@article{gulyuk_lajeunesse_collazo_ivanisevic_2021, title={Tuning Microbial Activity via Programmatic Alteration of Cell/Substrate Interfaces}, volume={5}, ISSN={["1521-4095"]}, DOI={10.1002/adma.202004655}, abstractNote={AbstractA wide portfolio of advanced programmable materials and structures has been developed for biological applications in the last two decades. Particularly, due to their unique properties, semiconducting materials have been utilized in areas of biocomputing, implantable electronics, and healthcare. As a new concept of such programmable material design, biointerfaces based on inorganic semiconducting materials as substrates introduce unconventional paths for bioinformatics and biosensing. In particular, understanding how the properties of a substrate can alter microbial biofilm behavior enables researchers to better characterize and thus create programmable biointerfaces with necessary characteristics on demand. Herein, the current status of advanced microorganism–inorganic biointerfaces is summarized along with types of responses that can be observed in such hybrid systems. This work identifies promising inorganic material types along with target microorganisms that will be critical for future research on programmable biointerfacial structures.}, journal={ADVANCED MATERIALS}, author={Gulyuk, Alexey V. and LaJeunesse, Dennis R. and Collazo, Ramon and Ivanisevic, Albena}, year={2021}, month={May} }
 @article{gleco_reddy_kirste_collazo_lajeunesse_ivanisevic_2020, title={Modulating the Stress Response of E. coli at GaN Interfaces Using Surface Charge, Surface Chemistry, and Genetic Mutations}, volume={3}, ISSN={["2576-6422"]}, url={https://doi.org/10.1021/acsabm.0c01007}, DOI={10.1021/acsabm.0c01007}, abstractNote={The surface properties of inorganic materials can be used to modulate the response of microorganisms at the interface. We used the persistent photoconductivity properties of chemically treated gallium nitride substrates to evaluate the stress response of wild-type, ΔfliC, and ΔcsgG mutant E. coli exposed to charged surfaces. Substrate surface characterization and biological assays were used to correlate the physiological response to substrate surface charge. The physiological response was evaluated by measuring the intracellular levels of reactive oxygen species (ROS) and Ca2+ cations using fluorescent probes. We evaluated the response 1, 2, and 3 h after a short exposure to the surfaces to determine generational effects of the initial exposure on the physiology of the bacteria. In general, the ROS levels 1 h after exposure were not different. However, there were differences in Ca2+ levels in E. coli 1 h after the initial exposure to charged GaN surfaces, primarily in the wild-type E. coli. The differences in Ca2+ levels depended on the substrate surface chemistry and genetic mutation that suggests the involvement of multiple factors for modulating the interactions of bacteria at interfaces.}, number={10}, journal={ACS APPLIED BIO MATERIALS}, publisher={American Chemical Society (ACS)}, author={Gleco, Sara and Reddy, Pramod and Kirste, Ronny and Collazo, Ramon and LaJeunesse, Dennis and Ivanisevic, Albena}, year={2020}, month={Oct}, pages={7211–7218} }
 @article{gleco_romanyuk_gordeev_kuldova_paskova_ivanisevic_2019, title={Modification of the Surface Properties of AlxGa1-xN Substrates with Gradient Aluminum Composition Using Wet Chemical Treatments}, volume={4}, ISSN={["2470-1343"]}, DOI={10.1021/acsomega.9b01467}, abstractNote={The surface properties of biomolecular gradients are widely known to be important for controlling cell dynamics, but there is a lack of platforms for studying them in vitro using inorganic materials. The changes in various surface properties of an AlxGa1–xN film (0.173 ≤ x ≤ 0.220) with gradient aluminum content were quantified to demonstrate the ability to modify interfacial characteristics. Four wet chemical treatments were used to modify the surface of the film: (i) oxide passivation by hydrogen peroxide, (ii) two-step functionalization with a carboxylic acid following hydrogen peroxide pretreatment, (iii) phosphoric acid etch, and (iv) in situ functionalization with a phosphonic acid in phosphoric acid. The characterization confirmed changes in the topography, nanostructures, and hydrophobicity after chemical treatment. Additionally, X-ray photoelectron spectroscopy was used to confirm that the chemical composition of the surfaces, in particular, Ga2O3 and Al2O3 content, was dependent on both the chemical treatment and the Al content of the gradient. Spectroscopic evaluation showed red shifts in strain-sensitive Raman peaks as the Al content gradually increased, but the same peaks blue-shifted after chemical treatment. Kelvin probe force microscopy measurements demonstrated that one can modify the surface charge using the chemical treatments. There were no predictable or controllable surface charge trends because of the spontaneous oxide-based nanostructured formations of the bulk material that varied based on treatment and were defect-dependent. The reported methodology and characterization can be utilized in future interfacial studies that rely on water-based wet chemical functionalization of inorganic materials.}, number={7}, journal={ACS OMEGA}, author={Gleco, Sara and Romanyuk, Oleksandr and Gordeev, Ivan and Kuldova, Karla and Paskova, Tania and Ivanisevic, Albena}, year={2019}, month={Jul}, pages={11760–11769} }
 @article{adams_vinueza_romanyuk_gordeev_paskova_ivanisevic_2019, title={Nanostructured GaOOH modified with reactive yellow, red and blue water-soluble dyes}, volume={9}, ISSN={["2158-3226"]}, DOI={10.1063/1.5080353}, abstractNote={Water soluble reactive dyes are used to modify nanostructured GaOOH. The resulting particles showed excellent stability in water solutions. The materials were characterized by Scanning electron microscopy (SEM) and X-ray Photoelectron Spectroscopy (XPS) to assess changes due to the dye functionalization. SEM revealed changes in size after dye modification. XPS confirmed the presence of the dyes on the nanostructured materials and assessed changes in functional groups due to use of different type of modification and concentrations of dyes. The reported approach to stabilize the nanostructured GaOOH provides a simple and environmentally friendly route to tune the properties of wide band gap semiconductor materials.}, number={2}, journal={AIP ADVANCES}, author={Adams, W. Taylor and Vinueza, Nelson R. and Romanyuk, Oleksandr and Gordeev, Ivan and Paskova, Tania and Ivanisevic, Albena}, year={2019}, month={Feb} }
 @article{adams_ivanisevic_2019, title={Nanostructured Oxides Containing Ga: Materials with Unique Properties for Aqueous-Based Applications}, volume={4}, ISSN={["2470-1343"]}, DOI={10.1021/acsomega.9b00461}, abstractNote={Oxides containing Ga have been studied by various research communities due to their stability under harsh conditions as well as conductivity and luminescence properties. Nanostructured forms of such oxides can be fabricated by a variety of methods. Advances in synthesis approaches have focused on control over size and shape that can permit adaptation in applied interfaces related to medicine, energy, and the environment. Chemical functionalization can enhance the stability of nanostructured oxides containing Ga in aqueous solutions. In this prospective, we summarize progress in making these materials as well as functionalizing them in water solutions. The prospective also identifies future opportunities with these materials in applied and fundamental materials chemistry research.}, number={4}, journal={ACS OMEGA}, author={Adams, W. Taylor and Ivanisevic, Albena}, year={2019}, month={Apr}, pages={6876–6882} }
 @article{snyder_lajeunesse_reddy_kirste_collazo_ivanisevic_2018, title={Bioelectronics communication: encoding yeast regulatory responses using nanostructured gallium nitride thin films}, volume={10}, ISSN={2040-3364 2040-3372}, url={http://dx.doi.org/10.1039/C8NR03684E}, DOI={10.1039/C8NR03684E}, abstractNote={Baker's yeast, S. cerevisiae, is a model organism that is used in synthetic biology.}, number={24}, journal={Nanoscale}, publisher={Royal Society of Chemistry (RSC)}, author={Snyder, Patrick J. and LaJeunesse, Dennis R. and Reddy, Pramod and Kirste, Ronny and Collazo, Ramon and Ivanisevic, Albena}, year={2018}, pages={11506–11516} }
 @misc{snyder_reddy_kirste_collazo_ivanisevic_2018, title={Bulk and Surface Electronic Properties of Inorganic Materials: Tools to Guide Cellular Behavior}, volume={2}, ISSN={["2366-9608"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85072577277&partnerID=MN8TOARS}, DOI={10.1002/smtd.201800016}, abstractNote={AbstractClassical concepts associated with the electronic properties of inorganic materials in the context of conditions used in biointerface studies are summarized. Electronic properties provide unique ways for stimulating a variety of biological systems; however, here the major focus is on mammallian cells. An additional focus is placed on bulk and electronic properties prior to chemical functionalization of inorganic materials. Representative studies, challenges, and opportunities toward utilization of charge, conductivity, photoconductivity, polarity, and piezoelectricity‐dependent mamallian cell interfaces are highlighted.}, number={9}, journal={SMALL METHODS}, author={Snyder, Patrick J. and Reddy, Pramod and Kirste, Ronny and Collazo, Ramon and Ivanisevic, Albena}, year={2018}, month={Sep} }
 @article{gulyuk_lajeunesse_collazo_ivanisevic_2018, title={Characterization of Pseudomonas aeruginosa Films on Different Inorganic Surfaces before and after UV Light Exposure}, volume={34}, ISSN={["0743-7463"]}, DOI={10.1021/acs.langmuir.8b02079}, abstractNote={The changes of the surface properties of Au, GaN, and SiO x after UV light irradiation were used to actively influence the process of formation of Pseudomonas aeruginosa films. The interfacial properties of the substrates were characterized by X-ray photoelectron spectroscopy and atomic force microscopy. The changes in the P. aeruginosa film properties were accessed by analyzing adhesion force maps and quantifying the intracellular Ca2+ concentration. The collected analysis indicates that the alteration of the inorganic materials' surface chemistry can lead to differences in biofilm formation and variable response from P. aeruginosa cells.}, number={36}, journal={LANGMUIR}, author={Gulyuk, Alexey V and LaJeunesse, Dennis R. and Collazo, Ramon and Ivanisevic, Albena}, year={2018}, month={Sep}, pages={10806–10815} }
 @article{adams_nolan_ivanisevic_2018, title={Ga Ion-Enhanced and Particle Shape-Dependent Generation of Reactive Oxygen Species in X-ray-Irradiated Composites}, volume={3}, ISSN={["2470-1343"]}, DOI={10.1021/acsomega.8b00524}, abstractNote={The reported results test the effects of the collective behavior hypothesized to contribute to the production of more reactive oxygen species (ROS) in vitro and result in an enhanced radiosensitization. The role of particle shape in composites with gallium oxyhydroxide (GaOOH) particles and Matrigel is studied. Particles of two different shapes are embedded into the gel to understand only the materials effect on the generation of ROS rather than cell penetrating variations. The paper reports materials characterization by scanning electron microscopy and X-ray diffraction. The stability of the particles within the composite is assessed by quantification of leached metal using inductively coupled plasma mass spectrometry. The amount of ROS in each construct under variable radiation conditions is quantified in the presence and absence of PC12 cells seeded on top of the composites. The viability of cells is also recorded under different in vitro conditions. The collective materials characterization and the results from the bioassays are used to explain the role of anisotropy on the radiosensitization of nanostructures containing Ga. The presence of Ga ions in composites can have a radiosensitizing effect, and the amount of the available Ga3+ determines the magnitude of the radiosensitization. The shape of the particles determines the stability in aqueous solutions and release of Ga3+ that triggers ROS production. The concentration and shape of Ga-containing materials can be combined to generate an additive effect by increasing the amount of available free metal ions in solution. The studies with GaOOH containing composites enable one to explore the role of key parameters that lead to an increased efficiency of radiation treatments.}, number={5}, journal={ACS OMEGA}, author={Adams, W. T. and Nolan, Michael W. and Ivanisevic, Albena}, year={2018}, month={May}, pages={5252–5259} }
 @article{snyder_reddy_kirste_lajeunesse_collazo_ivanisevic_2018, title={Noninvasive Stimulation of Neurotypic Cells Using Persistent Photoconductivity of Gallium Nitride}, volume={3}, ISSN={2470-1343 2470-1343}, url={http://dx.doi.org/10.1021/ACSOMEGA.7B01894}, DOI={10.1021/ACSOMEGA.7B01894}, abstractNote={The persistent photoconductivity (PPC) of the n-type Ga-polar GaN was used to stimulate PC12 cells noninvasively. Analysis of the III-V semiconductor material by atomic force microscopy, Kelvin probe force microscopy, photoconductivity, and X-ray photoelectron spectroscopy quantified bulk and surface charge, as well as chemical composition before and after exposure to UV light and cell culture media. The semiconductor surface was made photoconductive by illumination with UV light and experienced PPC, which was utilized to stimulate PC12 cells in vitro. Stimulation was confirmed by measuring the changes in intracellular calcium concentration. Control experiments with gallium salt verified the stimulation of neurotypic cells. Inductively coupled plasma mass spectrometry data confirmed the lack of gallium leaching and toxic effects during the stimulation.}, number={1}, journal={ACS Omega}, publisher={American Chemical Society (ACS)}, author={Snyder, Patrick J. and Reddy, Pramod and Kirste, Ronny and LaJeunesse, Dennis R. and Collazo, Ramon and Ivanisevic, Albena}, year={2018}, month={Jan}, pages={615–621} }
 @article{snyder_davis_berg_pearce_romanyuk_jiricek_paskova_ivanisevic_2019, title={Passivation of semipolar (10-1-1) GaN with different organic adsorbates}, volume={236}, ISSN={["1873-4979"]}, DOI={10.1016/j.matlet.2018.10.109}, abstractNote={Expanding the functionality of electronic materials is often reliant on the attachment of organic molecules to the surface. In this study, several methods for passivating the surface of semipolar (10-1-1) GaN with different chemistries were examined; this included simple physisorption, in-situ functionalization using phosphonic acids, and a two-step carboxylic acid attachment with a peroxide pretreatment. The binding of a variety of different organic adsorbates on semipolar substrates was quantified using X-ray photoelectron spectroscopy (XPS). Our results confirm binding at the organic-inorganic interface through the presence of amine/amide species on the surface. The wide variety of organic molecules, and their binding to inorganic electronic materials, can be exploited to impart specific functionalities in technologies spanning fields of energy, biomedical science, and chemical sensing.}, journal={MATERIALS LETTERS}, author={Snyder, Patrick J. and Davis, Hailey and Berg, Nora G. and Pearce, Brady and Romanyuk, Oleksandr and Jiricek, Petr and Paskova, Tania and Ivanisevic, Albena}, year={2019}, month={Feb}, pages={201–204} }
 @article{snyder_reddy_kirste_lajeunesse_collazo_ivanisevic_2018, title={Variably doped nanostructured gallium nitride surfaces can serve as biointerfaces for neurotypic PC12 cells and alter their behavior}, volume={8}, ISSN={["2046-2069"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85056316378&partnerID=MN8TOARS}, DOI={10.1039/c8ra06836d}, abstractNote={Neurotypic PC12 cells behavior was studied on nanostructured GaN and rationalized with respect to surface charge, doping level, and chemical functionalization.}, number={64}, journal={RSC ADVANCES}, author={Snyder, Patrick J. and Reddy, Pramod and Kirste, Ronny and LaJeunesse, Dennis R. and Collazo, Ramon and Ivanisevic, Albena}, year={2018}, pages={36722–36730} }
 @article{snyder_kirste_collazo_ivanisevic_2017, title={Persistent Photoconductivity, Nanoscale Topography, and Chemical Functionalization Can Collectively Influence the Behavior of PC12 Cells on Wide Bandgap Semiconductor Surfaces}, volume={13}, ISSN={["1613-6829"]}, DOI={10.1002/smll.201700481}, abstractNote={Wide bandgap semiconductors such as gallium nitride (GaN) exhibit persistent photoconductivity properties. The incorporation of this asset into the fabrication of a unique biointerface is presented. Templates with lithographically defined regions with controlled roughness are generated during the semiconductor growth process. Template surface functional groups are varied using a benchtop surface functionalization procedure. The conductivity of the template is altered by exposure to UV light and the behavior of PC12 cells is mapped under different substrate conductivity. The pattern size and roughness are combined with surface chemistry to change the adhesion of PC12 cells when the GaN is made more conductive after UV light exposure. Furthermore, during neurite outgrowth, surface chemistry and initial conductivity difference are used to facilitate the extension to smoother areas on the GaN surface. These results can be utilized for unique bioelectronics interfaces to probe and control cellular behavior.}, number={24}, journal={SMALL}, author={Snyder, Patrick J. and Kirste, Ronny and Collazo, Ramon and Ivanisevic, Albena}, year={2017}, month={Jun} }
 @article{pearce_berg_jiang_ivanisevic_2016, title={Aqueous stability of nanostructured aluminum and gallium oxyhydroxide before and after functionalization with lysine}, volume={184}, ISSN={["1873-4979"]}, DOI={10.1016/j.matlet.2016.08.071}, abstractNote={Composites of nanostructured aluminum and gallium oxyhydroxide (AlOOH and GaOOH) and l-lysine were synthesized using an environmentally friendly approach. These composites were investigated to determine the effects of the functionalization on the aqueous stability and leaching of aluminum and gallium. The organic and inorganic components present in the samples were assessed with X-Ray photoelectron spectroscopy (XPS) and Fourier transformed-infrared spectroscopy (FT-IR). In the GaOOH-lysine composite, XPS provided evidence of both the presence of gallium and lysine. Crystallographic information was gathered using X-Ray diffraction (XRD). The FT-IR and XRD spectra of the composite materials were dominated by peaks related to lysine, due to the nature of these samples. Inductively coupled plasma-mass spectrometry (ICP-MS) data were collected of the functionalized and non-functionalized samples left in solution for periods of 1 days, 5 days and 7 days. This provided evidence of improved aqueous stability of the AlOOH-lysine composite with no effect seen in the GaOOH-lysine composite. The findings of this study will be used in determining the importance of lysine functionalization for future biomolecule-nanomaterial composites.}, journal={MATERIALS LETTERS}, author={Pearce, Brady L. and Berg, Nora G. and Jiang, Lin and Ivanisevic, Albena}, year={2016}, month={Dec}, pages={278–281} }
 @article{berg_pearce_rohrbaugh_jiang_nolan_ivanisevic_2017, title={Gallium containing composites as a tunable material to understand neuronal behavior under variable stiffness and radiation conditions}, volume={71}, ISSN={["1873-0191"]}, DOI={10.1016/j.msec.2016.10.022}, abstractNote={We report a composite biomaterial containing nanostructured GaOOH and Matrigel™ that can be modulated with respect to its stiffness and radiosensitization properties. A variety of concentrations of GaOOH were added to the composite to alter the mechanical properties of the material as well as to tune the radiosensitizing properties to the composite. PC-12 cells were used to study the combined effects of different stimuli on cell behavior. NGF was given to the cells to record their morphology as well as viability. An increase in the substrate stiffness caused an increase in neurite outgrowth but a decrease in cell viability. In addition, increasing the radiation dose decreased neurite outgrowth but increased cell viability when radiosensitizing particles were present. A subtractive effect between radiosensitizing and mechanical stimuli was observed when PC-12 cells were grown on the GaOOH containing composite.}, journal={MATERIALS SCIENCE & ENGINEERING C-MATERIALS FOR BIOLOGICAL APPLICATIONS}, author={Berg, Nora G. and Pearce, Brady L. and Rohrbaugh, Nathaniel and Jiang, Lin and Nolan, Michael W. and Ivanisevic, Albena}, year={2017}, month={Feb}, pages={317–321} }
 @article{rohrbaugh_hernandez-balderrama_kaess_kirste_collazo_ivanisevic_2016, title={HgNO3 sensitivity of AlGaN/GaN field effect transistors functionalized with phytochelating peptides}, volume={6}, ISSN={["2158-3226"]}, DOI={10.1063/1.4953806}, abstractNote={This study examined the conductance sensitivity of AlGaN/GaN field effect transistors in response to varying Hg/HNO3 solutions. FET surfaces were covalently functionalized with phytochelatin-5 peptides in order to detect Hg in solution. Results showed a resilience of peptide-AlGaN/GaN bonds in the presence of strong HNO3 aliquots, with significant degradation in FET ID signal. However, devices showed strong and varied response to Hg concentrations of 1, 10, 100, and 1000 ppm. The gathered statistically significant results indicate that peptide terminated AlGaN/GaN devices are capable of differentiating between Hg solutions and demonstrate device sensitivity.}, number={6}, journal={AIP ADVANCES}, author={Rohrbaugh, Nathaniel and Hernandez-Balderrama, Luis and Kaess, Felix and Kirste, Ronny and Collazo, Ramon and Ivanisevic, Albena}, year={2016}, month={Jun} }
