@article{movahed_nguyen_goering_skoog_narayan_2020, title={Argon and oxygen plasma treatment increases hydrophilicity and reduces adhesion of silicon-incorporated diamond-like coatings}, volume={15}, ISSN={["1559-4106"]}, DOI={10.1116/6.0000356}, abstractNote={In this study, the structure, adhesion, and cell viability characteristics of silicon-incorporated diamond-like carbon (Si-DLC) coatings on fused silica substrates were investigated. The effects of argon and oxygen postprocessing plasma treatments on the Si-DLC coatings were also studied. The contact angle results showed that the Si-DLC coatings were more hydrophilic than the uncoated surfaces, and postprocessing plasma treatment increased the hydrophilicity of the Si-DLC coatings. Atomic force microscopy and profilometry confirmed that postprocessing plasma treatment increased the thickness and roughness of the Si-DLC coatings. The results of microscratch testing indicated that the plasma treatments reduced the adhesion of the coatings. The x-ray photoelectron spectroscopy (XPS) showed the presence of carbon, oxygen, and silicon in the Si-DLC coatings before and after the plasma treatments. These results show that the postprocessing plasma treatment significantly reduced the atomic percentage of the carbon in the Si-DLC coatings. XPS also confirmed the presence of carbon in the form of sp3(C—C), sp2(C=C), C—O, and C=O bonds in the Si-DLC coatings; it showed that postprocessing treatments significantly increased the percentage of oxygen in the Si-DLC coatings. Fourier transform infrared spectroscopy (FTIR) analysis showed features associated with C—OH stretching, C—H bending, as well as Si—CH2 and C—H bending in the Si-DLC coating. The XPS and FTIR results confirmed that the plasma treatment caused dissociation of the sp2 and sp3 bonds and formation of C—OH bonds. The contact angle data indicated that postprocessing treatment increased the hydrophilicity of the Si-DLC coating. Similar to the uncoated substrates, L929 cells showed no change in cell viability when cultured on Si-DLC coatings. These results of the study indicate the suitability of Si-DLC coatings as inert coatings for medical and biotechnology applications.}, number={4}, journal={BIOINTERPHASES}, author={Movahed, Saeid and Nguyen, Alexander K. and Goering, Peter L. and Skoog, Shelby A. and Narayan, Roger J.}, year={2020}, month={Jul} }
 @article{liu_movahed_dangi_pan_kaur_bilinovich_faison_leighton_wang_williams_et al._2020, title={DNA looping by two 5-methylcytosine-binding proteins quantified using nanofluidic devices}, volume={13}, ISSN={["1756-8935"]}, DOI={10.1186/s13072-020-00339-7}, abstractNote={Abstract
Background
MeCP2 and MBD2 are members of a family of proteins that possess a domain that selectively binds 5-methylcytosine in a CpG context. Members of the family interact with other proteins to modulate DNA packing. Stretching of DNA–protein complexes in nanofluidic channels with a cross-section of a few persistence lengths allows us to probe the degree of compaction by proteins.

Results
We demonstrate DNA compaction by MeCP2 while MBD2 does not affect DNA configuration. By using atomic force microscopy (AFM), we determined that the mechanism for compaction by MeCP2 is the formation of bridges between distant DNA stretches and the formation of loops.

Conclusions
Despite sharing a similar specific DNA-binding domain, the impact of full-length 5-methylcytosine-binding proteins can vary drastically between strong compaction of DNA and no discernable large-scale impact of protein binding. We demonstrate that ATTO 565-labeled MBD2 is a good candidate as a staining agent for epigenetic mapping.
}, number={1}, journal={EPIGENETICS & CHROMATIN}, author={Liu, Ming and Movahed, Saeid and Dangi, Saroj and Pan, Hai and Kaur, Parminder and Bilinovich, Stephanie M. and Faison, Edgar M. and Leighton, Gage O. and Wang, Hong and Williams, David C., Jr. and et al.}, year={2020}, month={Mar} }
 @article{jahromi_amani_movahed_2019, title={An improved hybrid continuum-atomistic four-way coupled model for electrokinetics in nanofluidics}, volume={40}, ISSN={["1522-2683"]}, DOI={10.1002/elps.201800307}, abstractNote={AbstractIn this study, an efficient hybrid continuum‐atomistic method is proposed to study electrokinetic transport of aqueous solutions in nanofluidics. The aqueous phase is considered as a continuous phase containing immersed ion particles. The behavior of the system is then simulated through utilization of an improved hybrid continuum‐atomistic four‐way coupled approach, including the MultiPhase Particle‐In‐Cell method for the short‐ranged interaction between the ion particles, the Brownian force for the collision between the aqueous phase molecules and the ion particles, and a wall force accounting for the short‐ranged interaction of ions and walls. The validation of the proposed model with the results of Molecular Dynamics simulations suggests that this model can be a promising approach for studying the electrokinetic phenomena in more complicated geometries where the Molecular Dynamics approach is computationally prohibitive. Finally, the effects of electrokinetic parameters, such as the height of the channel, the external electric field, and bulk ionic concentration, on the electroosmotic flow in a nanochannel are investigated and discussed.}, number={12-13}, journal={ELECTROPHORESIS}, author={Jahromi, Saeed and Amani, Ehsan and Movahed, Saeid}, year={2019}, month={Jul}, pages={1678–1690} }
 @article{roushan_azad_movahed_ray_livshits_lim_weninger_riehn_2018, title={Motor-like DNA motion due to an ATP-hydrolyzing protein under nanoconfinement}, volume={8}, journal={Scientific Reports}, author={Roushan, M. and Azad, Z. and Movahed, S. and Ray, P. D. and Livshits, G. I. and Lim, S. F. and Weninger, K. R. and Riehn, R.}, year={2018} }