 @article{pearce_berg_rahn_ivanisevic_2016, title={In situ and ex situ functionalization of nanostructured gallium oxy-hydroxide with a porphyrin dye}, volume={38}, ISSN={["1932-8745"]}, DOI={10.1002/sca.21315}, abstractNote={SummaryThe surface attachment of a porphyrin dye to nanocrystalline GaOOH was performed using two routes of solution‐based functionalization. The first method of functionalization utilized an in situ incorporation of dissolved porphyrin salt in solution during the microwave synthesis step. Additionally, synthesized GaOOH nanorods were mixed in porphyrin solution after the microwave process to make an ex situ GaOOH/TTP‐PO­3. X‐ray photoelectron spectroscopy confirmed the presence of expected surface species and provided evidence of increased surface coverage of TTP‐PO3 on GaOOH in the ex situ­ GaOOH/TTP‐PO3 as compared to the in situ one. Size and morphology changes were investigated using SEM and, along with analysis of XRD, the in situ samples showed larger crystallite sizes. This was confirmed with PL due to the higher bandgap energy evident in the ex situ GaOOH/TTP‐PO3 compared to the in situ sample. A stability study was performed using fluorescence spectroscopy which indicated no leaching of porphyrin from the in situ GaOOH/TTP‐PO3. However, porphyrin leaching was evident from the ex situ GaOOH/TTP‐PO3 sample. The stability of the in situ GaOOH/TTP‐PO3 makes it attractive for a number of interfacial applications. SCANNING 38:671–683, 2016. © 2016 Wiley Periodicals, Inc.}, number={6}, journal={SCANNING}, author={Pearce, Brady L. and Berg, Nora G. and Rahn, Matthew S. and Ivanisevic, Albena}, year={2016}, month={Dec}, pages={671–683} }
 @article{berg_pearce_snyder_rohrbaugh_nolan_adhikari_khan_ivanisevic_2016, title={Interfaces with Tunable Mechanical and Radiosensitizing Properties}, volume={8}, ISSN={["1944-8252"]}, DOI={10.1021/acsami.5b11639}, abstractNote={We report the fabrication of a composite containing nanostructured GaOOH and Matrigel with tunable radiosensitizing and stiffness properties. Composite characterization was done with microscopy and rheology. The utility of the interface was tested in vitro using fibroblasts. Cell viability and reactive oxygen species assays quantified the effects of radiation dosages and GaOOH concentrations. Fibroblasts' viability decreased with increasing concentration of GaOOH and composite stiffness. During ionizing radiation experiments the presence of the scintillating GaOOH triggered a different cellular response. Reactive oxygen species data demonstrated that one can reduce the amount of radiation needed to modulate the behavior of cells on interfaces with different stiffness containing a radiosensitizing material.}, number={34}, journal={ACS APPLIED MATERIALS & INTERFACES}, author={Berg, Nora G. and Pearce, Brady L. and Snyder, Patrick J. and Rohrbaugh, Nathaniel and Nolan, Michael W. and Adhikari, Prajesh and Khan, Saad A. and Ivanisevic, Albena}, year={2016}, month={Aug}, pages={21956–21961} }
 @article{snyder_kirste_collazoa_ivanisevic_2016, title={Nanoscale topography, semiconductor polarity and surface functionalization: additive and cooperative effects on PC12 cell behavior}, volume={6}, ISSN={["2046-2069"]}, DOI={10.1039/c6ra21936e}, abstractNote={This work compares the behavior of PC12 cells on planar and patterned III-nitride materials with nanostructured topographies.}, number={100}, journal={RSC ADVANCES}, author={Snyder, Patrick J. and Kirste, Ronny and Collazoa, Ramon and Ivanisevic, Albena}, year={2016}, pages={97873–97881} }
 @article{berg_franke_kirste_collazo_ivanisevic_2016, title={Photoluminescence changes of III-Nitride lateral polarity structures after chemical functionalization}, volume={3}, ISSN={["2053-1591"]}, DOI={10.1088/2053-1591/3/12/125906}, abstractNote={The photoluminescence changes of a III-Nitride semiconductor with various surface topographies were studied after chemical functionalization. AlxGa1−xN with a composition of 70% aluminum was used and the surfaces were functionalized with a fluorophore dye-terminated peptide using a linker molecule. The stability of the wafers in water was studied using inductively coupled plasma mass spectrometry prior to modifying the material. The leaching data demonstrated that the AlGaN material in highly stable in biological conditions over 7 d. The attachment of the dye to the wafer was investigated using x-ray photoelectron spectroscopy and photoluminescence spectroscopy (PL). The PL spectrum showed a clear signature of the dye with a pronounced emission peak at approximately 260 nm, indicating a successful attachment to the surface.}, number={12}, journal={MATERIALS RESEARCH EXPRESS}, author={Berg, Nora G. and Franke, Alexander and Kirste, Ronny and Collazo, Ramon and Ivanisevic, Albena}, year={2016}, month={Dec} }
 @article{pearce_berg_ivanisevic_2017, title={Synthesis and optical characterization of mixed nanostructured aluminum-gallium oxy-hydroxide}, volume={5}, ISSN={["2166-3831"]}, DOI={10.1080/21663831.2016.1232317}, abstractNote={ABSTRACT Nanostructured oxy-hydroxide materials with varied compositions of aluminum and gallium were synthesized in an environmentally friendly way with water as the only solvent. The tunability of optical properties of these materials through concentration ranges is particularly of interest for organic/inorganic hybrid materials in optoelectronic devices. Size comparisons of the materials were performed using dynamic light scattering measurements. The measured size of the particles decreased with increasing Al. This supports the blue shift seen from the GaOOH emission wavelength to the Al0.5Ga0.5OOH emission wavelength in the photoluminescence spectra. The X-ray diffraction showed the formation of a possible amorphous layer in Al0.5Ga0.5OOH and Al0.2Ga0.8OOH. GRAPHICAL ABSTRACT IMPACT STATEMENT A water-based synthesis for mixed aluminum–gallium nanostructured oxides is presented with size comparisons and optical characteristics demonstrating emission wavelength tunability.}, number={2}, journal={MATERIALS RESEARCH LETTERS}, author={Pearce, Brady L. and Berg, Nora G. and Ivanisevic, Albena}, year={2017}, pages={124–127} }
 @article{berg_paskova_ivanisevic_2017, title={Tuning the biocompatibility of aluminum nitride}, volume={189}, ISSN={["1873-4979"]}, DOI={10.1016/j.matlet.2016.11.041}, abstractNote={High-quality, electronic-grade, aluminum nitride thin films grown by reactive sputtering were studied in vitro. The semiconductor material showed high degree of stability in cell culture with very little Al leaching over time. Unlike other III-nitride materials, clean AlN does not promote the adhesion of cells to its surface. The work demonstrates that functionalization with peptides can be used to reverse this behavior. The presence of AlN in cell culture does not have any adverse effects on neurotypic cell behavior as confirmed by cell viability and reactive oxygen species assays.}, journal={MATERIALS LETTERS}, author={Berg, Nora G. and Paskova, Tania and Ivanisevic, Albena}, year={2017}, month={Feb}, pages={1–4} }
 @misc{pearce_wilkins_paskova_ivanisevic_2015, title={A review of in situ surface functionalization of gallium nitride via beaker wet chemistry}, volume={30}, ISSN={["2044-5326"]}, DOI={10.1557/jmr.2015.132}, abstractNote={Abstract}, number={19}, journal={JOURNAL OF MATERIALS RESEARCH}, author={Pearce, Brady L. and Wilkins, Stewart J. and Paskova, Tania and Ivanisevic, Albena}, year={2015}, month={Oct}, pages={2859–2870} }
 @article{wilkins_paskova_reynolds_ivanisevic_2015, title={Comparison of the Stability of Functionalized GaN and GaP}, volume={16}, ISSN={["1439-7641"]}, DOI={10.1002/cphc.201500105}, abstractNote={AbstractSurface functionalization via 1 H,1 H,2 H,2H‐perfluoro octanephosphonic acid was done in the presence of phosphoric acid to provide a simplified surface passivation technique for gallium nitride (GaN) and gallium phosphide (GaP). In an effort to identify the leading causes of surface instabilities, hydrogen peroxide was utilized as an additional chemical modification to cap unsatisfied bonds. The stability of the surfaces was studied in an aqueous environment and subsequently characterized. A physical characterization was carried out to evaluate the surface roughness and water hydrophobicity pre and post stability testing via atomic force microscopy and water goniometry. Surface‐chemistry changes and solution leaching were quantified by X‐ray photoelectron spectroscopy and inductively coupled plasma mass spectrometry. The results indicate a sensitivity to hydroxyl terminated species for both GaN and GaP under aqueous environments, as the increase of the degree of leaching was more significant for hydrogen peroxide treated samples. The results support the notion that hydroxyl species act as precursors to gallium oxide formation and lead to subsequent instability in aqueous solutions.}, number={8}, journal={CHEMPHYSCHEM}, author={Wilkins, Stewart J. and Paskova, Tania and Reynolds, C. Lewis, Jr. and Ivanisevic, Albena}, year={2015}, month={Jun}, pages={1687–1694} }
 @article{kirste_rohrbaugh_bryan_bryan_collazo_ivanisevic_2015, title={Electronic Biosensors Based on III-Nitride Semiconductors}, volume={8}, ISSN={["1936-1327"]}, DOI={10.1146/annurev-anchem-071114-040247}, abstractNote={ We review recent advances of AlGaN/GaN high-electron-mobility transistor (HEMT)-based electronic biosensors. We discuss properties and fabrication of III-nitride-based biosensors. Because of their superior biocompatibility and aqueous stability, GaN-based devices are ready to be implemented as next-generation biosensors. We review surface properties, cleaning, and passivation as well as different pathways toward functionalization, and critically analyze III-nitride-based biosensors demonstrated in the literature, including those detecting DNA, bacteria, cancer antibodies, and toxins. We also discuss the high potential of these biosensors for monitoring living cardiac, fibroblast, and nerve cells. Finally, we report on current developments of covalent chemical functionalization of III-nitride devices. Our review concludes with a short outlook on future challenges and projected implementation directions of GaN-based HEMT biosensors. }, journal={ANNUAL REVIEW OF ANALYTICAL CHEMISTRY, VOL 8}, author={Kirste, Ronny and Rohrbaugh, Nathaniel and Bryan, Isaac and Bryan, Zachary and Collazo, Ramon and Ivanisevic, Albena}, year={2015}, pages={149–169} }
 @article{pearce_wilkins_rahn_ivanisevic_2015, title={In situ functionalization of gallium nitride powder with a porphyrin dye}, volume={30}, ISSN={["2044-5326"]}, DOI={10.1557/jmr.2015.152}, abstractNote={Abstract}, number={19}, journal={JOURNAL OF MATERIALS RESEARCH}, author={Pearce, Brady L. and Wilkins, Stewart J. and Rahn, Matthew S. and Ivanisevic, Albena}, year={2015}, month={Oct}, pages={2910–2918} }
 @article{rohrbaugh_bryan_bryan_collazo_ivanisevic_2015, title={Long-term stability assessment of AlGaN/GaN field effect transistors modified with peptides: Device characteristics vs. surface properties}, volume={5}, ISSN={["2158-3226"]}, DOI={10.1063/1.4930192}, abstractNote={AlGaN/GaN Field Effect Transistors (FETs) are promising biosensing devices. Functionalization of these devices is explored in this study using an in situ approach with phosphoric acid etchant and a phosphonic acid derivative. Devices are terminated on peptides and soaked in water for up to 168 hrs to examine FETs for both device responses and surface chemistry changes. Measurements demonstrated threshold voltage shifting after the functionalization and soaking processes, but demonstrated stable FET behavior throughout. X-ray photoelectron spectroscopy and atomic force microscopy confirmed peptides attachment to device surfaces before and after water soaking. Results of this work point to the stability of peptide coated functionalized AlGaN/GaN devices in solution and support further research of these devices as disposable, long term, in situ biosensors.}, number={9}, journal={AIP ADVANCES}, author={Rohrbaugh, Nathaniel and Bryan, Isaac and Bryan, Zachary and Collazo, Ramon and Ivanisevic, Albena}, year={2015}, month={Sep} }
 @article{wilkins_slomski_paskova_weyher_ivanisevic_2015, title={Modulated optical sensitivity with nanostructured gallium nitride}, volume={106}, ISSN={["1077-3118"]}, DOI={10.1063/1.4918739}, abstractNote={Surface functionalization via etching of high aspect ratio gallium nitride (GaN) nanostructures provides a way to modulate the optical properties in addition to properties gained from unique topographical formations. In this study, planar layered (heteroepitaxy) and bulk free-standing gallium nitride were modified via a phosphonic acid (1H,1H,2H,2H-perfluorooctanephosphonic acid) assisted phosphoric acid etch in conjunction with an aqueous KOH + K2S2O8 formed gallium nitride nanostructured surface. Despite the high defect concentrations in the thin planar and nanostructured GaN layer, the nanostructured GaN sample produced improved photoluminescence intensities versus the high quality bulk free-standing gallium nitride. Subsequent treatments with additive and additive-free phosphoric etches provided a means of additional optical manipulation in the form of red-shifting the near-band-edge (NBE) emission of the nanostructured GaN sample and increasing the maximum NBE photoluminescence intensity.}, number={15}, journal={APPLIED PHYSICS LETTERS}, author={Wilkins, S. J. and Slomski, M. J. and Paskova, T. and Weyher, J. L. and Ivanisevic, A.}, year={2015}, month={Apr} }
 @article{berg_ivanisevic_2015, title={Nanostructured gallium nitride powder functionalized with a fluorophore terminated peptide}, volume={2}, ISSN={["2053-1591"]}, DOI={10.1088/2053-1591/2/9/095018}, abstractNote={Nanostructured gallium nitride (GaN) powder was functionalized with a biomolecule terminated with a fluorophore. The fluorophore was used to enhance and modulate the luminescent properties of the semiconductor powder. A simple two-step wet-chemistry in situ modification approach resulted in covalent attachment of the peptide to the powder. X-ray photoelectron spectroscopy survey data confirmed qualitatively that the peptide molecules were successfully attached to the surface of the powder with the presence of a phosphorus peak as well as an increase in nitrogen atomic percentage on the surface of the material. The bonding and stability of the modification to the nanostructured surface was assessed by quantitatively analyzing high-resolution regional scans. Photoluminescence Spectroscopy mapped changes to the optical properties of the powder upon dye terminated peptide attachment. A clear shift in the luminescence peak was recorded after the powder was functionalized. The results demonstrate a straight-forward way to alter the emission characteristics of a nanostructured semiconductor material. The role of material defects on the powder surface is used to explain the initial and altered luminescence properties.}, number={9}, journal={MATERIALS RESEARCH EXPRESS}, author={Berg, Nora and Ivanisevic, Albena}, year={2015}, month={Sep} }
 @article{bain_kirste_johnson_ghashghaei_collazo_ivanisevic_2016, title={Neurotypic cell attachment and growth on III-nitride lateral polarity structures}, volume={58}, ISSN={["1873-0191"]}, DOI={10.1016/j.msec.2015.09.084}, abstractNote={III-nitride materials have recently received increasing levels of attention for their potential to successfully interface with, and sense biochemical interactions in biological systems. Expanding on available sensing schemes (including transistor-based devices,) a III-N lateral polarity structure capable of introducing quasi-phase matching through a periodic polarity grating presents a novel platform for second harmonic generation. This platform constitutes a non-linear optical phenomenon with exquisite sensitivity to the chemical state of a surface or interface. To characterize the response of a biological system to the nanostructured lateral polarity structures, we cultured neurotypic PC12 cells on AlGaN with varying ratios of Al:Ga - 0, 0.4, 0.6, and 1 - and on surfaces of varying pitch to the III-polar vs. N-polar grating - 5, 10, 20 and 50 μm. While some toxicity associated with increasing Al is observed, we documented and quantified trends in cell responses to the local material polarity and nanoscale roughness. The nitrogen-polar material has a significantly higher nanoscale roughness than III-polar regions, and a 80-200 nm step height difference between the III-polar and N-polar materials in the lateral polarity configuration generates adequate changes in topography to influence cell growth, improves cell adhesion and promotes cell migration along the direction of the features. As the designed material configuration is further explored for biochemical sensing, the lateral polarity scheme may provide a route in assessing the non-specific protein adsorption to this varying nano-topography that drives the subsequent cell response.}, journal={MATERIALS SCIENCE & ENGINEERING C-MATERIALS FOR BIOLOGICAL APPLICATIONS}, author={Bain, L. E. and Kirste, R. and Johnson, C. A. and Ghashghaei, H. T. and Collazo, R. and Ivanisevic, A.}, year={2016}, month={Jan}, pages={1194–1198} }
 @article{bain_hoffmann_bryan_collazo_ivanisevic_2015, title={Adsorption and adhesion of common serum proteins to nanotextured gallium nitride}, volume={7}, ISSN={["2040-3372"]}, DOI={10.1039/c4nr06353h}, abstractNote={Morphology can be used to modulate the adsorption of proteins onto gallium nitride.}, number={6}, journal={NANOSCALE}, author={Bain, Lauren E. and Hoffmann, Marc P. and Bryan, Isaac and Collazo, Ramon and Ivanisevic, Albena}, year={2015}, pages={2360–2365} }
 @article{rohrbaugh_bryan_bryan_arellano_collazo_ivanisevic_2014, title={AlGaN/GaN field effect transistors functionalized with recognition peptides}, volume={105}, ISSN={0003-6951 1077-3118}, url={http://dx.doi.org/10.1063/1.4896962}, DOI={10.1063/1.4896962}, abstractNote={Recognition peptides are used to modify AlGaN/GaN field effect transistors. The recognition sequence, SVSVGMKPSPRP, was compared to other biomolecules and subsequently the device stability was examined. Changes in the electrical characteristic were recorded using current-voltage measurements at a VD of 1 V and VG of −1 V. The recognition sequence coatings yielded an average increase in ID of 96.43% compared to initial values. Exposure to solution removed the peptides from the devices indicating a weak interaction between adsorbate and the semiconductor surfaces. The peptide coatings are suitable for simple device modification for short-term recognition studies.}, number={13}, journal={Applied Physics Letters}, publisher={AIP Publishing}, author={Rohrbaugh, N. and Bryan, I. and Bryan, Z. and Arellano, C. and Collazo, R. and Ivanisevic, A.}, year={2014}, month={Sep}, pages={134103} }
 @article{rohrbaugh_bryan_bryan_arellano_collazo_ivanisevic_2014, title={AlGaN/GaN field effect transistors functionalized with recognition peptides}, volume={105}, number={13}, journal={Applied Physics Letters}, author={Rohrbaugh, N. and Bryan, I. and Bryan, Z. and Arellano, C. and Collazo, R. and Ivanisevic, A.}, year={2014} }
 @article{rohrbaugh_bryan_bryan_collazo_ivanisevic_2014, title={Effects of Environmental Exposure on Stability and Conductance Poly-l-lysine Coated AlGaN/GaN High Electron Mobility Transistors}, volume={61}, ISSN={["1938-6737"]}, DOI={10.1149/06104.0147ecst}, abstractNote={AlGaN/GaN HEMTs have been shown promise to be used as in-situ biosensors. An inquiry was done into the stability of physisorption as a method of adhering surface bioactive molecules to the surface of the HEMT gate contacts. Poly-l-lysine (30,000 MW) was used to coat AlGaN/GaN field effect transistors as a representative charged biomolecule for biosensing applications. Coated FETs were then exposed to 1 and 4 hour soaks in DI water at ambient temperature. Atomic force microscopy (AFM) and conductance measurements (IV) were used to quantify current decay and surface morphology changes. Analysis of the results showed that charged analytes readily adsorbed onto the surface.  Upon adsorption an immediate signal decay was observed. The changes after soaking in solution were variable.  The results point to the need to develop specific chemistry that will result in stable immobilization of biomolecules onto the device surface.  Such stability is necessary for long- term reliable device operation.}, number={4}, journal={WIDE BANDGAP SEMICONDUCTOR MATERIALS AND DEVICES 15}, author={Rohrbaugh, N. and Bryan, I. and Bryan, Z. and Collazo, R. and Ivanisevic, A.}, year={2014}, pages={147–151} }
 @misc{bain_ivanisevic_2015, title={Engineering the Cell-Semiconductor Interface: A Materials Modification Approach using II-VI and III-V Semiconductor Materials}, volume={11}, ISSN={["1613-6829"]}, DOI={10.1002/smll.201401450}, abstractNote={Developing functional biomedical devices based on semiconductor materials requires an understanding of interactions taking place at the material-biosystem interface. Cell behavior is dependent on the local physicochemical environment. While standard routes of material preparation involve chemical functionalization of the active surface, this review emphasizes both biocompatibility of unmodified surfaces as well as use of topographic features in manipulating cell-material interactions. Initially, the review discusses experiments involving unmodified II-VI and III-V semiconductors - a starting point for assessing cytotoxicity and biocompatibility - followed by specific surface modification, including the generation of submicron roughness or the potential effect of quantum dot structures. Finally, the discussion turns to more recent work in coupling topography and specific chemistry, enhancing the tunability of the cell-semiconductor interface. With this broadened materials approach, researchers' ability to tune the interactions between semiconductors and biological environments continues to improve, reaching new heights in device function.}, number={7}, journal={SMALL}, author={Bain, Lauren E. and Ivanisevic, Albena}, year={2015}, month={Feb}, pages={768–780} }
 @article{wilkins_greenough_arellano_paskova_ivanisevic_2014, title={In Situ Chemical Functionalization of Gallium Nitride with Phosphonic Acid Derivatives during Etching}, volume={30}, ISSN={0743-7463 1520-5827}, url={http://dx.doi.org/10.1021/LA404511B}, DOI={10.1021/la404511b}, abstractNote={In situ functionalization of polar (c plane) and nonpolar (a plane) gallium nitride (GaN) was performed by adding (3-bromopropyl) phosphonic acid or propyl phosphonic acid to a phosphoric acid etch. The target was to modulate the emission properties and oxide formation of GaN, which was explored through surface characterization with atomic force microscopy, X-ray photoelectron spectroscopy, photoluminescence (PL), inductively coupled plasma-mass spectrometry, and water contact angle. The use of (3-bromopropyl) phosphonic acid and propyl phosphonic acid in phosphoric acid demonstrated lower amounts of gallium oxide formation and greater hydrophobicity for both sample sets, while also improving PL emission of polar GaN samples. In addition to crystal orientation, growth-related factors such as defect density in bulk GaN versus thin GaN films residing on sapphire substrates were investigated as well as their responses to in situ functionalization. Thin nonpolar GaN layers were the most sensitive to etching treatments due in part to higher defect densities (stacking faults and threading dislocations), which accounts for large surface depressions. High-quality GaN (both free-standing bulk polar and bulk nonpolar) demonstrated increased sensitivity to oxide formation. Room-temperature PL stands out as an excellent technique to identify nonradiative recombination as observed in the spectra of heteroepitaxially grown GaN samples. The chemical methods applied to tune optical and physical properties of GaN provide a quantitative framework for future novel chemical and biochemical sensor development.}, number={8}, journal={Langmuir}, publisher={American Chemical Society (ACS)}, author={Wilkins, Stewart J. and Greenough, Michelle and Arellano, Consuelo and Paskova, Tania and Ivanisevic, Albena}, year={2014}, month={Feb}, pages={2038–2046} }
 @article{wilkins_paskova_ivanisevic_2015, title={Modified surface chemistry, potential, and optical properties of polar gallium nitride via long chained phosphonic acids}, volume={327}, ISSN={["1873-5584"]}, DOI={10.1016/j.apsusc.2014.11.179}, abstractNote={Surface potential, chemistry, topography, and optical properties were modulated utilizing the attachment of phosphonic acids (11-mercaptoundecylphosphonic acid, 1H,1H,2H,2H-perfluorooctanephosphonic acid, and 1,8-octanediphosphonic acid) with phosphoric acid to polar (c-plane) GaN. These changes were identified using X-ray photoelectron spectroscopy (XPS), atomic force microscopy (AFM) with kelvin probe force microscopy (KPFM), photoluminescence (PL), and water contact angle. The results indicated that the attachment of phosphonic groups to gallium nitride strongly depends on the formation of a native oxide layer and subsequent passivation. It was seen that a fluorine terminated phosphonic acid increased the overall surface oxide versus other groups, as well as reduced the surface potential and improved the photoluminescence relative to other treatments. Sulfur terminated phosphonic acid demonstrated a similar reduction in surface potential and oxide formation to fluorine based phosphonic acid; however, improvements of optical luminescence on the same scale were not achieved.}, journal={APPLIED SURFACE SCIENCE}, author={Wilkins, Stewart J. and Paskova, Tania and Ivanisevic, Albena}, year={2015}, month={Feb}, pages={498–503} }
 @article{wilkins_paskova_ivanisevic_2014, title={Modulated optical properties of nonpolar gallium nitride via surface in-situ functionalization with cysteamine assisted phosphoric acid}, volume={295}, ISSN={["1873-5584"]}, DOI={10.1016/j.apsusc.2014.01.035}, abstractNote={In-situ functionalization of nonpolar a-plane gallium nitride (GaN) surface was achieved by adding cysteamine to phosphoric acid, aiming to modulate its optical properties. The emission properties and oxide formation were explored through surface characterization with atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), photoluminescence (PL), and water contact angle. Nonpolar a-plane bulk GaN sample sliced from a GaN boule and nonpolar a-plane GaN thin layer heteroepitaxially grown on r-plane sapphire were used to elucidate the effects of in-situ functionalization of identical surface orientation of GaN crystals with different defect ensembles. The addition of cysteamine to the phosphoric acid solution was found to result in: (i) increased surface roughness, (ii) no change to hydrophobicity, (iii) decreased oxygen content at high solution temperatures and increased gallium and nitrogen content versus phosphoric acid solutions at similar temperatures without cysteamine. The in-situ functionalization resulted in enhanced PL intensity from the nonpolar bulk GaN, while the PL intensity from the nonpolar heteroepitaxially grown GaN layer on sapphire was significantly reduced. The opposite PL modulation was explained by the effects of different defects present in the two samples on the nonradiative recombination.}, journal={APPLIED SURFACE SCIENCE}, author={Wilkins, Stewart J. and Paskova, Tania and Ivanisevic, Albena}, year={2014}, month={Mar}, pages={207–213} }
 @article{berg_nolan_paskova_ivanisevic_2014, title={Surface Characterization of Gallium Nitride Modified with Peptides before and after Exposure to Ionizing Radiation in Solution}, volume={30}, ISSN={0743-7463 1520-5827}, url={http://dx.doi.org/10.1021/la5040245}, DOI={10.1021/la5040245}, abstractNote={An aqueous surface modification of gallium nitride was employed to attach biomolecules to the surface. The modification was a simple two-step process using a single linker molecule and mild temperatures. The presence of the peptide on the surface was confirmed with X-ray photoelectron spectroscopy. Subsequently, the samples were placed in water baths and exposed to ionizing radiation to examine the effects of the radiation on the material in an environment similar to the body. Surface analysis confirmed degradation of the surface of GaN after radiation exposure in water; however, the peptide molecules successfully remained on the surface following exposure to ionizing radiation. We hypothesize that during radiation exposure of the samples, the radiolysis of water produces peroxide and other reactive species on the sample surface. Peroxide exposure promotes the formation of a more stable layer of gallium oxyhydroxide which passivates the surface better than other oxide species.}, number={51}, journal={Langmuir}, publisher={American Chemical Society (ACS)}, author={Berg, Nora G. and Nolan, Michael W. and Paskova, Tania and Ivanisevic, Albena}, year={2014}, month={Dec}, pages={15477–15485} }
 @article{bain_collazo_hsu_latham_manfra_ivanisevic_2014, title={Surface topography and chemistry shape cellular behavior on wide band-gap semiconductors}, volume={10}, ISSN={1742-7061}, url={http://dx.doi.org/10.1016/J.ACTBIO.2014.02.038}, DOI={10.1016/j.actbio.2014.02.038}, abstractNote={The chemical stability and electrical properties of gallium nitride make it a promising material for the development of biocompatible electronics, a range of devices including biosensors as well as interfaces for probing and controlling cellular growth and signaling. To improve the interface formed between the probe material and the cell or biosystem, surface topography and chemistry can be applied to modify the ways in which the device interacts with its environment. PC12 cells are cultured on as-grown planar, unidirectionally polished, etched nanoporous and nanowire GaN surfaces with and without a physisorbed peptide sequence that promotes cell adhesion. While cells demonstrate preferential adhesion to roughened surfaces over as-grown flat surfaces, the topography of that roughness also influences the morphology of cellular adhesion and differentiation in neurotypic cells. Addition of the peptide sequence generally contributes further to cellular adhesion and promotes development of stereotypic long, thin neurite outgrowths over alternate morphologies. The dependence of cell behavior on both the topographic morphology and surface chemistry is thus demonstrated, providing further evidence for the importance of surface modification for modulating bio-inorganic interfaces.}, number={6}, journal={Acta Biomaterialia}, publisher={Elsevier BV}, author={Bain, Lauren E. and Collazo, Ramon and Hsu, Shu-han and Latham, Nicole Pfiester and Manfra, Michael J. and Ivanisevic, Albena}, year={2014}, month={Jun}, pages={2455–2462} }
 @article{bain_jewett_mukund_bedair_paskova_ivanisevic_2013, title={Biomolecular Gradients via Semiconductor Gradients: Characterization of Amino Acid Adsorption to InxGa1–xN Surfaces}, volume={5}, ISSN={1944-8244 1944-8252}, url={http://dx.doi.org/10.1021/AM4015555}, DOI={10.1021/am4015555}, abstractNote={The band gap of indium gallium nitride can be tuned by varying the compositional ratio of indium to gallium, spanning the entire visible region and extending into the near-infrared and near-ultraviolet. This tunability allows for device optimization specific to different applications, including as a biosensor or platform for studying biological interactions. However, these rely on chemically dependent interactions between the device surface and the biostructures of interest. This study presents a material gradient of changing In:Ga composition and the subsequent evaluation of amino acid adsorption to this surface. Arginine is adsorbed to the surface in conditions both above and below the isoelectric point, providing insight to the role of electrostatic interactions in interface formation. These electrostatics are the driving force of the observed adsorption behaviors, with protonated amino acid demonstrating increased adsorption as a function of native surface oxide buildup. We thus present a gradient inorganic substrate featuring varying affinity for amino acid adhesion, which can be applied in generating gradient architectures for biosensors and studying cellular behaviors without application of specialized patterning processes.}, number={15}, journal={ACS Applied Materials & Interfaces}, publisher={American Chemical Society (ACS)}, author={Bain, Lauren E and Jewett, Scott A and Mukund, Aadhithya Hosalli and Bedair, Salah M and Paskova, Tania M and Ivanisevic, Albena}, year={2013}, month={Jul}, pages={7236–7243} }
 @article{foster_collazo_sitar_ivanisevic_2013, title={Cell Behavior on Gallium Nitride Surfaces: Peptide Affinity Attachment versus Covalent Functionalization}, volume={29}, ISSN={["0743-7463"]}, DOI={10.1021/la401503b}, abstractNote={Gallium nitride is a wide band gap semiconductor that demonstrates a unique set of optical and electrical properties as well as aqueous stability and biocompatibility. This combination of properties makes gallium nitride a strong candidate for use in chemical and biological applications such as sensors and neural interfaces. Molecular modification can be used to enhance the functionality and properties of the gallium nitride surface. Here, gallium nitride surfaces were functionalized with a PC12 cell adhesion promoting peptide using covalent and affinity driven attachment methods. The covalent scheme proceeded by Grignard reaction and olefin metathesis while the affinity driven scheme utilized the recognition peptide isolated through phage display. This study shows that the method of attaching the adhesion peptide influences PC12 cell adhesion and differentiation as measured by cell density and morphological analysis. Covalent attachment promoted monolayer and dispersed cell adhesion while affinity driven attachment promoted multilayer cell agglomeration. Higher cell density was observed on surfaces modified using the recognition peptide. The results suggest that the covalent and affinity driven attachment methods are both suitable for promoting PC12 cell adhesion to the gallium nitride surface, though each method may be preferentially suited for distinct applications.}, number={26}, journal={LANGMUIR}, author={Foster, Corey M. and Collazo, Ramon and Sitar, Zlatko and Ivanisevic, Albena}, year={2013}, month={Jul}, pages={8377–8384} }
 @article{wilkins_paskova_ivanisevic_2013, title={Effect of etching with cysteamine assisted phosphoric acid on gallium nitride surface oxide formation}, volume={114}, ISSN={["1089-7550"]}, DOI={10.1063/1.4817899}, abstractNote={In-situ functionalization of polar GaN was performed by adding cysteamine to a phosphoric acid etchant in order to study its effect on photoluminescence and oxide formation on the surfaces. The functionalization was characterized by atomic force microscopy, x-ray photoelectron spectroscopy, photoluminescence (PL), and water contact angle measurements. Two sets of polar GaN samples with different dislocation densities were evaluated, thin GaN layers residing on sapphire and thick free-standing GaN separated from sapphire substrate aiming to reveal the effect of material quality on in-situ functionalization. The addition of cysteamine to the phosphoric acid solution was found to result in: (i) decreased surface roughness, (ii) no change to hydrophobicity, (iii) decreased oxygen content especially at high-temperature treatments. The effect of the in-situ functionalization on the PL efficiency was more pronounced in the free-standing sample than in the film residing on the sapphire, which was attributed to a higher crystal quality free from strain.}, number={6}, journal={JOURNAL OF APPLIED PHYSICS}, author={Wilkins, S. J. and Paskova, T. and Ivanisevic, A.}, year={2013}, month={Aug} }
 @article{makowski_bryan_sitar_arellano_xie_collazo_ivanisevic_2013, title={Erratum: “Kinase detection with gallium nitride based high electron mobility transistors” [Appl. Phys. Lett. 103, 013701 (2013)]}, volume={103}, ISSN={0003-6951 1077-3118}, url={http://dx.doi.org/10.1063/1.4819200}, DOI={10.1063/1.4819200}, abstractNote={[This corrects the article on p. 013701 in vol. 103.].}, number={8}, journal={Applied Physics Letters}, publisher={AIP Publishing}, author={Makowski, Matthew S. and Bryan, Isaac and Sitar, Zlatko and Arellano, Consuelo and Xie, Jinqiao and Collazo, Ramon and Ivanisevic, Albena}, year={2013}, month={Aug}, pages={089902} }
 @article{makowski_bryan_sitar_arellano_xie_collazo_ivanisevic_2013, title={Kinase detection with gallium nitride based high electron mobility transistors}, volume={103}, ISSN={0003-6951 1077-3118}, url={http://dx.doi.org/10.1063/1.4812987}, DOI={10.1063/1.4812987}, abstractNote={A label-free kinase detection system was fabricated by the adsorption of gold nanoparticles functionalized with kinase inhibitor onto AlGaN/GaN high electron mobility transistors (HEMTs). The HEMTs were operated near threshold voltage due to the greatest sensitivity in this operational region. The Au NP/HEMT biosensor system electrically detected 1 pM SRC kinase in ionic solutions. These results are pertinent to drug development applications associated with kinase sensing.}, number={1}, journal={Applied Physics Letters}, publisher={AIP Publishing}, author={Makowski, Matthew S. and Bryan, Isaac and Sitar, Zlatko and Arellano, Consuelo and Xie, Jinqiao and Collazo, Ramon and Ivanisevic, Albena}, year={2013}, month={Jul}, pages={013701} }
 @misc{hugar_ivanisevic_2013, title={Materials characterization and mechanobiology of the eye}, volume={33}, ISSN={["1873-0191"]}, DOI={10.1016/j.msec.2013.02.009}, abstractNote={The eye responds to a great deal of internal and external stimuli throughout its normal function. Due to this, a mechanical or chemical analysis alone is insufficient. A systematic materials characterization is needed. A mechanobiological approach is required for a full understanding of the unique properties and function of the eye. This review compiles the mechanical properties of select eye components, summarizes mechanical and chemical testing platforms, and overviews modeling approaches. Analysis is done across studies, experimental methods, and between species in order to summarize what is known about the mechanobiology of the eye. Several opportunities for future research are identified.}, number={4}, journal={MATERIALS SCIENCE & ENGINEERING C-MATERIALS FOR BIOLOGICAL APPLICATIONS}, author={Hugar, Daniel L. and Ivanisevic, Albena}, year={2013}, month={May}, pages={1867–1875} }
 @inbook{bain_hosalli_bedair_paskova_ivanisevic_2014, place={New York}, series={Conference Proceedings of the Society for Experimental Mechanics Series}, title={Molecular Interactions on InxGa1−xN}, volume={5}, ISBN={9783319007793 9783319007809}, ISSN={2191-5644 2191-5652}, url={http://dx.doi.org/10.1007/978-3-319-00780-9_14}, DOI={10.1007/978-3-319-00780-9_14}, abstractNote={Atomic force microscopy in solution offers a platform for assessing interactions on chemically modified surfaces. In this study a biologically relevant molecule, an amino acid, is adsorbed onto a compositionally varied semiconductor substrate. AFM is used to assess the effect of the substrate composition on the adhesion of the amino acid. We report adsorption of L-arginine to an indium-gallium-nitride (InGaN) substrate with a gradient of In:Ga composition. Data are collected above and below the isoelectric point of arginine to highlight the effect of protonation on the adhesive behavior across the InGaN. Characterization is also performed using X-ray photoelectron spectroscopy to establish the presence of amino acid on the surface and determine the general composition of a given region of the substrate both with and without amino acid. Combining these factors, we are able to better evaluate the significance of substrate properties in influencing the behavior of surface molecules. Determining the dynamics of amino acid behavior as a function of both the substrate and the environment provides new insight into the preparation of semiconductor materials for biological applications.}, booktitle={MEMS and Nanotechnology}, publisher={Springer International Publishing}, author={Bain, L. E. and Hosalli, A. M. and Bedair, S. M. and Paskova, T. and Ivanisevic, A.}, editor={Shaw, Gordon, III and Starman, LaVern and Prorok, Barton C. and Furlong, CosmeEditors}, year={2014}, pages={109–114}, collection={Conference Proceedings of the Society for Experimental Mechanics Series} }
 @article{makowski_kim_gaillard_janes_manfra_bryan_sitar_arellano_xie_collazo_et al._2013, title={Physisorption of functionalized gold nanoparticles on AlGaN/GaN high electron mobility transistors for sensing applications}, volume={102}, ISSN={0003-6951 1077-3118}, url={http://dx.doi.org/10.1063/1.4791788}, DOI={10.1063/1.4791788}, abstractNote={AlGaN/GaN high electron mobility transistors (HEMTs) were used to measure electrical characteristics of physisorbed gold nanoparticles (Au NPs) functionalized with alkanethiols with a terminal methyl, amine, or carboxyl functional group. Additional alkanethiol was physisorbed onto the NP treated devices to distinguish between the effects of the Au NPs and alkanethiols on HEMT operation. Scanning Kelvin probe microscopy and electrical measurements were used to characterize the treatment effects. The HEMTs were operated near threshold voltage due to the greatest sensitivity in this region. The Au NP/HEMT system electrically detected functional group differences on adsorbed NPs which is pertinent to biosensor applications.}, number={7}, journal={Applied Physics Letters}, publisher={AIP Publishing}, author={Makowski, M. S. and Kim, S. and Gaillard, M. and Janes, D. and Manfra, M. J. and Bryan, I. and Sitar, Z. and Arellano, C. and Xie, J. and Collazo, R. and et al.}, year={2013}, month={Feb}, pages={074102} }
 @article{foster_collazo_sitar_ivanisevic_2013, title={Aqueous Stability of Ga- and N-Polar Gallium Nitride}, volume={29}, ISSN={["0743-7463"]}, DOI={10.1021/la304039n}, abstractNote={The stability of III-nitride semiconductors in various solutions becomes important as researchers begin to integrate them into sensing platforms. This study quantitatively compares the stability of GaN surfaces with different polarities. This type of quantification is important because it represents the first step toward designing semiconductor material interfaces compatible with solution conditions. A stability study of Ga- and N-polar GaN was conducted by immersion of the surfaces in deionized H(2)O, pH 5, pH 9, and H(2)O(2) solutions for 7 days. Inductively coupled plasma mass spectrometry of the solutions was conducted to determine the amount of gallium leached from the surface. X-ray photoelectron spectroscopy and atomic force microscopy were used to compare the treated surfaces to untreated surfaces. The results show that both gallium nitride surface types exhibit the greatest stability in acidic and neutral solutions. Gallium polar surfaces were found to exhibit superior stability to nitrogen polar surfaces in the solutions studied. Our findings highlight the need for further research on surface passivation and functionalization techniques for polar III-nitride semiconductors.}, number={1}, journal={LANGMUIR}, author={Foster, Corey M. and Collazo, Ramon and Sitar, Zlatko and Ivanisevic, Albena}, year={2013}, month={Jan}, pages={216–220} }
 @article{valentin-rodriguez_tezel_ivanisevic_2012, title={Deposition of Triamcinolone Acetonide and Its Effect on Soft Tissue Topography}, volume={1}, ISSN={["2192-2659"]}, DOI={10.1002/adhm.201200049}, abstractNote={AbstractBimodal imaging is utilized to characterize the topography of human tissue samples. The deposition of triamcinolone acetonide (TA) on various surfaces – including surgical human inner limiting membrane (ILM) samples and collagen fibrillar sheets – was studied. Changes in composition were well defined with bimodal imaging when TA deposition was examined on mica. TA sedimentation resulted in observable changes in ILM topography when compared to collagen fibrillar sheets. The heterogeneous chemical and topographical features of the ILM tissues promoted the TA crystallization compared to the flatter and homogeneous collagen surfaces. Higher spatial resolution was achieved by imaging ILM samples in the new bimodal imaging mode. The most apparent difference was observed in the imaging of ILM samples which had been exposed to the steroid TA. The study demonstrated the usefulness of bimodal imaging to evaluate tissue samples.}, number={4}, journal={ADVANCED HEALTHCARE MATERIALS}, author={Valentin-Rodriguez, Celimar and Tezel, Tongalp H. and Ivanisevic, Albena}, year={2012}, month={Jul}, pages={520–525} }
 @article{richards_zemlyanov_ivanisevic_2012, title={Kelvin Probe Force Microscopy Analysis of the Covalent Functionalization and DNA Modification of Gallium Phosphide Nanorods}, volume={116}, ISSN={["1932-7455"]}, DOI={10.1021/jp302307j}, abstractNote={The growth, covalent functionalization, and subsequent DNA modification of gallium phosphide (GaP) nanorods is presented. Analysis of the nanorods by scanning electron microscopy (SEM), transmission electron microscopy (TEM), and X-ray diffraction (XRD) revealed important information regarding their physical properties such as the presence of twinning defects. The nanorods were deposited onto glass substrates for further functionalization and biomolecule immobilization. Plasma cleaning was employed to remove the surfactant present on the nanorods’ surfaces. Kelvin probe force microscopy (KPFM) was used to analyze the extent of plasma cleaning and how it affected the functionalization that employed thiol chemistry. KFPM analysis of the subsequent modification of functionalized nanorods with single-stranded DNA (ssDNA) revealed that immobilization was dependent on the amount of plasma cleaning to which the nanorods had been exposed. Nanorods were then exposed to the cDNA strand and KPFM was again used to de...}, number={23}, journal={JOURNAL OF PHYSICAL CHEMISTRY C}, author={Richards, David N. and Zemlyanov, Dmitry Y. and Ivanisevic, Albena}, year={2012}, month={Jun}, pages={12613–12620} }
 @article{kramer_ivanisevic_2012, title={Parallel Dip-Pen Nanolithography using Spore- and Colloid-Terminated Cantilevers}, volume={8}, ISSN={1613-6810}, url={http://dx.doi.org/10.1002/smll.201200378}, DOI={10.1002/smll.201200378}, abstractNote={Parallel dip-pen nanolithography is used to generate micrometer-scale patterns with protein and lipid dyes on both a glass surface and spore layer. Spore- and colloid-based tips are used to facilitate parallel patterning.}, number={24}, journal={Small}, publisher={Wiley}, author={Kramer, Marcus A. and Ivanisevic, Albena}, year={2012}, month={Aug}, pages={3791–3794} }
 @article{richards_luce_zemlyanov_ivanisevic_2012, title={Quantitative Analysis of the Functionalization of Gallium Phosphide With Organic Azides}, volume={34}, ISSN={["1932-8745"]}, DOI={10.1002/sca.21012}, abstractNote={SummaryGallium phosphide (GaP) surfaces were functionalized with two different molecules that contain an azide moiety at their terminus. Compound 4‐azidophenacyl bromide (4AB) is an aryl azide with a bromine group at its opposite terminus that provides easy identification of the molecule's presence on the surface with x‐ray photoelectron spectroscopy (XPS). O‐(2‐aminoethyl)‐O′‐(2‐azidoethyl)pentaethylene glycol (AAP) is a small poly(ethylene glycol) molecule with an amine group at its opposite terminus. Atomic force microscopy was used to identify the uniformity of the clean and functionalized GaP surfaces. Water contact angle revealed a more hydrophobic surface with AAP functionalization (33°) and even more hydrophobic (53°) with the 4AB functionalized surface compared to a clean surface (16°). XPS confirmed the presence of each of the organic azides on the surface. XPS was further used to calculate the adlayer thickness of each functionalization. This analysis revealed an adlayer thickness of about 8 Å for the 4AB functionalized surfaces compared to 1 Å for the AAP adlayer, which led to the conclusion that AAP functionalization only provided partial coverage. A stability study using 4AB‐functionalized surfaces showed good stability in saline solutions with varying concentrations of hydrogen peroxide. Finally, inductively coupled plasma mass spectrometry was used to evaluate the gallium concentration in the stability solutions. While the functionalization with the organic azides did not provide complete suppression of gallium leaching, both of the azides decreased the leaching by 10–50%. SCANNING 34: 332–340, 2012. © 2012 Wiley Periodicals, Inc.}, number={5}, journal={SCANNING}, author={Richards, David and Luce, Philip and Zemlyanov, Dmitry and Ivanisevic, Albena}, year={2012}, pages={332–340} }
 @article{jewett_yoder_ivanisevic_2012, title={Surface modifications on InAs decrease indium and arsenic leaching under physiological conditions}, volume={261}, ISSN={["1873-5584"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84867742842&partnerID=MN8TOARS}, DOI={10.1016/j.apsusc.2012.08.115}, abstractNote={Devices containing III–V semiconductors such as InAs are increasingly being used in the electronic industry for a variety of optoelectronic applications. Furthermore, the attractive chemical, material, electronic properties make such materials appealing for use in devices designed for biological applications, such as biosensors. However, in biological applications the leaching of toxic materials from these devices could cause harm to cells or tissue. Additionally, after disposal, toxic inorganic materials can leach from devices and buildup in the environment, causing long-term ecological harm. Therefore, the toxicity of these materials along with their stability in physiological conditions are important factors to consider. Surface modifications are one common method of stabilizing semiconductor materials in order to chemically and electronically passivate them. Such surface modifications could also prevent the leaching of toxic materials by preventing the regrowth of the unstable surface oxide layer and by creating an effective barrier between the semiconductor surface and the surrounding environment. In this study, various surface modifications on InAs are developed with the goal of decreasing the leaching of indium and arsenic. The leaching of indium and arsenic from modified substrates was assessed in physiological conditions using inductively coupled plasma mass spectrometry (ICP-MS). Substrates modified with 11-mercapto-1-undecanol (MU) and graft polymerized with poly(ethylene) glycol (PEG) were most effective at preventing indium and arsenic leaching. These surfaces were characterized using contact angle analysis, ellipsometry, atomic force microscopy (AFM), and X-ray photoelectron spectroscopy (XPS). Substrates modified with collagen and synthetic polyelectrolytes were least effective, due to the destructive nature of acidic environments on InAs. The toxicity of modified and unmodified InAs, along with raw indium, arsenic, and PEG components was assessed using zebrafish embryos.}, journal={APPLIED SURFACE SCIENCE}, author={Jewett, Scott A. and Yoder, Jeffrey A. and Ivanisevic, Albena}, year={2012}, month={Nov}, pages={842–850} }
 @misc{jewett_ivanisevic_2012, title={Wet-Chemical Passivation of InAs: Toward Surfaces with High Stability and Low Toxicity}, volume={45}, ISSN={["1520-4898"]}, DOI={10.1021/ar200282f}, abstractNote={In a variety of applications where the electronic and optical characteristics of traditional, siliconbased materials are inadequate, recently researchers have employed semiconductors made from combinations of group III and V elements such as InAs. InAs has a narrow band gap and very high electron mobility in the near-surface region, which makes it an attractive material for high performance transistors, optical applications, and chemical sensing. However, silicon-based materials remain the top semiconductors of choice for biological applications, in part because of their relatively low toxicity. In contrast to silicon, InAs forms an unstable oxide layer under ambient conditions, which can corrode over time and leach toxic indium and arsenic components. To make InAs more attractive for biological applications, researchers have investigated passivation, chemical and electronic stabilization, of the surface by adlayer adsorption. Because of the simplicity, low cost, and flexibility in the type of passivating molecule used, many researchers are currently exploring wet-chemical methods of passivation. This Account summarizes much of the recent work on the chemical passivation of InAs with a particular focus on the chemical stability of the surface and prevention of oxide regrowth. We review the various methods of surface preparation and discuss how crystal orientation affects the chemical properties of the surface. The correct etching of InAs is critical as researchers prepare the surface for subsequent adlayer adsorption. HCl etchants combined with a postetch annealing step allow the tuning of the chemical properties in the near-surface region to either arsenic- or indium-rich environments. Bromine etchants create indium-rich surfaces and do not require annealing after etching; however, bromine etchants are harsh and potentially destructive to the surface. The simultaneous use of NH(4)OH etchants with passivating molecules prevents contact with ambient air that can occur during sample transfer between solutions. The passivation of InAs is dominated by sulfur-based molecules, which form stable In-S bonds on the InAs surface. Both sulfides and alkanethiols form well-defined monolayers on InAs and are dominated by In-S interactions. Sulfur-passivated InAs surfaces prevent regrowth of the surface oxide layer and are more stable in air than unpassivated surfaces. Although functionalization of InAs with sulfur-based molecules effectively passivates the surface, future sensing applications may require the adsorption of functional biomolecules onto the InAs surface. Current research in this area focuses on the passivation abilities of biomolecules such as collagen binding peptides and amino acids. These biomolecules can physically adsorb onto InAs, and they demonstrate some passivation ability but not to the extent of sulfur-based molecules. Because these adsorbents do not form covalent bonds with the InAs surface, they do not effectively block oxide regrowth. A mixed adlayer containing a biomolecule and a thiol on the InAs surface provides one possible solution: these hybrid surfaces enhance passivation but also maintain the presence of a biomolecule on the surface. Such surface functionalization strategies on InAs could provide long-term stability and make these surfaces suitable for biological applications.}, number={9}, journal={ACCOUNTS OF CHEMICAL RESEARCH}, author={Jewett, Scott A. and Ivanisevic, Albena}, year={2012}, month={Sep}, pages={1451–1459} }
 @article{jewett_zemlyanov_ivanisevic_2011, title={Adsorption of Mixed Peptide/Thiol Adlayers on InAs: Assessment of Different Functionalization Strategies Using X-ray Photoelectron Spectroscopy}, volume={115}, ISSN={["1932-7447"]}, DOI={10.1021/jp203203x}, abstractNote={Mixed adlayers are commonly used to create surfaces with multiple functional groups or molecular gradients. The resulting surfaces are designed to have the combined effects of each adsorbed functional group. In this work, we combine the passivation ability of a thiol with the functionality of a peptide by assembling mixed peptide/thiol adlayers on InAs. Both sequential (insertion) and simultaneous (co-assembly) methods are used to functionalize InAs and are analyzed by contact angle measurements and X-ray photoelectron spectroscopy (XPS). Peptide coverage, thiol coverage, and oxide layer thicknesses are estimated from XPS data. For each method, oxide layer thicknesses were significantly lower than the oxide thicknesses for as-received samples. Surfaces functionalized using the insertion methods had lower oxide layer thicknesses than peptide only samples, indicating that the addition of the thiol helped block oxide regrowth. Functionalization with the thiol followed by the peptide yielded surfaces with the...}, number={29}, journal={JOURNAL OF PHYSICAL CHEMISTRY C}, author={Jewett, Scott and Zemlyanov, Dmitry and Ivanisevic, Albena}, year={2011}, month={Jul}, pages={14244–14252} }
 @article{jewett_zemlyanov_ivanisevic_2011, title={Characterization of Peptide Adsorption on InAs Using X-ray Photoelectron Spectroscopy}, volume={27}, ISSN={0743-7463 1520-5827}, url={http://dx.doi.org/10.1021/la104963v}, DOI={10.1021/la104963v}, abstractNote={The well-defined structure and high stability of peptides make them attractive biotemplates for low-temperature synthesis of semiconductor nanocrystals. Adsorbed peptide monolayers could also potentially passivate semiconductors by preventing regrowth of the oxide layer. In this work, the adsorption and passivation capabilities of different collagen-binding peptides on InAs surfaces were analyzed by X-ray photoelectron spectroscopy (XPS). Before peptide functionalization, Br(2)- and HCl-based etches were used to remove the native oxide layer on the InAs surfaces. The presence of the N 1s peak for peptide-functionalized samples confirms the adsorption of peptides onto the etched InAs surfaces. Calculated coverages were similar for all peptide sequences and ranged from ∼20 to 40% of a monolayer using the deconvoluted C 1s spectra and from ∼2 to 5% for the N 1s spectra. The passivation ability of the peptides was analyzed by comparing the ratios of the oxide components to the nonoxide components in the XPS spectra. The thickness of the oxide layer was also approximated by accounting for the attenuation of the substrate photoelectrons through the oxide layer. We find that the oxide layer regrowth still occurs after peptide functionalization. However, the oxide layer thicknesses for peptide-functionalized samples do not reach as received levels, indicating that the peptides do have some passivation ability on InAs.}, number={7}, journal={Langmuir}, publisher={American Chemical Society (ACS)}, author={Jewett, Scott and Zemlyanov, Dmitry and Ivanisevic, Albena}, year={2011}, month={Apr}, pages={3774–3782} }
 @article{makowski_zemlyanov_lindsey_bernhard_hagen_chan_petersohn_medow_wendel_chen_et al._2011, title={Covalent attachment of a peptide to the surface of gallium nitride}, volume={605}, ISSN={0039-6028}, url={http://dx.doi.org/10.1016/j.susc.2011.05.015}, DOI={10.1016/j.susc.2011.05.015}, abstractNote={The properties of GaN have made it not only an ideal material for high power and high frequency electronic devices, but also a semiconductor suitable for application in biosensing devices. The utilization of GaN in electronic biosensors has increased the importance of characterizing robust and easily implemented organic functionalization methods for GaN surfaces. This work demonstrates and characterizes a route to functionalize the GaN (0001) surface with two organic molecules, hexylamine and a peptide, through olefin cross-metathesis with Grubbs first generation catalyst. The GaN (0001) surface was chlorinated, functionalized with a terminal alkene group using a Grignard reaction, and then terminated with a carboxyl group using an olefin cross-metathesis reaction. With a condensation reaction, the final step in the reaction scheme bound hexylamine or a peptide to the carboxyl terminated GaN surface. Qualitative and quantitative X-ray photoelectron spectroscopy (XPS) data verified the success of each step in the reaction scheme. Surface element composition, adlayer coverages, and adlayer thicknesses were calculated based on the XPS data. At least a monolayer of surface molecules covered the GaN surface.}, number={15-16}, journal={Surface Science}, publisher={Elsevier BV}, author={Makowski, Matthew S. and Zemlyanov, Dmitry Y. and Lindsey, Jason A. and Bernhard, Jonathan C. and Hagen, Evan M. and Chan, Burke K. and Petersohn, Adam A. and Medow, Matthew R. and Wendel, Lindsay E. and Chen, Dafang and et al.}, year={2011}, month={Aug}, pages={1466–1475} }
 @article{jaganathan_wang_klein_lossie_ivanisevic_2011, title={Detecting DNA methylation through changes in transverse proton relaxation}, volume={136}, ISSN={0003-2654 1364-5528}, url={http://dx.doi.org/10.1039/c1an15146k}, DOI={10.1039/c1an15146k}, abstractNote={We present a facile, simple method to detect DNA methylation by measuring the transverse proton relaxation behaviour. Positively charged nanoparticles are arranged along the negatively charged backbone of DNA strands through electrostatic interactions. The arrangement of NPs along DNA strands aids to amplify and compare the transverse proton relaxation signal for un-cut versus cut DNA strands cleaved by sequence specific restriction enzymes. Results from this study suggest that the presence of methylation on DNA can be detected using superparamagnetic NPs using NMR.}, number={12}, journal={The Analyst}, publisher={Royal Society of Chemistry (RSC)}, author={Jaganathan, Hamsa and Wang, Pengfei and Klein, Jonathon and Lossie, Amy C. and Ivanisevic, Albena}, year={2011}, pages={2441} }
 @article{jaganathan_hugar_ivanisevic_2011, title={Examining MRI Contrast in Three-Dimensional Cell Culture Phantoms with DNA-Templated Nanoparticle Chains}, volume={3}, ISSN={1944-8244 1944-8252}, url={http://dx.doi.org/10.1021/am200086r}, DOI={10.1021/am200086r}, abstractNote={DNA-templated nanoparticle (NP) chains were examined as potential magnetic resonance imaging (MRI) contrast agents using in vitro environments of the extracellular matrix and tissue. A 3-T clinical MRI scanner was utilized to examine and compare image contrast enhanced by dispersed NPs, DNA-templated NP chains, gold-superparamagnetic multicomponent NP chains, and polyelectrolyte encapsulated, multicomponent NP chains in both T(1)-weighted and T(2)-weighted images. In addition, the longitudinal and transverse relaxivity (r(1) and r(2)) changes were measured both in the basement membrane, using Matrigel, and in the tissue environment, using in vitro 3D cell culture scaffolds. Results suggest that MRI contrast was significantly enhanced from NP chains compared to dispersed NPs in the basement membrane and polyelectrolyte encapsulation for NP chains produced similar relaxivity to nonencapsulated NP chains due to the enhanced cell uptake of encapsulated NP chains.}, number={4}, journal={ACS Applied Materials & Interfaces}, publisher={American Chemical Society (ACS)}, author={Jaganathan, Hamsa and Hugar, Daniel L. and Ivanisevic, Albena}, year={2011}, month={Mar}, pages={1282–1288} }
 @article{jewett_makowski_andrews_manfra_ivanisevic_2012, title={Gallium nitride is biocompatible and non-toxic before and after functionalization with peptides}, volume={8}, ISSN={["1878-7568"]}, DOI={10.1016/j.actbio.2011.09.038}, abstractNote={The toxicity of semiconductor materials can significantly hinder their use for in vitro and in vivo applications. Gallium nitride (GaN) is a material with remarkable properties, including excellent chemical stability. This work demonstrated that functionalized and etched GaN surfaces were stable in aqueous environments and leached a negligible amount of Ga in solution even in the presence of hydrogen peroxide. Also, GaN surfaces in cell culture did not interfere with nearby cell growth, and etched GaN promoted the adhesion of cells compared to etched silicon surfaces. A model peptide, "IKVAV", covalently attached to GaN and silicon surfaces increased the adhesion of PC12 cells. Peptide terminated GaN promoted greater cell spreading and extension of neurites. The results suggest that peptide modified GaN is a biocompatible and non-toxic material that can be used to probe chemical and electrical stimuli associated with neural interfaces.}, number={2}, journal={ACTA BIOMATERIALIA}, author={Jewett, Scott A. and Makowski, Matthew S. and Andrews, Benjamin and Manfra, Michael J. and Ivanisevic, Albena}, year={2012}, month={Feb}, pages={728–733} }
 @misc{richards_ivanisevic_2012, title={Inorganic material coatings and their effect on cytotoxicity}, volume={41}, ISSN={["1460-4744"]}, DOI={10.1039/c1cs15252a}, abstractNote={Inorganic materials have become an increasingly researched topic due to their applications in many areas especially health care. One major problem with them is the effect that their surface coatings have on cells. The same coatings that are meant to increase biocompatibility can actually invoke cytotoxicity. This tutorial review focuses on the various types of coatings and how their properties, such as electrostatic charge and hydrophobicity, affect the observed toxicity. The theorized mechanisms by which the coatings induce toxicity are also presented. Finally, the prospects for the future of this field are discussed.}, number={6}, journal={CHEMICAL SOCIETY REVIEWS}, author={Richards, David and Ivanisevic, Albena}, year={2012}, pages={2052–2060} }
 @misc{makowski_ivanisevic_2011, title={Molecular Analysis of Blood with Micro-/Nanoscale Field-Effect-Transistor Biosensors}, volume={7}, ISSN={["1613-6829"]}, DOI={10.1002/smll.201100211}, abstractNote={AbstractRapid and accurate molecular blood analysis is essential for disease diagnosis and management. Field‐effect transistor (FET) biosensors are a type of device that promise to advance blood point‐of‐care testing by offering desirable characteristics such as portability, high sensitivity, brief detection time, low manufacturing cost, multiplexing, and label‐free detection. By controlling device parameters, desired FET biosensor performance is obtained. This review focuses on the effects of sensing environment, micro‐/nanoscale device structure, operation mode, and surface functionalization on device performance and long‐term stability.}, number={14}, journal={SMALL}, author={Makowski, Matthew S. and Ivanisevic, Albena}, year={2011}, month={Jul}, pages={1863–1875} }
 @article{wang_jaganathan_ivanisevic_2011, title={Multicomponent DNA-Templated Nanoparticle Chains with Controllable Dimension and Composition}, volume={7}, ISSN={1613-6810}, url={http://dx.doi.org/10.1002/smll.201100067}, DOI={10.1002/smll.201100067}, abstractNote={Multicomponent DNA-templated nanoparticle chains with controllable dimension and composition are fabricated by joining nanoparticle (NP)-coated DNA fragments with asymmetric sticky overhangs in a specific pattern. Nuclear magnetic resonance spectroscopy is used to investigate the proton relaxation properties for two- segmented multicomponent structures. The position, composition, and the pattern of the NP chains has an influence on proton relaxation.}, number={14}, journal={Small}, publisher={Wiley}, author={Wang, Pengfei and Jaganathan, Hamsa and Ivanisevic, Albena}, year={2011}, month={May}, pages={2021–2026} }
 @article{kramer_gieseck_andrews_ivanisevic_2011, title={Spore-Terminated Cantilevers for Chemical Patterning on Complex Architectures}, volume={133}, ISSN={0002-7863 1520-5126}, url={http://dx.doi.org/10.1021/ja201331j}, DOI={10.1021/ja201331j}, abstractNote={Atomic force microscope tips terminated with spore cells are used to directly pattern onto glass and tissue surfaces. The spore cells act as sponges and eliminate the need to use microfabricated ink reservoirs during lithography.}, number={25}, journal={Journal of the American Chemical Society}, publisher={American Chemical Society (ACS)}, author={Kramer, Marcus A. and Gieseck, Richard L. and Andrews, Benjamin and Ivanisevic, Albena}, year={2011}, month={Jun}, pages={9627–9629} }
 @article{valentin-rodriguez_tezel_ivanisevic_2011, title={Surface modification of vitreoretinal surgical instruments with layer-by-layer films}, volume={33}, ISSN={0161-0457}, url={http://dx.doi.org/10.1002/sca.20240}, DOI={10.1002/sca.20240}, abstractNote={AbstractCommercially available vitreoretinal surgical forceps were modified with layer‐by‐layer (LbL) films designed to render them the ability to specifically adhere human the inner limiting membrane. Surgical forceps with two different geometries were etched, polished, and silanized before deposition of the films composed of poly (allylamine hydrochloride), poly (styrene sulfonate), and cationic gold nanoparticles. Stability and integrity of the LbL films was scrutinized by exposing the modified forceps to commercial disinfectant Cidex‐OPA and then placing the instruments in a physiological‐like HEPES buffer (pH 7.4, 5 mM, 154 mM NaCl). Surface topography analysis with scanning electron microscopy revealed that the geometry of the surgical instrument may affect the integrity of the film. Analysis of the HEPES buffer with inductively coupled plasma mass spectrometry demonstrated that gold nanoparticles did not leach from the LbL film after 60 min. SCANNING 33:397–401, 2011. © 2011 Wiley Periodicals, Inc.}, number={6}, journal={Scanning}, publisher={Wiley}, author={Valentin-Rodriguez, Celimar and Tezel, Tongalp H. and Ivanisevic, Albena}, year={2011}, month={May}, pages={397–401} }
 @article{valentín-rodríguez_he_chodavarapu_smith_roach_lewis_vaid_lin_lord_green_et al._2011, title={Tuning the adhesion of layer-by-layer films to the physicochemical properties of inner limiting membranes using nanoparticles}, volume={42}, ISSN={0968-4328}, url={http://dx.doi.org/10.1016/j.micron.2011.02.007}, DOI={10.1016/j.micron.2011.02.007}, abstractNote={Retinal trauma is a serious concern for patients undergoing inner limiting membrane (ILM) peeling to correct for various vitreoretinal interface conditions. This mechanical trauma can be prevented by modifying the surface of surgical instruments to increase adhesion to the ILM. To this effect, we have studied the effects of roughness and surface charge on the adhesive properties of ILMs by utilizing layer-by-layer (LbL) films with embedded gold nanoparticles (LbL-AuNP films). LbL films were assembled on atomic force microscopy (AFM) tipless cantilevers. Topographical analysis of these films, with and without nanoparticles, showed that LbL films with nanoparticles had a higher rms roughness compared to films alone or unmodified cantilevers. Nanoparticle-modified LbL films significantly increased the adhesion forces at the cantilever-ILM interface, compared to LbL films without particles. Surprisingly, adsorption of gold nanoparticles onto the AFM cantilevers caused increases in adhesion forces greater than those measured with LbL-AuNP films. These results have important implications for the design of surface modifications for vitreoretinal surgical instruments.}, number={6}, journal={Micron}, publisher={Elsevier BV}, author={Valentín-Rodríguez, Celimar and He, Yuanzu and Chodavarapu, Sai S. and Smith, Mackenzie and Roach, Alexander S. and Lewis, Nicole R. and Vaid, Sonal and Lin, Teresa and Lord, Derek E. and Green, Sara M. and et al.}, year={2011}, month={Aug}, pages={616–624} }
 @article{murthy_bailey_valentin-rodriguez_ivanisevic_grunlan_2010, title={Amphiphilic silicones prepared from branched PEO-silanes with siloxane tethers}, volume={48}, ISSN={0887-624X}, url={http://dx.doi.org/10.1002/pola.24203}, DOI={10.1002/pola.24203}, abstractNote={AbstractAmphiphilic silicones were prepared by the covalent incorporation of branched polyethylene oxide (PEO) via a siloxane tether. This was achieved by using six novel branched PEO‐silanes with varying siloxane tether lengths and PEO molecular weight (Mn). Each PEO‐silane was crosslinked via acid‐catalyzed sol–gel condensation with α,ω‐bis(Si‐OH)polydimethylsiloxane (PDMS) (Mn = 3000 g/mol) to yield six amphiphilic silicone films. Film surface hydrophilicity increased with siloxane tether length, particularly after exposure to an aqueous environment, indicating that the PEO segments were more readily driven to the surface. This effect was more pronounced for films prepared with PEO‐silanes containing lower Mn PEO segments. AFM was used to study surface reconstruction of films upon exposure to an aqueous environment. Adsorption of bovine serum albumin (BSA) and human fibrinogen (HF) proteins decreased with siloxane tether length, particularly after first exposing films to an aqueous environment. For a given siloxane tether length, relatively less BSA adsorbed onto films prepared with PEO‐silanes with lower Mn PEO segments whereas less HF adsorbed onto films prepared with PEO‐silanes with higher Mn PEO segments. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 4108–4119, 2010}, number={18}, journal={Journal of Polymer Science Part A: Polymer Chemistry}, publisher={Wiley}, author={Murthy, Ranjini and Bailey, Brennan M. and Valentin-Rodriguez, Celimar and Ivanisevic, Albena and Grunlan, Melissa A.}, year={2010}, month={Aug}, pages={4108–4119} }
 @article{richards_zemlyanov_ivanisevic_2010, title={Assessment of the Passivation Capabilities of Two Different Covalent Chemical Modifications on GaP(100)}, volume={26}, ISSN={0743-7463 1520-5827}, url={http://dx.doi.org/10.1021/la904451x}, DOI={10.1021/la904451x}, abstractNote={Gallium phosphide is a semiconductor material that can be used for the fabrication of optoelectronic devices. The report compares the ability of two similar organic molecules to form covalent bonds with the GaP(100) surface. Undecenoic acid (UDA) is a terminal alkene that can potentially form Ga-C bonds, and mercaptoundecanoic acid (MUA) is a thiol that can be used to generate Ga-S bonds. The chemical passivation capabilities of the functionalized surfaces exposed to different media were investigated by contact angle measurements, atomic force microscopy (AFM), and X-ray photoelectron spectroscopy (XPS). Toxicity levels, which are important for sensing applications, were evaluated by inductively coupled plasma mass spectrometry (ICP-MS) on the media in which surfaces were stored in order to identify any gallium leaching from the substrates. Both molecules formed fairly disordered monolayers demonstrated by comparable oxide thicknesses. The UDA molecules demonstrated better stability compared to MUA molecules based on contact angle measurements and tilt angle data extracted from XPS results. According to the XPS data, the UDA molecules formed a more dense adlayer compared to MUA molecules. With respect to toxicity, the UDA-functionalized GaP provided better passivation which was confirmed by less gallium leaching into water and saline solutions. Overall, the superior passivation provided by UDA demonstrates that alkene grafting has better potential for modifying GaP based devices such as implantable sensors.}, number={11}, journal={Langmuir}, publisher={American Chemical Society (ACS)}, author={Richards, David and Zemlyanov, Dmitry and Ivanisevic, Albena}, year={2010}, month={Jun}, pages={8141–8146} }
 @article{kramer_andrews_hugar_jaitli_larsen_kline_mcellen_agrawal_su_dammu_et al._2010, title={Characterization of Conformational Adsorbate Changes on a Tissue-Derived Substrate Using Fourier Transform Infrared Spectroscopy}, volume={26}, ISSN={0743-7463 1520-5827}, url={http://dx.doi.org/10.1021/la1038766}, DOI={10.1021/la1038766}, abstractNote={Fourier transform infrared (FT-IR) spectroscopy is utilized to observe adsorbate interactions with a tissue-derived collagen scaffold extracted from the Bruch's membrane of pig eyes. The characterization includes conformational changes in isoleucine, polyisoleucine, collagen-binding peptide, RGD-tagged collagen-binding peptide, and laminin after adsorption onto the substrate. Isotopically labeled isoleucine is further utilized to understand changes in the biomolecular structure upon binding to a tissue-derived surface. The adsorbates associated with the collagen scaffold predominately through hydrophobic interactions and hydrogen bonding. The results of this study can be used to improve our understanding of surface chemistry changes during the engineering of biomimetic scaffolds before and after biomolecule adsorption.}, number={23}, journal={Langmuir}, publisher={American Chemical Society (ACS)}, author={Kramer, Marcus A. and Andrews, Benjamin and Hugar, Daniel L. and Jaitli, Arjun and Larsen, Seij B. and Kline, Benjamin P. and McEllen, Kristin N. and Agrawal, Namita and Su, Si Min and Dammu, Sandhya A. and et al.}, year={2010}, month={Dec}, pages={18083–18088} }
 @article{jaganathan_gieseck_ivanisevic_2010, title={Characterizing proton relaxation times for metallic and magnetic layer-by-layer-coated, DNA-templated nanoparticle chains}, volume={21}, ISSN={0957-4484 1361-6528}, url={http://dx.doi.org/10.1088/0957-4484/21/24/245103}, DOI={10.1088/0957-4484/21/24/245103}, abstractNote={Metallic and superparamagnetic DNA-templated nanoparticle (NP) chains are examined as potential imaging agents. Proton relaxation times (T1 and T2) are measured for DNA nanostructures using nuclear magnetic resonance (NMR) spectroscopy. The layer-by-layer (LBL) method was used to encapsulate the DNA-templated NP chains and demonstrated a change in proton relaxation times. Results from this study suggest that LBL-coated, DNA-templated nanostructures can serve as effective imaging agents for magnetic resonance imaging (MRI) applications.}, number={24}, journal={Nanotechnology}, publisher={IOP Publishing}, author={Jaganathan, Hamsa and Gieseck, Richard L and Ivanisevic, Albena}, year={2010}, month={May}, pages={245103} }
 @article{richards_zemlyanov_asrar_chokshi_cook_hinton_lu_nguyen_patel_usher_et al._2010, title={DNA Immobilization on GaP(100) Investigated by Kelvin Probe Force Microscopy}, volume={114}, ISSN={1932-7447 1932-7455}, url={http://dx.doi.org/10.1021/jp105927t}, DOI={10.1021/jp105927t}, abstractNote={Understanding changes in the properties of semiconductor materials after immobilization of biomolecules on the surface is essential for the fabrication of well-tuned and programmable devices. The work examines changes in the properties of gallium phosphide (GaP) after modification with an organic linker, a single stranded DNA, and its complementary strand. We investigated changes in surface potential with Kelvin probe force microscopy (KPFM). Analysis revealed that a more ordered adlayer of ssDNA was present when a lower concentration of linker molecule was used. KPFM data combined with coverage data obtained from X-ray photoelectron spectroscopy (XPS) further confirmed this result. Successful hybridization with the complementary strand was confirmed by both KPFM and Raman spectroscopy. The results indicate that one can control the amount of DNA on the surface by changing the initial concentration of the organic linker, and thus modulate the surface potential of the semiconductor material.}, number={36}, journal={The Journal of Physical Chemistry C}, publisher={American Chemical Society (ACS)}, author={Richards, David N. and Zemlyanov, Dmitry Y. and Asrar, Rafay M. and Chokshi, Yena Y. and Cook, Emily M. and Hinton, Thomas J. and Lu, Xinran and Nguyen, Viet Q. and Patel, Neil K. and Usher, Jonathan R. and et al.}, year={2010}, month={Aug}, pages={15486–15490} }
 @article{jaganathan_ivanisevic_2011, title={Gold–iron oxide nanoparticle chains scaffolded on DNA as potential magnetic resonance imaging agents}, volume={21}, ISSN={0959-9428 1364-5501}, url={http://dx.doi.org/10.1039/c0jm02754e}, DOI={10.1039/c0jm02754e}, abstractNote={We present a unique nanostructure design using DNA that can serve as potential magnetic resonance imaging (MRI) agents. By attaching gold and iron oxide NPs on linear strands of DNA, NP chains are easily formed by self-assembly and through DNA-based enzymes. Furthermore, gold–iron oxide NP chains exhibit fast proton relaxation times that improve MRI signals and do not induce in vitro toxicity. This report highlights the use of DNA to create NP chains as a cost-effective, promising technology for the detection of diseases through MRI.}, number={4}, journal={J. Mater. Chem.}, publisher={Royal Society of Chemistry (RSC)}, author={Jaganathan, Hamsa and Ivanisevic, Albena}, year={2011}, pages={939–943} }
 @article{jaganathan_ivanisevic_2010, title={In vitro Cytotoxic Evaluation of Metallic and Magnetic DNA-Templated Nanostructures}, volume={2}, ISSN={1944-8244 1944-8252}, url={http://dx.doi.org/10.1021/am1000568}, DOI={10.1021/am1000568}, abstractNote={We evaluate the potential in vitro cytotoxicity that may arise from metallic and magnetic DNA-templated nanostructures. By using a fluorescence-based assay, the viability of cells was examined after treatment with DNA-templated nanostructures. Inductively coupled plasma mass spectrometry (ICP-MS) was used to quantify the amount of nanoparticles internalized by the cells. Cell uptake of DNA-templated nanostructures was enhanced after encapsulating the nanostructure with layers of polyelectrolytes (PSS and PAH) and targeting ligands. Transmission electron microscope (TEM) images provided evidence that the nanostructures were localized in vesicles in the cytoplasm of the cells. The results from this study suggest that gold, iron oxide, and cobalt iron oxide DNA-templated nanostructures do not induce in vitro toxicity.}, number={5}, journal={ACS Applied Materials & Interfaces}, publisher={American Chemical Society (ACS)}, author={Jaganathan, Hamsa and Ivanisevic, Albena}, year={2010}, month={Apr}, pages={1407–1413} }
 @article{jaganathan_gieseck_hudson_kellogg_ramaswamy_raver_smith_vacchiano_wager_ivanisevic_2010, title={Mechanism of Proton Relaxation for Enzyme‐Manipulated, Multicomponent Gold–Magnetic Nanoparticle Chains}, volume={11}, ISSN={1439-4235 1439-7641}, url={http://dx.doi.org/10.1002/cphc.201000397}, DOI={10.1002/cphc.201000397}, abstractNote={AbstractLongitudinal and transverse relaxation times of multicomponent nanoparticle (NP) chains are investigated for their potential use as multifunctional imaging agents in magnetic resonance imaging (MRI). Gold NPs (ca. 5 nm) are arranged linearly along double‐stranded DNA, creating gold NP chains. After cutting gold NP chains with restriction enzymes (EcoRI or BamHI), multicomponent NP chains are formed through a ligation reaction with enzyme‐cut, superparamagnetic NP chains. We evaluate the changes in relaxation times for different constructs of gold–iron oxide NP chains and gold–cobalt iron oxide NP chains using 300 MHz 1H NMR. In addition, the mechanism of proton relaxation for multicomponent NP chains is examined. The results indicate that relaxation times are dependent on the one‐dimensional structure and the amount of superparamagnetic NP chains present in the multicomponent constructs. Multicomponent NP chains arranged on double‐stranded DNA provide a feasible method for fabrication of multifunctional imaging agents that improve relaxation times effectively for MRI applications.}, number={17}, journal={ChemPhysChem}, publisher={Wiley}, author={Jaganathan, Hamsa and Gieseck, Richard L. and Hudson, Katherine and Kellogg, Michael and Ramaswamy, Aneesh K. and Raver, Kimberly E. and Smith, Tyler and Vacchiano, Ashley N. and Wager, Andrew and Ivanisevic, Albena}, year={2010}, month={Nov}, pages={3664–3672} }
 @article{johanes_mihelc_sivasankar_ivanisevic_2011, title={Morphological Properties of Collagen Fibers in Porcine Lamina Propria}, volume={25}, ISSN={0892-1997}, url={http://dx.doi.org/10.1016/j.jvoice.2009.09.006}, DOI={10.1016/j.jvoice.2009.09.006}, abstractNote={Objectives Collagen influences the biomechanical properties of vocal folds. Altered collagen morphology has been implicated in dysphonia associated with aging and scarring. Documenting the morphological properties of native collagen in healthy vocal folds is essential to understand the structural and functional alterations to collagen with aging and disease. Our primary objective was to quantify the morphological properties of collagen in the vocal fold lamina propria. Our secondary exploratory objective was to investigate the effects of pepsin exposure on the morphological properties of collagen in the lamina propria. Study Design Experimental, in vitro study with porcine model. Methods Lamina propria was dissected from 26 vocal folds and imaged with atomic force microscopy (AFM). Morphological data on d-periodicity, diameter, and roughness of collagen fibers were obtained. To investigate the effects of pepsin exposure on collagen morphology, vocal fold surface was exposed to pepsin or sham challenge before lamina propria dissection and AFM imaging. Results The d-periodicity, diameter, and roughness values for native vocal fold collagen are consistent with literature reports of collagen fibers in other body tissues. Pepsin exposure on vocal fold surface did not appear to change the morphological properties of collagen fibers in the lamina propria. Conclusions Quantitative data on collagen morphology were obtained at nanoscale resolution. Documenting collagen morphology in healthy vocal folds is critical for understanding the physiological changes to collagen with aging and scarring and for designing biomaterials that match the native topography of lamina propria.}, number={2}, journal={Journal of Voice}, publisher={Elsevier BV}, author={Johanes, Iecun and Mihelc, Elaine and Sivasankar, Mahalakshmi and Ivanisevic, Albena}, year={2011}, month={Mar}, pages={254–257} }
 @article{makowski_zemlyanov_ivanisevic_2011, title={Olefin metathesis reaction on GaN (0001) surfaces}, volume={257}, ISSN={0169-4332}, url={http://dx.doi.org/10.1016/j.apsusc.2010.12.100}, DOI={10.1016/j.apsusc.2010.12.100}, abstractNote={Proof-of-concept reactions were performed on GaN (0 0 0 1) surfaces to demonstrate surface termination with desired chemical groups using an olefin cross-metathesis reaction. To prepare the GaN surfaces for olefin metathesis, the surfaces were hydrogen terminated with hydrogen plasma, chlorine terminated with phosphorous pentachloride, and then terminated with an alkene group via a Grignard reaction. The olefin metathesis reaction then bound 7-bromo-1-heptene. The modified surfaces were characterized by X-ray photoelectron spectroscopy (XPS), atomic force microscopy, and water contact angle measurements following each step in the reaction scheme. The XPS data was used to qualitatively identify surface chemical species and to quantitatively determine molecular surface coverage. The bromine atom in 7-bromo-1-heptene served as a heteroatom for identification with XPS. The reaction scheme resulted in GaN substrates with a surface coverage of 0.10 monolayers and excellent stability towards oxidation when exposed to oxygen plasma.}, number={10}, journal={Applied Surface Science}, publisher={Elsevier BV}, author={Makowski, Matthew S. and Zemlyanov, Dmitry Y. and Ivanisevic, Albena}, year={2011}, month={Mar}, pages={4625–4632} }
 @article{valentín-rodríguez celimar_tezel_ivanisevic_2010, title={Quantitative Analysis of Human Internal Limiting Membrane Extracted from Patients with Macular Holes}, volume={26}, ISSN={0743-7463 1520-5827}, url={http://dx.doi.org/10.1021/la101797e}, DOI={10.1021/la101797e}, abstractNote={We report the study of the morphology, topography, and adhesion properties of internal limiting membrane (ILM) from patients with macular holes. The quantitative analysis of human ILM could provide essential information toward the improvement of existing surgical instruments for more efficient and safer surgical removal of ILM. Imaging in air revealed the presence of globular structures in most of the samples analyzed which were coupled with fibrillar structures in some of the samples. Modification of silicon nitride AFM tips with oppositely charged functional groups showed changes in adhesion force at the membrane-tip interface. Defining the surface characteristics of the human ILM is an initial step in the development of improved surgical tools that may allow nontraumatic stripping of ILM during surgery.}, number={15}, journal={Langmuir}, publisher={American Chemical Society (ACS)}, author={Valentín-Rodríguez Celimar and Tezel, Tongalp H. and Ivanisevic, Albena}, year={2010}, month={Aug}, pages={12810–12816} }
 @article{kramer_jaganathan_ivanisevic_2010, title={Serial and Parallel Dip-Pen Nanolithography Using a Colloidal Probe Tip}, volume={132}, ISSN={0002-7863 1520-5126}, url={http://dx.doi.org/10.1021/ja1003137}, DOI={10.1021/ja1003137}, abstractNote={AFM tips terminated with PMMA colloids are used to pattern molecules in both serial and parallel modes by allowing the polymer on the tip to swell under different humidity conditions. This extension of the dip-pen nanolithography technique provides an easy methodology to place inks on different substrates without the need to perform specialized tip alignment.}, number={13}, journal={Journal of the American Chemical Society}, publisher={American Chemical Society (ACS)}, author={Kramer, Marcus A. and Jaganathan, Hamsa and Ivanisevic, Albena}, year={2010}, month={Apr}, pages={4532–4533} }
 @article{jaganathan_gieseck_ivanisevic_2010, title={Transverse Relaxivity Changes after Layer-by-Layer Encapsulation of Multicomponent DNA Templated Nanostructures}, volume={114}, ISSN={1932-7447 1932-7455}, url={http://dx.doi.org/10.1021/jp109131q}, DOI={10.1021/jp109131q}, abstractNote={We examine the effects on transverse proton relaxivity after layer-by-layer encapsulation of one-dimensional (1D), DNA templated nanostructures for potential applications as magnetic resonance imaging contrast agents. Multicomponent DNA templated nanostructures made with gold−iron oxide and gold−cobalt iron oxide were electrostatically encapsulated by polyelectrolytes (PSS and PAH) and ligands (RGD peptide) in order to stabilize the DNA nanostructure. Transverse relaxivity was measured by 300 MHz H1 nuclear magnetic resonance (NMR) spectroscopy. The results indicate that the transverse proton relaxivity was greater for 1D DNA-templated nanostructures when compared to zero-dimensional (0D) nanoparticles, but relaxivity decreased after the layer-by-layer encapsulation.}, number={51}, journal={The Journal of Physical Chemistry C}, publisher={American Chemical Society (ACS)}, author={Jaganathan, Hamsa and Gieseck, Richard L. and Ivanisevic, Albena}, year={2010}, month={Dec}, pages={22508–22513} }
 @article{cho_shi_ivanisevic_ben borgens_2009, title={A mesoporous silica nanosphere-based drug delivery system using an electrically conducting polymer}, volume={20}, ISSN={0957-4484 1361-6528}, url={http://dx.doi.org/10.1088/0957-4484/20/27/275102}, DOI={10.1088/0957-4484/20/27/275102}, abstractNote={In this study, a mesoporous silica nanoparticle (MSN)-based nerve growth factor (NGF) delivery system has been successfully embedded within an electroactive polypyrrol (Ppy). The spherical particles with ∼100 nm diameter possess a large surface-to-volume ratio for the entrapment of NGF into the pores of MSNs while retaining their bioactivity. Direct incorporation of MSN-NGF within Ppy was achieved during electrochemical polymerization. The loading amount and release profile of NGF from the composite was investigated by sandwich ELISA. The NGF incorporation can be controllable by varying particle concentration or by extending electrodeposition time. The morphology and chemical composition of the Ppy/MSN-NGF composite was evaluated by atomic force microscopy (AFM), transmission electron microscopy (TEM), scanning electron microscopy (SEM), and x-ray photoelectron spectroscopy (XPS). Optical and electron microscopy revealed a characteristic attachment of PC 12 cells and the outgrowth of their neurites when grown on the Ppy/MSN-NGF composite as a result of a sustained and controlled release of NGF. In order to observe the effectiveness of electrical stimulation, neurite extension of cells cultured on unstimulated and stimulated Ppy/MSN-NGF was compared. The NGF release in the presence of electrical stimulation promoted significantly greater neurite extension.}, number={27}, journal={Nanotechnology}, publisher={IOP Publishing}, author={Cho, Youngnam and Shi, Riyi and Ivanisevic, Albena and Ben Borgens, Richard}, year={2009}, month={Jun}, pages={275102} }
 @article{slavin_zemlyanov_ivanisevic_2009, title={Adsorption of amino acids on indium arsenide (100) surfaces: Assessment of passivation capabilities}, volume={603}, ISSN={0039-6028}, url={http://dx.doi.org/10.1016/j.susc.2009.02.005}, DOI={10.1016/j.susc.2009.02.005}, abstractNote={Abstract Angle-Resolved X-ray Photoelectron Spectroscopy (ARXPS) was used to examine amino acid bonding and oxide removal on InAs(1 0 0) surfaces. Five amino acids were studied, including cysteine, lysine, aspartic acid, glutamic acid and arginine. Observations on the ability of specific functional groups to prevent oxide formation were made by examining the thickness of oxide films on the functionalize surfaces. Amino acids that possessed more than one functional group having resonance were shown to most effectively affect oxide formation. The influence of these groups on the electronic structure of InAs(1 0 0) provides insight into how multifunctional passivation strategies could be beneficial, as well as showing how biological molecules might affect detection when InAs(1 0 0) is used as a platform.}, number={6}, journal={Surface Science}, publisher={Elsevier BV}, author={Slavin, John W.J. and Zemlyanov, Dmitry and Ivanisevic, Albena}, year={2009}, month={Mar}, pages={907–911} }
 @article{slavin_jarori_zemlyanov_ivanisevic_2009, title={Characterization of amino acid adlayers on InAs surfaces using X-ray photoelectron spectroscopy}, volume={172}, ISSN={0368-2048}, url={http://dx.doi.org/10.1016/j.elspec.2009.03.006}, DOI={10.1016/j.elspec.2009.03.006}, abstractNote={Removal of surface oxide layers and the prevention of their reformation is an essential step in the use of III-V semiconductor technologies. Highlighted here are data exploring the use of amino acid (AA) self-assembled monolayers (SAMs) to block the pre-growth of oxides on indium arsenide surfaces. Three different AAs were used: lysine, aspartic acid, and cysteine. The adlayers were characterized by atomic force microscopy (AFM), Raman, and angle resolved X-ray photoelectron spectroscopy (ARXPS). AFM data suggest that the AA functional groups affect the packing and orientation of the molecules on the surfaces, reinforced by contact angle data. Raman data provide proof that the type of functional group alters the intensity of the unscreened LO phonon, resulting in an electrostatic stabilization, in the case of lysine, which lends to the case of electrostatic interactions blocking oxide formation. ARXPS demonstrated that the degree of oxide blocking is dependent upon the type of functional group and further verifies inferences made from the Raman spectra. The degree of monolayer formation is also determined from this data. It is concluded that AA's can be useful means for blocking oxide growth on InAs (1 0 0) surfaces, which also provides insights into how protein and peptide side chains might interact with such surfaces.}, number={1-3}, journal={Journal of Electron Spectroscopy and Related Phenomena}, publisher={Elsevier BV}, author={Slavin, John W.J. and Jarori, Upasana and Zemlyanov, Dmitry and Ivanisevic, Albena}, year={2009}, month={May}, pages={47–53} }
 @article{kramer_park_ivanisevic_2010, title={Dip-pen nanolithography on SiO x and tissue-derived substrates: comparison with multiple biological inks}, volume={32}, ISSN={0161-0457 1932-8745}, url={http://dx.doi.org/10.1002/sca.20160}, DOI={10.1002/sca.20160}, abstractNote={AbstractThere has been extensive interest in the micro and nanoscale manipulation of various substrates in the past few decades. One promising technique is dip‐pen nanolithography which has shown the capability to pattern substrates of all forms including, tissue‐derived substrates. Patterning of tissue‐derived substrates is of particular interest, as it would facilitate studies into controlling cell morphology and cell–substrate interaction. To expand the field into this area both peptides and bioactive collagen‐binding peptide‐linked biomolecules were patterned to the inner collagenous zone of the Bruch's membrane (BM). Collagen‐binding peptide, and extra cellular matrix (ECM) proteins laminin and fibronectin were patterned on the BM and SiOx. The lithographic protocol was facilitated by Triton X‐100 which was used to clean the tissue‐derived construct after harvesting. This produced a collagen‐exposed BM which was more hydrophilic (contact angle 67°±8.49°) surface compared with other cleaning methods but it maintained similar surface roughness (root‐mean‐square) 80±18 nm and collagen exposure. This type of surface can be readily patterned with the chosen inks under lower humidity conditions. SCANNING 32: 30–34, 2010. © 2009 Wiley Periodicals, Inc.}, number={1}, journal={Scanning}, publisher={Wiley}, author={Kramer, Marcus A. and Park, Heyjin C. and Ivanisevic, Albena}, year={2010}, month={Jan}, pages={30–34} }
 @article{cho_shi_ivanisevic_ben borgens_2010, title={Functional silica nanoparticle-mediated neuronal membrane sealing following traumatic spinal cord injury}, volume={88}, ISSN={0360-4012}, url={http://dx.doi.org/10.1002/jnr.22309}, DOI={10.1002/jnr.22309}, abstractNote={AbstractThe mechanical damage to neurons and their processes induced by spinal cord injury (SCI) causes a progressive cascade of pathophysiological events beginning with the derangement of ionic equilibrium and collapse of membrane permeability. This leads to a cumulative deterioration of neurons, axons, and the tissue architecture of the cord. We have previously shown that the application of the hydrophilic polymer polyethylene glycol (PEG) following spinal cord or brain injury can rapidly restore membrane integrity, reduce oxidative stress, restore impaired axonal conductivity, and mediate functional recovery in rats, guinea pigs, and dogs. However there are limits to both the concentration and the molecular weight of the application that do not permit the broadest recovery across an injured animal population. In this study, PEG‐decorated silica nanoparticles (PSiNPs) sealed cells, as shown by the significantly reduced leakage of lactate dehydrogenase from damaged cells compared with uncoated particles or PEG alone. Further in vivo tests showed that PSiNPs also significantly reduced the formation of reactive oxygen species and the process of lipid peroxidation of the membrane. Fabrication of PSiNPs containing embedded dyes also revealed targeting of the particles to damaged, but not undamaged, spinal cord tissues. In an in vivo crush/contusion model of guinea pig SCI, every animal but one injected with PSiNPs recovered conduction through the cord lesion, whereas none of the control animals did. These findings suggest that the use of multifunctional nanoparticles may offer a novel treatment approach for spinal cord injury, traumatic brain injury, and possibly neurodegenerative disorders. © 2009 Wiley‐Liss, Inc.}, number={7}, journal={Journal of Neuroscience Research}, publisher={Wiley}, author={Cho, Youngnam and Shi, Riyi and Ivanisevic, Albena and Ben Borgens, Richard}, year={2010}, month={May}, pages={1433–1444} }
 @article{wampler_ivanisevic_2009, title={Nanoindentation of gold nanoparticles functionalized with proteins}, volume={40}, ISSN={0968-4328}, url={http://dx.doi.org/10.1016/j.micron.2009.01.002}, DOI={10.1016/j.micron.2009.01.002}, abstractNote={The hardness and Young's modulus of 10 and 20 nm gold nanoparticles (Au NPs) modified with bovine serum albumin and streptavidin were measured using a nanoindenter. The Au NPs were immobilized on a semiconductor surface through organic self-assembled monolayers. Changes in mechanical properties occurred when the Au NPs were immobilized on the surface. The hardness and Young's modulus were dependent on the size of the NPs, and the proteins on the particles showed highly plastic and elastic behavior compared to flat surfaces modified with self-assembled monolayers.}, number={4}, journal={Micron}, publisher={Elsevier BV}, author={Wampler, Heeyeon P. and Ivanisevic, Albena}, year={2009}, month={Jun}, pages={444–448} }
 @article{jaganathan_kinsella_ivanisevic_2008, title={Circular Dichroism Study of the Mechanism of Formation of DNA Templated Nanowires}, volume={9}, ISSN={1439-4235 1439-7641}, url={http://dx.doi.org/10.1002/cphc.200800509}, DOI={10.1002/cphc.200800509}, abstractNote={AbstractIn order to control the fabrication method, the mechanism used in the formation of DNA templated nanowires is investigated through circular dichroism (CD) spectroscopy. Metallic (Au) and magnetic (Fe2O3 and CoFe2O4) nanoparticles (NP) are aligned along the DNA strand at various mass ratios. The DNA templated nanowires are compared to the structure of B‐form dsDNA through CD experiments. Absorbance and thermal melting tests are performed to verify the structural changes of DNA templated nanowires. Low concentrations of nanoparticles preserve the DNA B‐form through electrostatic interactions. Conversely, at higher concentrations of nanoparticles aligned along the DNA strand, the template is denatured. Information on the mode of nanoparticle binding and DNA helix alterations are explored for metallic and magnetic nanowires based upon the results.}, number={15}, journal={ChemPhysChem}, publisher={Wiley}, author={Jaganathan, Hamsa and Kinsella, Joseph M. and Ivanisevic, Albena}, year={2008}, month={Oct}, pages={2203–2206} }
 @article{jaganathan_ivanisevic_2008, title={Circular dichroism study of enzymatic manipulation on magnetic and metallic DNA template nanowires}, volume={67}, ISSN={0927-7765}, url={http://dx.doi.org/10.1016/j.colsurfb.2008.08.024}, DOI={10.1016/j.colsurfb.2008.08.024}, abstractNote={Circular dichroism spectroscopy (CD) was used to examine the mechanism of endonuclease clipping and ligation of the DNA template nanowires. The biomolecular manipulation of the DNA template is compared for both metallic (Au) and magnetic (Fe2O3 and CoFe2O4) nanowires. The dependence of nanoparticle (NP) concentration on enzymatic clipping and DNA ligation was studied, in addition to performing absorbance and thermal melting experiments. Low-NP concentration preserved and digested the DNA template structure. Yet, at higher NP concentrations, the DNA template began to denature before enzyme addition. It was also observed that ligation of the digested DNA occurred more efficiently at low-NP concentrations. These results provide significant information on structural alteration and biorecognition effectiveness of the DNA template after enzymatic manipulation.}, number={2}, journal={Colloids and Surfaces B: Biointerfaces}, publisher={Elsevier BV}, author={Jaganathan, Hamsa and Ivanisevic, Albena}, year={2008}, month={Dec}, pages={279–283} }
 @article{sistiabudi_ivanisevic_2008, title={Collagen-Binding Peptide Interaction with Retinal Tissue Surfaces}, volume={24}, ISSN={0743-7463 1520-5827}, url={http://dx.doi.org/10.1021/la703561d}, DOI={10.1021/la703561d}, abstractNote={One of the current challenges in treating age-related macular degeneration (AMD) is the surface modification of the retinal Bruch membrane. In this study, the collagen fibers of the inner collagenous zone of the Bruch membrane were identified as type I and type III. Subsequently, the adsorption of a collagen-binding peptide onto the inner collagenous zone surface was investigated. The collagen-binding peptide was able to bind specifically to the collagen fibers while maintaining the biological activity of the N-terminus biotin tag. These results indicate that the collagen-binding peptide may be used as an anchor to immobilize bioactive molecules on the inner collagenous zone surface of the Bruch membrane.}, number={5}, journal={Langmuir}, publisher={American Chemical Society (ACS)}, author={Sistiabudi, Rizaldi and Ivanisevic, Albena}, year={2008}, month={Mar}, pages={1591–1594} }
 @article{flores-perez_zemlyanov_ivanisevic_2008, title={DNA Molecules on GaP (100) Surfaces: Spectroscopic Characterization and Biospecificity Assessment}, volume={9}, ISSN={1439-4235 1439-7641}, url={http://dx.doi.org/10.1002/cphc.200800166}, DOI={10.1002/cphc.200800166}, abstractNote={DNA-modified surfaces have been the subject of considerable research activity in the field of bionanotechnology. Such surfaces can be incorporated into novel diagnostic devices that utilize sequencing and gene mapping technologies. 3] For example, the use of DNAbased sensors shows promise for rapid, economical and accurate detection of genetic diseases. In such sensor devices it is very important to have a robust and reproducible packing of DNA molecules. Different research groups have explored the absorption of biomolecules and the integration of biological systems on inorganic materials such as gold and silicon. Recently, there has been an interest in extending such studies to III–V semiconductor substrates. Gallium phosphide (GaP) is an attractive semiconductor material due to its usage in charge storage devices and low-noise detection photodiodes. This material offers promise for the fabrication of novel biosensors. Our previous work demonstrated that GaP ACHTUNGTRENNUNG(100) remains stable after surface functionalization with well-parked adlayers and high molecular coverages. Herein, we describe the covalent functionalization and characterization of H-doped GaP ACHTUNGTRENNUNG(100) with modified DNA strands. We demonstrate that photochemical functionalization with undecylenic acid (UDA) can modify GaP substrates and that the terminal carboxylic acid groups can be used for the successful immobilzation of biomolecules (Scheme 1). In our approach, we control the orientation of modified DNAs by reacting the carboxylic acid-terminated GaP ACHTUNGTRENNUNG(100) surfaces with a mixture of amine-terminated ssDNA and a spacer, hexylamine (HA). We also confirm the bioactivity of biotin-modified DNA by the use of streptavidin-modified nanoparticles and Cy3-labeled streptavidin. The following techniques are used to complete the physical characterization of the surfaces: water contact angle (WCA), atomic force microscopy (AFM), Fourier transform infrared reflectance absorbance spectroscopy (FT–IRRAS). Prior to any spectroscopic analysis each modified surface is evaluated using WCA and AFM. The data, summarized in the Supporting Information, follows the expected hydrophicilicity trend due to the nature of the end groups. In addition, no major changes in roughness are observed after each treatment. Initial spectroscopic analysis of the modified surfaces by FT–IRRAS spectroscopy provides us with information about the adsorbates’ orientation on the GaP surface. The FT–IRRAS vibrations for H-doped, Br-modified DNA/HA, biotin-modified DNA/HA and biotin-modified DNA/HA/streptavidin nanoparticles GaP ACHTUNGTRENNUNG(100) steps are shown in Figure 1. We place a Br-label at the 5’ end of the DNA so that we can use it as a way to prove that molecules are on the surface by X-ray photoelectron spectroscopy (XPS). The FT–IRRAS spectrum of H-doped GaP ACHTUNGTRENNUNG(100) does not show any peaks in the low and high frequency regions, as one would expect to be the case immedi[a] Dr. R. Flores-Perez, Prof. A. Ivanisevic Department of Chemistry Weldon School of Biomedical Engineering, Purdue University 206 S. Martin Jischke Drive, West Lafayette, IN 47907 (USA) Fax: (+1)7654961459 E-mail : albena@purdue.edu [b] Dr. D. Y. Zemlyanov Birck Nanotechnology Center Purdue University, West Lafayette, IN 47907 (USA) Supporting information for this article is available on the WWW under http://dx.doi.org/10.1002/cphc.200800166. Scheme 1. Surface coupling chemistry used to modify GaP with DNA molecules.}, number={11}, journal={ChemPhysChem}, publisher={Wiley}, author={Flores-Perez, Rosangelly and Zemlyanov, Dmitry Y. and Ivanisevic, Albena}, year={2008}, month={Aug}, pages={1528–1530} }
 @article{sistiabudi_ivanisevic_2008, title={Dip-Pen Nanolithography of Bioactive Peptides on Collagen-Terminated Retinal Membrane}, volume={20}, ISSN={0935-9648 1521-4095}, url={http://dx.doi.org/10.1002/adma.200800950}, DOI={10.1002/adma.200800950}, abstractNote={Dip-pen nanolithography (DPN) is a direct-write lithographic technique that utilizes atomic force microscopy (AFM). [1,2] DPN uses a modified AFM tip that has been physisorbed with molecules to be transferred onto a surface. The transport of molecules onto the surface is facilitated by a water meniscus that forms between the AFM tip and the surface. Meanwhile, the resulting pattern size can be controlled through parameters such as temperature, relative humidity, write speed, contact force between tip and surface, as well as the tip-coating conditions. [3] For biotechnological applications, DPN is an attractive method that has been widely investigated for the deposition of biomolecules onto different substrates. [4–8] Thus far, these efforts have demonstrated the capability to produce specific patterns of biologically active molecules on highly homogeneous surfaces (e}, number={19}, journal={Advanced Materials}, publisher={Wiley}, author={Sistiabudi, Rizaldi and Ivanisevic, Albena}, year={2008}, month={Oct}, pages={3678–3681} }
 @article{lee_nair_alam_janes_wampler_zemlyanov_ivanisevic_2008, title={Electrical detection of the biological interaction of a charged peptide via gallium arsenide junction-field-effect transistors}, volume={103}, ISSN={0021-8979 1089-7550}, url={http://dx.doi.org/10.1063/1.2936853}, DOI={10.1063/1.2936853}, abstractNote={GaAs junction-field-effect transistors (JFETs) are utilized to achieve label-free detection of biological interaction between a probe transactivating transcriptional activator (TAT) peptide and the target trans-activation-responsive (TAR) RNA. The TAT peptide is a short sequence derived from the human immunodeficiency virus-type 1 TAT protein. The GaAs JFETs are modified with a mixed adlayer of 1-octadecanethiol (ODT) and TAT peptide, with the ODT passivating the GaAs surface from polar ions in physiological solutions and the TAT peptide providing selective binding sites for TAR RNA. The devices modified with the mixed adlayer exhibit a negative pinch-off voltage (VP) shift, which is attributed to the fixed positive charges from the arginine-rich regions in the TAT peptide. Immersing the modified devices into a TAR RNA solution results in a large positive VP shift (>1 V) and a steeper subthreshold slope (∼80 mV/decade), whereas “dummy” RNA induced a small positive VP shift (∼0.3 V) without a significant change in subthreshold slopes (∼330 mV/decade). The observed modulation of device characteristics is analyzed with analytical modeling and two-dimensional numerical device simulations to investigate the electronic interactions between the GaAs JFETs and biological molecules.}, number={11}, journal={Journal of Applied Physics}, publisher={AIP Publishing}, author={Lee, Kangho and Nair, Pradeep R. and Alam, Muhammad A. and Janes, David B. and Wampler, Heeyeon P. and Zemlyanov, Dmitry Y. and Ivanisevic, Albena}, year={2008}, month={Jun}, pages={114510} }
 @article{jaganathan_ivanisevic_2008, title={Heterostructured DNA templates: A combined magnetic force microscopy and circular dichroism study}, volume={93}, ISSN={0003-6951 1077-3118}, url={http://dx.doi.org/10.1063/1.3058711}, DOI={10.1063/1.3058711}, abstractNote={The effect of nanoparticle (NP) concentration was examined on the formation of heterostructured nanowires fabricated using DNA as a template. At mass ratios of 1:1 DNA:NP, the circular dichroism (CD) data showed a distinct characteristic, a plateau at 260 nm. The magnetic force microscopy (MFM) data revealed segments that showed variable interaction with the magnetized tip. At high NP concentrations both the CD and MFM data confirmed that the DNA template denatures and the control over the assembly process is poor.}, number={26}, journal={Applied Physics Letters}, publisher={AIP Publishing}, author={Jaganathan, Hamsa and Ivanisevic, Albena}, year={2008}, month={Dec}, pages={263104} }
 @article{flores-perez_zemlyanov_ivanisevic_2008, title={Lithography on GaP(100) surfaces}, volume={602}, ISSN={0039-6028}, url={http://dx.doi.org/10.1016/j.susc.2008.04.002}, DOI={10.1016/j.susc.2008.04.002}, abstractNote={Abstract Two types of lithographic methods were used to modify GaP(1 0 0) surfaces with commercially available alkanethiol molecules: microcontact printing (μCP) and “dip-pen” nanolithography (DPN). The patterned surfaces were characterized by atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS) and Fourier transform infrared reflection absorption spectroscopy (FT-IRRAS). The characterization was done in order to understand the quality of each type of pattern, its chemical composition, and the organization of the molecules on the surface. Differences between the two lithographic methods used to do lithography on the GaP(1 0 0) in this study were dependent on the chosen molecular “ink”.}, number={11}, journal={Surface Science}, publisher={Elsevier BV}, author={Flores-Perez, Rosangelly and Zemlyanov, Dmitry Y. and Ivanisevic, Albena}, year={2008}, month={Jun}, pages={1993–1998} }
 @article{kinsella_ivanisevic_2008, title={Magnetotransport of One-Dimensional Chains of CoFe2O4 Nanoparticles Ordered along DNA}, volume={112}, ISSN={1932-7447 1932-7455}, url={http://dx.doi.org/10.1021/jp712002a}, DOI={10.1021/jp712002a}, abstractNote={We have investigated the magnetotransport properties of 5 nm CoFe 2 O 4 nanoparticles aligned into one-dimensional chains using a DNA guide. The chemically synthesized particles were capped with a positively charged ligand molecule that drives the electrostatic assembly when incubated in solutions containing DNA. To test the transport, these nanoparticle-coated DNA strands were adsorbed onto microfabricated devices. Large room-temperature magnetoresistance is observed at high fields in these samples.}, number={9}, journal={The Journal of Physical Chemistry C}, publisher={American Chemical Society (ACS)}, author={Kinsella, Joseph M. and Ivanisevic, Albena}, year={2008}, month={Mar}, pages={3191–3193} }
 @article{wampler_zemlyanov_lee_janes_ivanisevic_2008, title={Mixed Adlayer of Alkanethiol and Peptide on GaAs(100):  Quantitative Characterization by X-ray Photoelectron Spectroscopy}, volume={24}, ISSN={0743-7463 1520-5827}, url={http://dx.doi.org/10.1021/la703543g}, DOI={10.1021/la703543g}, abstractNote={Homogeneous and mixed adlayers composed of an alkanethiol (1-octadecanethiol, ODT) and a peptide (CGISYGRKKRRQRRR) on GaAs(100) were formed in two different solvent systems: phosphate-buffered saline (PBS) and N,N-dimethylformamide (DMF). The chemical composition of each adlayer was characterized by X-ray photoelectron spectroscopy (XPS). The data showed that the makeup of the adlayer and its stability largely depends on the solvent used. Angle-resolved XPS also revealed that the adlayer thickness and tilt angles were different from values obtained from ellipsometry measurements and vastly varied between the two solvents used. The coverage data extracted from the XPS measurements indicated that homogeneous adlayers of peptide in PBS buffer form a multilayered film. Homogeneous alkanethiol adlayers exhibited monolayer coverage under all solvent treatments. Coadsorbed layers containing both alkanethiol and peptide have fractional monolayer coverage in both solvents.}, number={7}, journal={Langmuir}, publisher={American Chemical Society (ACS)}, author={Wampler, Heeyeon P. and Zemlyanov, Dmitry Y. and Lee, Kangho and Janes, David B. and Ivanisevic, Albena}, year={2008}, month={Apr}, pages={3164–3170} }
 @article{sistiabudi_paderi_panitch_ivanisevic_2009, title={Modification of native collagen with cell-adhesive peptide to promote RPE cell attachment on Bruch's membrane}, volume={102}, ISSN={0006-3592 1097-0290}, url={http://dx.doi.org/10.1002/bit.22215}, DOI={10.1002/bit.22215}, abstractNote={AbstractCurrent efforts to reverse loss of visual function due to Age‐related Macular Degeneration point to the restoration of the Retinal Pigment Epithelial (RPE) layer. Restoration of the RPE layer involves replacing lost RPE cells as well as addressing the degeneration of the underlying Bruch's membrane (BM). To advance the potential of using donor BM, we present a strategy to achieve specific and controllable modification of the inner collagenous layer (ICL) of the Bruch's membrane. In particular, interaction between a collagen binding peptide (CBP) sequence with exposed collagen fibers on the ICL surface is utilized to anchor bioactive molecules. Here, a cell‐adhesion sequence is added to the collagen binding sequence to promote attachment and survival of ARPE‐19. First, the binding specificity of the CBP sequence is verified with a fluorescent binding assay. Subsequently, the effect of modification using the peptide is studied qualitatively using confocal fluorescent imaging and quantitatively through a cell proliferation assay. Results of these experiments indicate that the peptide sequence binds specifically to collagen fibers. Additionally, modification using the peptide enhanced cell adhesion, allowing large uniform cell networks to be formed on the surface. Furthermore, modification with the peptide also delayed the onset of apoptosis on adherent cells. Biotechnol. Bioeng. 2009;102: 1723–1729. © 2008 Wiley Periodicals, Inc.}, number={6}, journal={Biotechnology and Bioengineering}, publisher={Wiley}, author={Sistiabudi, Rizaldi and Paderi, John and Panitch, Alyssa and Ivanisevic, Albena}, year={2009}, month={Apr}, pages={1723–1729} }
 @article{flores-perez_zemlyanov_ivanisevic_2008, title={Quantitative Evaluation of Covalently Bound Molecules on GaP (100) Surfaces}, volume={112}, ISSN={1932-7447 1932-7455}, url={http://dx.doi.org/10.1021/jp710437v}, DOI={10.1021/jp710437v}, abstractNote={The study utilizes surface sensitive techniques in order to quantitatively characterize the nature of organization and bonding of alkanethiol adsorbates on GaP (100) surfaces. The evaluation was performed using water contact angle, atomic force microscopy (AFM), Fourier transform infrared (FT-IR) spectroscopy, and X-ray photoelectron spectroscopy (XPS). The hydrophobicity and consistency of surface roughness were studied via water contact angle and AFM. The FT-IR experimental protocol permitted the identification of characteristic functional groups on the surface and enabled insight into the organization within the adlayers on the GaP surface. XPS data showed evidence for the formation of a covalent bond between the sulfur and the surface and was used to calculate the adlayer thicknesses, tilt angles, and molecular coverages for different adsorbates. The thickness and tilt angles values were comparable to other modified semiconductor materials. High coverages were observed for all alkanethiols on GaP (100...}, number={6}, journal={The Journal of Physical Chemistry C}, publisher={American Chemical Society (ACS)}, author={Flores-Perez, Rosangelly and Zemlyanov, Dmitry Y. and Ivanisevic, Albena}, year={2008}, month={Feb}, pages={2147–2155} }
 @article{cho_shi_borgens_ivanisevic_2008, title={Repairing the Damaged Spinal Cord and Brain with Nanomedicine}, volume={4}, ISSN={1613-6810 1613-6829}, url={http://dx.doi.org/10.1002/smll.200800838}, DOI={10.1002/smll.200800838}, abstractNote={There is no medical therapy for severe spinal-cord or brain injury that can restore behavioral loss in the chronic condition, or rapidly repair the membranes of damaged nerve cells in the acute stage of the injury. The latter permits rapid recovery of physiological functioning after injury, and largely vitiates continuing and progressive cell death. Here we describe for the first time a microcolloid composite, ranging from 50 to 300 nm, made of nonbiological, inert, and nontoxic components that fulfill all of the requirements of the latter therapy. From an applied-engineering standpoint, tools fabricated by nanotechnology have the potential to lead to more effective ways to treat and predict disease, though a particular therapy for central nervous system (CNS) injury or disease has yet to be realized. Recent activity in nanotechnology has substantially improved colloid-based systems. The versatility of materials with inherent unique properties (optical, electrical, magnetic, and chemical) can be realized with the incorporation of a variety of biocompatible and biodegradable materials such as synthetic or natural polymers, lipids, or solid (metal, semiconductor, magnetic, or insulator) components. Of these, silica particles have several advantages: i) they ride upon a wealth of well-established methods for the synthesis and incorporation with other substances through surface modification and bioconjugation; ii) they have great potential to perform multifunctional activity; and iii) they exhibit intrinsic hydrophilicity, biocompatibility, and nontoxicity. In addition, inorganic cores, rather than organic cores such as micelles, have a longer ‘‘shelf life’’.}, number={10}, journal={Small}, publisher={Wiley}, author={Cho, Youngnam and Shi, Riyi and Borgens, Richard and Ivanisevic, Albena}, year={2008}, month={Oct}, pages={1676–1681} }
 @article{flores-perez_gupta_bashir_ivanisevic_2007, title={Cantilever-Based Sensor for the Detection of Different Chromophore Isomers}, volume={79}, ISSN={0003-2700 1520-6882}, url={http://dx.doi.org/10.1021/ac0703000}, DOI={10.1021/ac0703000}, abstractNote={We report the use of microcantilevers (MCs) for the detection of three retinoid isomers: 9-cis-retinal, 13-cis-retinal and all-trans-retinal. Detection of synthetic and natural retinoids in topical cosmetic products is important, and their presence can be used to predict reactions with the skin surface. In this study the MC surfaces were functionalized in order to promote the formation of covalent bonds with the chromophores. The lowest mass shift we detected with the functionalized MCs was 1.2 ppt, which is in the range needed by the cosmetics industry. Our results indicate that properly designed and functionalized microcantilevers can be used to construct economical, fast, and sensitive sensors for quality control in cosmetics.}, number={12}, journal={Analytical Chemistry}, publisher={American Chemical Society (ACS)}, author={Flores-Perez, Rosangelly and Gupta, Amit K. and Bashir, Rashid and Ivanisevic, Albena}, year={2007}, month={Jun}, pages={4702–4708} }
 @article{kinsella_ivanisevic_2007, title={DNA-Templated Magnetic Nanowires with Different Compositions:  Fabrication and Analysis}, volume={23}, ISSN={0743-7463 1520-5827}, url={http://dx.doi.org/10.1021/la0628571}, DOI={10.1021/la0628571}, abstractNote={The structure and magnetic properties of different types of templated wires are compared in this study. A long DNA molecule was used to guide the assembly of pyrrolidinone-capped Fe2O3 and CoFe2O3 particles as well as polylysine-coated gold nanoparticles. The resulting DNA-templated wires were stretched onto silicon oxide surfaces using a receding meniscus procedure. The coated, stretched, and surface-bound wires were characterized using atomic force microscopy (AFM), magnetic force microscopy (MFM), and spectroscopic methods. The results with respect to the wire properties were correlated with those determined from the bulk properties of the nanoparticles and with the properties of the bulk DNA. The MFM measurements allowed us to visualize the formation of domains along the wires as well as qualitatively compare the magnetic properties of each templated structure.}, number={7}, journal={Langmuir}, publisher={American Chemical Society (ACS)}, author={Kinsella, Joseph M. and Ivanisevic, Albena}, year={2007}, month={Mar}, pages={3886–3890} }
 @article{song_ye_ivanisevic_2007, title={Elastomeric Nanoparticle Composites Covalently Bound to Al2O3/GaAs Surfaces}, volume={23}, ISSN={0743-7463 1520-5827}, url={http://dx.doi.org/10.1021/la700979r}, DOI={10.1021/la700979r}, abstractNote={This article reports the modification of Al2O3/GaAs surfaces with multifunctional soft materials. Siloxane elastomers were covalently bound to dopamine-modified Al2O3/GaAs semiconductor surfaces using MPt (M = Fe, Ni) nanoparticles. The sizes of the monodisperse FePt and NiPt nanoparticles were less than 5 nm. The surfaces of the nanoparticles as well as the Al2O3/GaAs substrates were modified with allyl-functionalized dopamine that utilized a dihydroxy group as a strong ligand. The immobilization of the elastomers was performed via a hydrosilation reaction of the allyl-functionalized dopamines with the siloxane backbones. X-ray photoelectron spectroscopy (XPS) experiments confirmed the covalent bonding of the siloxane elastomers to the oxide layer on the semiconductor surface. Fourier transform-infrared reflection absorption spectroscopy (FT-IRRAS) measurements revealed that the allyl functional groups are bonded to the siloxane backbones. The FT-IRRAS data also showed that the density of the allyl groups on the surface was lower than that of the siloxane backbones. The mechanical properties of the surface-bound nanocomposites were tested using nanoindentation experiments. The nanoindentation data showed that the soft matrix composed of the elastomeric coating on the surfaces behaves differently from the inner, hard Al2O3/GaAs substrate.}, number={18}, journal={Langmuir}, publisher={American Chemical Society (ACS)}, author={Song, Hyon Min and Ye, Peide D. and Ivanisevic, Albena}, year={2007}, month={Aug}, pages={9472–9480} }
 @article{kinsella_ivanisevic_2008, title={Fabrication of ordered metallic and magnetic heterostructured DNA—Nanoparticle hybrids}, volume={63}, ISSN={0927-7765}, url={http://dx.doi.org/10.1016/j.colsurfb.2007.12.004}, DOI={10.1016/j.colsurfb.2007.12.004}, abstractNote={Here we provide a method based on enzymatically catalyzed reactions to cleave and ligate DNA molecules coated with nanoparticles to fabricate multi-component structures. This is done by simultaneously digesting two solutions of nanoparticle coated DNA, one with iron oxide particles the other gold particles, which yields short DNA fragments with complementary single stranded overhangs. When added together and re-attached using ligase enzymes multi-component nanoparticle coated structures are formed providing a novel method to fabricate complicated nanoparticle arrangements from the bottom up. We evaluated the fabrication by characterizing the samples with gel electrophoresis and magnetic force microscopy (MFM). The electrophoresis provides proof that the coated DNA molecules were digested with restriction enzymes and ligated by the T4 ligase enzymes. MFM experiments allow us to visualize the multi-component strands and analyze the magnetic versus metallic segments.}, number={2}, journal={Colloids and Surfaces B: Biointerfaces}, publisher={Elsevier BV}, author={Kinsella, Joseph M. and Ivanisevic, Albena}, year={2008}, month={Jun}, pages={296–300} }
 @article{park_ivanisevic_2007, title={Formation and Characterization of Homogeneous and Mixed Self-Assembled Monolayers of Peptides and Alkanethiols on Indium Phosphide Surfaces}, volume={111}, ISSN={1932-7447 1932-7455}, url={http://dx.doi.org/10.1021/jp066109w}, DOI={10.1021/jp066109w}, abstractNote={This report describes the detailed characterization of alkanethiol and cysteine-terminated peptide layers on InP(100). Contact angle measurements, atomic force microscopy, X-ray photoelectron spectroscopy, and ellipsometry were performed. The surface characterization techniques showed that the composition of the mixed monolyers can be controlled through the concentration of each adsorbate solution. The surface coverage of the adsorbates on the InP(100) surface was lower than that of similar self-assembled monolayers (SAMs) on gold. The tilt angles for all adsorbates were higher than those of similar adsorbates on metal surfaces. The data from this report is important for the successful chemical functionalization of III−V semiconductor surfaces that are part of biosensor platforms such as light-emitting diodes.}, number={9}, journal={The Journal of Physical Chemistry C}, publisher={American Chemical Society (ACS)}, author={Park, Heeyeon H. and Ivanisevic, Albena}, year={2007}, month={Feb}, pages={3710–3718} }
 @article{kinsella_shalaev_ivanisevic_2007, title={Ligation of Nanoparticle Coated DNA Cleaved with Restriction Enzymes}, volume={19}, ISSN={0897-4756 1520-5002}, url={http://dx.doi.org/10.1021/cm070850e}, DOI={10.1021/cm070850e}, abstractNote={In nature, DNA is a dynamic molecule regulated, reproduced, and destroyed using a host of enzymatic reactions. This report describes how templated DNA can be used as a dynamic material scaffold capable of being enzymatically reduced to smaller fragments and subsequently rejoined to become a long strand.}, number={15}, journal={Chemistry of Materials}, publisher={American Chemical Society (ACS)}, author={Kinsella, Joseph M. and Shalaev, Margarita V. and Ivanisevic, Albena}, year={2007}, month={Jul}, pages={3586–3588} }
 @article{sistiabudi_ivanisevic_2007, title={Patterning of Polypeptides on a Collagen-Terminated Tissue Surface}, volume={111}, ISSN={1932-7447 1932-7455}, url={http://dx.doi.org/10.1021/jp072757j}, DOI={10.1021/jp072757j}, abstractNote={Collagen is a ubiquitous component of the extracellular matrix environment, and numerous studies have been devoted toward the development of collagen-based tissue scaffolds. These efforts have been primarily focused on synthetic collagenous materials made from purified collagen. In this article, we present a preliminary study toward the development of a technique that can result in a tissue-derived collagen scaffold. The tissue-derived collagenous matrix was isolated from the retinal Bruch's membrane, and dip pen nanolithography was investigated as a mean to modify the collagenous surface. Characterization experiments of the collagenous surface indicate a fairly hydrophobic surface. Minimal swelling (<7%) of the collagen fibers was observed under elevated humidity conditions with negligible rearrangement of the surface. The hydrophobicity and roughness of the surface can pose a barrier for the deposition of molecules via scanning probe lithography. However, deposition of poly(glutamic acid) and polyargini...}, number={31}, journal={The Journal of Physical Chemistry C}, publisher={American Chemical Society (ACS)}, author={Sistiabudi, Rizaldi and Ivanisevic, Albena}, year={2007}, month={Aug}, pages={11676–11681} }
 @article{kinsella_ivanisevic_2007, title={Taking charge of biomolecules}, volume={2}, ISSN={1748-3387 1748-3395}, url={http://dx.doi.org/10.1038/nnano.2007.313}, DOI={10.1038/nnano.2007.313}, number={10}, journal={Nature Nanotechnology}, publisher={Springer Science and Business Media LLC}, author={Kinsella, Joseph M. and Ivanisevic, Albena}, year={2007}, month={Sep}, pages={596–597} }
 @article{mallick_bhagwandin_ivanisevic_2006, title={Characterization of collagen fibers in Bruch’s membrane using chemical force microscopy}, volume={386}, ISSN={1618-2642 1618-2650}, url={http://dx.doi.org/10.1007/S00216-006-0538-7}, DOI={10.1007/S00216-006-0538-7}, abstractNote={Bruch's membrane is a layer composed of collagen fibers located just beneath the retina. This study validates a strategy used to map the morphological and adhesion characteristics of collagen fibers in Bruch's membrane. Atomic force microscopy tips were functionalized with different chemical groups and used to map the hydrophilic and hydrophobic regions on the surface of the eye tissue. The largest adhesion forces were observed when tips functionalized with NH(2) groups were used. The trend in the adhesion forces was rationalized based on the distribution of different functional groups in the triple-helical structure of the collagen fibers. The results of this study can be used to design more effective strategies to treat eye diseases such as age-related macular degeneration.}, number={3}, journal={Analytical and Bioanalytical Chemistry}, publisher={Springer Science and Business Media LLC}, author={Mallick, Shrestha Basu and Bhagwandin, Sandhya and Ivanisevic, Albena}, year={2006}, month={Jul}, pages={652–657} }
 @article{cho_ivanisevic_2006, title={In vitro assessment of the biocompatibility of chemically modified GaAs surfaces}, volume={2}, ISSN={1551-1286 1551-1294}, url={http://dx.doi.org/10.1007/S12030-006-0007-6}, DOI={10.1007/S12030-006-0007-6}, abstractNote={GaAs has excellent optical, electrical, and mechanical properties and shows promise to be used in the fabrication of novel devices. However, the unprotected GaAs surface can release heavy metal compounds such as AsOx, which are toxic to living cells. A promising approach to reduce or eliminate this release relies on the passivation of the GaAs surface using different chemical approaches. In this work, we compared three different passivation methods aimed at enhancing the viability of cells on GaAs. Protective layers composed of self-assembled alkyl thiols, polypeptides, thick polymer layers, and shells of polyelectrolytes were tested. We confirmed that the GaAs surface can be made biocompatible for several days based on in vitro tests with HeLa and KB cells. In addition, we compared the cell spreading behavior on the GaAs substrates modified by different chemical approaches. Our results suggest that when the toxicity of the GaAs surface is reduced or eliminated, the cells'viability and spreading depend on the chemical and topographical nature of the surface.}, number={1-2}, journal={NanoBiotechnology}, publisher={Springer Science and Business Media LLC}, author={Cho, Youngnam and Ivanisevic, Albena}, year={2006}, month={Mar}, pages={51–59} }
 @article{flores-perez_ivanisevic_2007, title={Molecular recognition of chromophore molecules to amine terminated surfaces}, volume={253}, ISSN={0169-4332}, url={http://dx.doi.org/10.1016/j.apsusc.2006.09.020}, DOI={10.1016/j.apsusc.2006.09.020}, abstractNote={We report the design and characterization of quartz surfaces that can bind to three retinal based chromophores. The amine terminated surfaces were engineered in order to mimic the environment of the opsin protein that accommodates binding of chromophore molecules in the human eye. Each surface coupling step was characterized by water contact angle measurements, ellipsometry, atomic force microscopy, X-ray photoelectron spectroscopy, and transmission infrared spectroscopy. The spectroscopic techniques confirmed that the three chromophore molecules can bind to the surface using a Schiff base mode. Our data suggests that the availability of the amine groups on the surface is critical in the accommodation of the binding of different chromophores.}, number={9}, journal={Applied Surface Science}, publisher={Elsevier BV}, author={Flores-Perez, Rosangelly and Ivanisevic, Albena}, year={2007}, month={Feb}, pages={4176–4181} }
 @article{cho_ivanisevic_2006, title={Peptides on GaAs Surfaces:  Comparison between Features Generated by Microcontact Printing and Dip-Pen Nanolithography}, volume={22}, ISSN={0743-7463 1520-5827}, url={http://dx.doi.org/10.1021/la060492e}, DOI={10.1021/la060492e}, abstractNote={Atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), and Fourier transform infrared reflection absorption spectroscopy (FT-IRRAS) were employed to understand the size, composition, and conformation of lithographic patterns composed of peptide molecules. GaAs surfaces were patterned by microcontact printing (microCP) and dip-pen nanolithography (DPN) using a peptide sequence composed of 15 amino acids. The detailed surface evaluation showed that the patterns have similar chemical compositions but differ in the bonding among the molecules anchored on the GaAs substrate. Both types of patterns were crystalline-like in nature. The features created by DPN exhibited interchain hydrogen bonding, while the ones generated by microCP displayed non-hydrogen bonding. The differences in the lithographic structures can be utilized in future biorecognition experiments that take advantage of the electronic properties of the GaAs substrate and the tunable behavior of the covalently anchored biomolecules on the surface.}, number={21}, journal={Langmuir}, publisher={American Chemical Society (ACS)}, author={Cho, Youngnam and Ivanisevic, Albena}, year={2006}, month={Oct}, pages={8670–8674} }
 @article{cho_ivanisevic_2005, title={Covalent Attachment of TAT Peptides and Thiolated Alkyl Molecules on GaAs Surfaces}, volume={109}, ISSN={1520-6106 1520-5207}, url={http://dx.doi.org/10.1021/jp0515737}, DOI={10.1021/jp0515737}, abstractNote={Four TAT peptide fragments were used to functionalize GaAs surfaces by adsorption from solution. In addition, two well-studied alkylthiols, mercaptohexadecanoic acid (MHA) and 1-octadecanethiol (ODT) were utilized as references to understand the structure of the TAT peptide monolayer on GaAs. The different sequences of TAT peptides were employed in recognition experiments where a synthetic RNA sequence was tested to verify the specific interaction with the TAT peptide. The modified GaAs surfaces were characterized by atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), and Fourier transform infrared reflection absorption spectroscopy (FT-IRRAS). AFM studies were used to compare the surface roughness before and after functionalization. XPS allowed us to characterize the chemical composition of the GaAs surface and conclude that the monolayers composed of different sequences of peptides have similar surface chemistries. Finally, FT-IRRAS experiments enabled us to deduce that the TAT peptide monolayers have a fairly ordered and densely packed alkyl chain structure. The recognition experiments showed preferred interaction of the RNA sequence toward peptides with high arginine content.}, number={26}, journal={The Journal of Physical Chemistry B}, publisher={American Chemical Society (ACS)}, author={Cho, Youngnam and Ivanisevic, Albena}, year={2005}, month={Jul}, pages={12731–12737} }
 @article{kinsella_ivanisevic_2005, title={Enzymatic Clipping of DNA Wires Coated with Magnetic Nanoparticles}, volume={127}, ISSN={0002-7863 1520-5126}, url={http://dx.doi.org/10.1021/ja043865b}, DOI={10.1021/ja043865b}, abstractNote={The study describes how DNA coated with magnetic nanoparticles remains biologically active and accessible to the BamH1 restriction enzyme. Long DNA molecules are coated with magnetic nanoparticles using electrostatic interactions. The coated, stretched, and surface-bound DNA is incubated in the restriction enzyme that specifically recognizes any strand containing the GGATCC base sequence and clips the DNA. We show that, despite the presence of the nanoparticles on the DNA, the enzyme is still able to recognize the cleavage site and effectively digest the assembly.}, number={10}, journal={Journal of the American Chemical Society}, publisher={American Chemical Society (ACS)}, author={Kinsella, Joseph M. and Ivanisevic, Albena}, year={2005}, month={Mar}, pages={3276–3277} }
 @article{yu_nyamjav_ivanisevic_2005, title={Fabrication of positively and negatively charged polyelectrolyte structures by dip-pen nanolithography}, volume={15}, ISSN={0959-9428 1364-5501}, url={http://dx.doi.org/10.1039/b409406a}, DOI={10.1039/b409406a}, abstractNote={Dip-Pen Nanolithography (DPN) is successfully used to pattern two polyelectrolytes: poly(diallyldimethylammonium) chloride, PDDA and poly(styrenesulfonate), PSS, on two types of surfaces: clean SiOx and SiOx coated with a layer of PDDA. Lateral Force Microscopy, Force Volume Imaging and X-ray Photoelectron Spectroscopy were used to verify the chemical composition of the patterns.}, number={6}, journal={Journal of Materials Chemistry}, publisher={Royal Society of Chemistry (RSC)}, author={Yu, Meng and Nyamjav, Dorjderem and Ivanisevic, Albena}, year={2005}, pages={649} }
 @article{nyamjav_kinsella_ivanisevic_2005, title={Magnetic wires with DNA cores: A magnetic force microscopy study}, volume={86}, ISSN={0003-6951 1077-3118}, url={http://dx.doi.org/10.1063/1.1875748}, DOI={10.1063/1.1875748}, abstractNote={Magnetic force microscopy (MFM) has been employed to study Fe3O4 nanowires containing DNA cores. The MFM experiments confirmed that long DNA molecules templated with Fe3O4 nanoparticles form a magnetic wire. The components of wires containing particles with sizes below 10 nm were recorded to behave as single domain particles with out-of-plane magnetization. The MFM study showed that one can change the magnetization states of the particles using a magnetic tip. The properties of the magnetic wires with DNA cores make them an attractive material for future magnetostatic devices.}, number={9}, journal={Applied Physics Letters}, publisher={AIP Publishing}, author={Nyamjav, Dorjderem and Kinsella, Joseph M. and Ivanisevic, Albena}, year={2005}, month={Feb}, pages={093107} }
 @article{cho_ivanisevic_2006, title={Mapping the Interaction Forces between TAR RNA and TAT Peptides on GaAs Surfaces Using Chemical Force Microscopy}, volume={22}, ISSN={0743-7463 1520-5827}, url={http://dx.doi.org/10.1021/la052729x}, DOI={10.1021/la052729x}, abstractNote={The complexation of the HIV transactivation response element (TAR) RNA with the viral regulatory protein TAT is of enormous interest for the design of new sensing and therapeutic strategies. In this work, we anchored TAT peptides on GaAs surfaces using microcontact printing. Atomic force microscopy was used to quantify the interaction between TAR RNA and model TAT peptide sequences. Different pH conditions were utilized in order to assess specific vs nonspecific interactions. AFM tips functionalized with TAR RNA molecules were used to collect adhesion maps that displayed stronger interaction with peptide sequences that contained a greater number of arginine residues. All of the studies consistently showed a pH dependence of the interaction between the surface bound peptides and the TAR RNA on the AFM tips. This work quantifies the TAR RNA/TAT peptide interaction after one of the molecules is anchored on a surface. The conclusions in this paper are consistent with previous work and demonstrate that cationic residues are responsible for the polyelectrolyte-like affinity of TAT peptides for TAR RNA.}, number={4}, journal={Langmuir}, publisher={American Chemical Society (ACS)}, author={Cho, Youngnam and Ivanisevic, Albena}, year={2006}, month={Feb}, pages={1768–1774} }
 @article{nyamjav_ivanisevic_2005, title={Structural and adhesion properties of surfaces functionalized with polyelectrolytes and polystyrene particles}, volume={67}, ISSN={0039-9140}, url={http://dx.doi.org/10.1016/j.talanta.2005.06.033}, DOI={10.1016/j.talanta.2005.06.033}, abstractNote={Surfaces functionalized with polystyrene particles and polyelectrolytes were used to investigate the morphological and adhesion properties of composite substrates. Atomic force microscopy (AFM) studies showed that surfaces with non-homogeneous topography have non-homogeneous adhesion properties. In addition, the homogeneity of the adhesion properties is dependent upon the chemical species used to functionalize the surface. Force volume (FV) imaging was utilized to map the adhesion of the fabricated substrates with high-resolution. The FV studies revealed that the hydrophobicity of the surface is not uniform despite the fact that the surface was functionalized with the same polyelectrolyte. The analysis methodology we report here opens the possibility to design better surfaces for future tissue engineering applications.}, number={3}, journal={Talanta}, publisher={Elsevier BV}, author={Nyamjav, D and Ivanisevic, A}, year={2005}, month={Sep}, pages={503–506} }
 @article{mallick_ivanisevic_2005, title={Study of the Morphological and Adhesion Properties of Collagen Fibers in the Bruch's Membrane}, volume={109}, ISSN={1520-6106 1520-5207}, url={http://dx.doi.org/10.1021/jp053605w}, DOI={10.1021/jp053605w}, abstractNote={The Bruch's membrane is located beneath the retina in vertebrate eyes. We have used atomic force microscopy to examine the morphological and adhesion properties of collagen fibers located in different portions of the membrane. The D-periodicity of the fibers was 62.54 +/- 4.25 nm and 63.78 +/- 4.14 nm for regions away from the optic nerve and close to it, respectively. The adhesion properties of the collagen fibers were evaluated using force volume imaging on a number of different eye samples. The adhesion force we recorded in regions away from the optic nerve was different compared to regions close to the optic nerve. The reported results allow us to understand the nanoscopic properties of connective tissues in the eye and are important for the design of new and improved biomaterials.}, number={41}, journal={The Journal of Physical Chemistry B}, publisher={American Chemical Society (ACS)}, author={Mallick, Shrestha Basu and Ivanisevic, Albena}, year={2005}, month={Oct}, pages={19052–19055} }
 @article{cho_ivanisevic_2005, title={TAT Peptide Immobilization on Gold Surfaces:  A Comparison Study with a Thiolated Peptide and Alkylthiols Using AFM, XPS, and FT-IRRAS}, volume={109}, ISSN={1520-6106 1520-5207}, url={http://dx.doi.org/10.1021/jp045731q}, DOI={10.1021/jp045731q}, abstractNote={A TAT peptide was used to functionalize a gold surface by three different methods: adsorption from solution, microcontact printing, and dip-pen nanolithography (DPN). The composition and structure of the modified gold was characterized by atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), and Fourier transform -infrared reflection absorption spectroscopy (FT-IRRAS). We used two well-studied alkylthiols, mercaptohexadecanoic acid and 1-octadecanethiol, as a comparison in order to understand the structure of the TAT peptide monolayers prepared by the three methods. AFM studies allowed us to assess the homogeneity after each modification protocol. XPS was used to characterize the chemical composition of the gold surface after each functionalization procedure. The XPS results showed that surfaces modified with the TAT peptide by the three methods exhibit similar surface chemistry. Finally, FT-IRRAS experiments allowed us to conclude that the structure of the alkyl chains of the TAT peptides is fairly disordered and different after each procedure. Regardless of the type of surface functionalization method used, the monolayer of TAT peptide formed on the surface was of "liquidlike" nature.}, number={13}, journal={The Journal of Physical Chemistry B}, publisher={American Chemical Society (ACS)}, author={Cho, Youngnam and Ivanisevic, Albena}, year={2005}, month={Apr}, pages={6225–6232} }
 @article{kinsella_ivanisevic_2005, title={Chromophore binding to in vitro engineered bio-mimetic surfaces}, volume={243}, ISSN={0169-4332}, url={http://dx.doi.org/10.1016/j.apsusc.2004.09.108}, DOI={10.1016/j.apsusc.2004.09.108}, abstractNote={In the retina, a chromophore isomerizes and the protein to which it binds changes shape. In this proof-of-concept experiment we engineer an artificial surface to mimic the physiochemical environment of the retina and the key reaction of the visual cycle. We immobilized small peptides on silicon and assessed changes in their surface properties upon chromophore binding via ellipsometry, X-ray photoelectron spectroscopy and atomic force microscopy. Our observations suggest that when binding occurs it is accompanied by changes in the properties of the film composed of surface-anchored peptides.}, number={1-4}, journal={Applied Surface Science}, publisher={Elsevier BV}, author={Kinsella, Joseph M. and Ivanisevic, Albena}, year={2005}, month={Apr}, pages={7–10} }
 @article{nyamjav_ivanisevic_2004, title={Properties of Polyelectrolyte Templates Generated by Dip-Pen Nanolithography and Microcontact Printing}, volume={16}, ISSN={0897-4756 1520-5002}, url={http://dx.doi.org/10.1021/cm049179t}, DOI={10.1021/cm049179t}, abstractNote={Patterns were generated with a single type of polyelectrolyte, poly(allylamine)hydrochloride, by two different lithographic methods and subsequently used in surface studies. The experiments allowed comparison and contrast of the properties of the features generated by each methodology.}, number={25}, journal={Chemistry of Materials}, publisher={American Chemical Society (ACS)}, author={Nyamjav, Dorjderem and Ivanisevic, Albena}, year={2004}, month={Dec}, pages={5216–5219} }
 @article{cho_ivanisevic_2004, title={SiOx Surfaces with Lithographic Features Composed of a TAT Peptide}, volume={108}, ISSN={1520-6106 1520-5207}, url={http://dx.doi.org/10.1021/jp048359n}, DOI={10.1021/jp048359n}, abstractNote={Synthetic TAT peptides designed to contain an arginine rich basic unit can bind to RNA with an affinity and specificity of a full-length TAT protein. Therefore, deducing strategies to immobilize such short peptides to surfaces can enable one to study their unique recognition properties in various types of sensor platforms. In this paper, we present a strategy to immobilize a 15-residue TAT peptide (CGISYGRKKRRQRRR) in the form of nanoscopic features on SiOx surfaces. The protocol is based on dip-pen nanolithography that results in the formation of a covalent attachment of the peptide to a SiOx surface rather than immobilization via electrostatic interactions or patterning on metal surfaces. The nanolithography was characterized by atomic force microscopy (AFM) and X-ray photoelectron spectroscopy. Critical parameters identified by this report include roughness quality and chemical composition of the surface prior to patterning, high humidity conditions, and concentration of ink solution needed to modify t...}, number={39}, journal={The Journal of Physical Chemistry B}, publisher={American Chemical Society (ACS)}, author={Cho, Youngnam and Ivanisevic, Albena}, year={2004}, month={Sep}, pages={15223–15228} }
 @article{nyamjav_ivanisevic_2005, title={Templates for DNA-templated Fe3O4 nanoparticles}, volume={26}, ISSN={0142-9612}, url={http://dx.doi.org/10.1016/j.biomaterials.2004.07.025}, DOI={10.1016/j.biomaterials.2004.07.025}, abstractNote={Two different strategies are reported that result in the site-specific placement of long DNA molecules, templated with Fe3O4 nanoparticles, on SiOx surfaces. The strategies combine solution templating of inorganic nanoparticles onto biomolecules, molecular combing, the layer-by-layer method, and dip-pen nanolithography (DPN). In one methodology, the first step is to place and stretch DNA molecules via a DPN template containing features of poly(allylamine hydrochloride) (PAH). In the second step the elongated DNA is templated with Fe3O4 nanoparticles allowing them to assemble onto the DNA molecules based on electrostatic interactions. In the second methodology, DPN templates composed of PSS patterns are used to comb in a site-specific manner DNA molecules that have been pre-tempated in solution with the Fe3O4 nanoparticles. The templates generated by the two methods can serve as building blocks for the fabrication of future higher order assemblies.}, number={15}, journal={Biomaterials}, publisher={Elsevier BV}, author={Nyamjav, Dorjderem and Ivanisevic, Albena}, year={2005}, month={May}, pages={2749–2757} }
 @article{yu_ivanisevic_2004, title={Encapsulated cells: an atomic force microscopy study}, volume={25}, ISSN={0142-9612}, url={http://dx.doi.org/10.1016/j.biomaterials.2003.10.061}, DOI={10.1016/j.biomaterials.2003.10.061}, abstractNote={Two types of cells--human platelets and spore cells--were encapsulated in polymer shells by adsorbing polyanions and polycations in a stepwise fashion. The encapsulated cells were attached to gold and silicon surfaces and their morphological and adhesion properties were studied in air using tapping mode atomic force microscopy (AFM). The roughness of the encapsulated cells increased upon the addition of a new polymer layer. The increase in roughness can be attributed to the formation of a shell around the cells, which is stabilized by electrostatic interactions, as well as to the drying effects associated with the immobilization and dehydration of the cells. Trigger mode was used to perform the force imaging and map out the adhesion characteristics of the cells. Systematic "maps" of the adhesion properties of the encapsulated cells to clean and amine terminated AFM tips were collected. The adhesion force data for the different tips and encapsulated cells showed dependence not only on the number and thickness of the polymer layers, but also on the interactions between these layers. The encapsulated cells' morphology and roughness characteristics remained intact over a substantial storage period. This stability and adhesion properties make them suitable building blocks for the design and construction of biomimetic templates where AFM is used as the primary tool to do the fabrication.}, number={17}, journal={Biomaterials}, publisher={Elsevier BV}, author={Yu, Meng and Ivanisevic, Albena}, year={2004}, month={Aug}, pages={3655–3662} }