@article{code_qiu_solov'yov_lee_shin_roland_sagui_houde_rand_jorgensen_2023, title={Conformationally Restricted Glycopeptide Backbone Inhibits Gas-Phase H/D Scrambling between Glycan and Peptide Moieties}, ISSN={["1520-5126"]}, DOI={10.1021/jacs.3c04068}, abstractNote={Protein glycosylation is a common post-translational modification on extracellular proteins. The conformational dynamics of several glycoproteins have been characterized by hydrogen/deuterium exchange mass spectrometry (HDX-MS). However, it is, in most cases, not possible to extract information about glycan conformation and dynamics due to the general difficulty of separating the deuterium content of the glycan from that of the peptide (in particular, for O-linked glycans). Here, we investigate whether the fragmentation of protonated glycopeptides by collision-induced dissociation (CID) can be used to determine the solution-specific deuterium content of the glycan. Central to this concept is that glycopeptides can undergo a facile loss of glycans upon CID, thereby allowing for the determination of their masses. However, an essential prerequisite is that hydrogen and deuterium (H/D) scrambling can be kept in check. Therefore, we have measured the degree of scrambling upon glycosidic bond cleavage in glycopeptides that differ in the conformational flexibility of their backbone and glycosylation pattern. Our results show that complete scrambling precedes the glycosidic bond cleavage in normal glycopeptides derived from a glycoprotein; i.e., all labile hydrogens have undergone positional randomization prior to loss of the glycan. In contrast, the glycosidic bond cleavage occurs without any scrambling in the glycopeptide antibiotic vancomycin, reflecting that the glycan cannot interact with the peptide moiety due to a conformationally restricted backbone as revealed by molecular dynamics simulations. Scrambling is also inhibited, albeit to a lesser degree, in the conformationally restricted glycopeptides ristocetin and its pseudoaglycone, demonstrating that scrambling depends on an intricate interplay between the flexibility and proximity of the glycan and the peptide backbone.}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Code, Christian and Qiu, Danwen and Solov'yov, Ilia A. and Lee, Jung-Goo and Shin, Hyeon-Cheol and Roland, Christopher and Sagui, Celeste and Houde, Damian and Rand, Kasper D. and Jorgensen, Thomas J. D.}, year={2023}, month={Oct} }
 @article{xu_zhang_pan_mahn_roland_sagui_weninger_2023, title={Frustration Between Preferred States of Complementary Trinucleotide Repeat DNA Hairpins Anticorrelates with Expansion Disease Propensity}, volume={435}, ISSN={["1089-8638"]}, DOI={10.1016/j.jmb.2023.168086}, abstractNote={DNA trinucleotide repeat (TRs) expansion beyond a threshold often results in human neurodegenerative diseases. The mechanisms causing expansions remain unknown, although the tendency of TR ssDNA to self-associate into hairpins that slip along their length is widely presumed related. Here we apply single molecule FRET (smFRET) experiments and molecular dynamics simulations to determine conformational stabilities and slipping dynamics for CAG, CTG, GAC and GTC hairpins. Tetraloops are favored in CAG (89%), CTG (89%) and GTC (69%) while GAC favors triloops. We also determined that TTG interrupts near the loop in the CTG hairpin stabilize the hairpin against slipping. The different loop stabilities have implications for intermediate structures that may form when TR-containing duplex DNA opens. Opposing hairpins in the (CAG) ∙ (CTG) duplex would have matched stability whereas opposing hairpins in a (GAC) ∙ (GTC) duplex would have unmatched stability, introducing frustration in the (GAC) ∙ (GTC) opposing hairpins that could encourage their resolution to duplex DNA more rapidly than in (CAG) ∙ (CTG) structures. Given that the CAG and CTG TR can undergo large, disease-related expansion whereas the GAC and GTC sequences do not, these stability differences can inform and constrain models of expansion mechanisms of TR regions.}, number={10}, journal={JOURNAL OF MOLECULAR BIOLOGY}, author={Xu, Pengning and Zhang, Jiahui and Pan, Feng and Mahn, Chelsea and Roland, Christopher and Sagui, Celeste and Weninger, Keith}, year={2023}, month={May} }
 @article{fakharzadeh_qu_pan_sagui_roland_2023, title={Structure and Dynamics of DNA and RNA Double Helices Formed by d(CTG), d(GTC), r(CUG), and r(GUC) Trinucleotide Repeats and Associated DNA-RNA Hybrids}, ISSN={["1520-5207"]}, DOI={10.1021/acs.jpcb.3c03538}, abstractNote={Myotonic dystrophy type 1 is the most frequent form of muscular dystrophy in adults caused by an abnormal expansion of the CTG trinucleotide. Both the expanded DNA and the expanded CUG RNA transcript can fold into hairpins. Co-transcriptional formation of stable RNA·DNA hybrids can also enhance the instability of repeat tracts. We performed molecular dynamics simulations of homoduplexes associated with the disease, d(CTG)n and r(CUG)n, and their corresponding r(CAG)n:d(CTG)n and r(CUG)n:d(CAG)n hybrids that can form under bidirectional transcription and of non-pathological d(GTC)n and d(GUC)n homoduplexes. We characterized their conformations, stability, and dynamics and found that the U·U and T·T mismatches are dynamic, favoring anti-anti conformations inside the helical core, followed by anti-syn and syn-syn conformations. For DNA, the secondary minima in the non-expanding d(GTC)n helices are deeper, wider, and longer-lived than those in d(CTG)n, which constitutes another biophysical factor further differentiating the expanding and non-expanding sequences. The hybrid helices are closer to A-RNA, with the A-T and A-U pairs forming two stable Watson-Crick hydrogen bonds. The neutralizing ion distribution around the non-canonical pairs is also described.}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Fakharzadeh, Ashkan and Qu, Jing and Pan, Feng and Sagui, Celeste and Roland, Christopher}, year={2023}, month={Sep} }
 @article{man_he_nguyen_sagui_roland_xie_wang_2023, title={Unpolarized laser method for infrared spectrum calculation of amide I C=O bonds in proteins using molecular dynamics simulation}, volume={159}, ISSN={["1879-0534"]}, DOI={10.1016/j.compbiomed.2023.106902}, abstractNote={The investigation of the strong infrared (IR)-active amide I modes of peptides and proteins has received considerable attention because a wealth of detailed information on hydrogen bonding, dipole-dipole interactions, and the conformations of the peptide backbone can be derived from the amide I bands. The interpretation of experimental spectra typically requires substantial theoretical support, such as direct ab-initio molecular dynamics simulation or mixed quantum-classical description. However, considering the difficulties associated with these theoretical methods and their applications are limited in small peptides, it is highly desirable to develop a simple yet efficient approach for simulating the amide I modes of any large proteins in solution. In this work, we proposed a comprehensive computational method that extends the well-established molecular dynamics (MD) simulation method to include an unpolarized IR laser for exciting the CO bonds of proteins. We showed the amide I frequency corresponding to the frequency of the laser pulse which resonated with the CO bond vibration. At this frequency, the protein energy and the CO bond length fluctuation were maximized. Overall, the amide I bands of various single proteins and amyloids agreed well with experimental data. The method has been implemented into the AMBER simulation package, making it widely available to the scientific community. Additionally, the application of the method to simulate the transient amide I bands of amyloid fibrils during the IR laser-induced disassembly process was discussed in details.}, journal={COMPUTERS IN BIOLOGY AND MEDICINE}, author={Man, Viet Hoang and He, Xibing and Nguyen, Phuong H. and Sagui, Celeste and Roland, Christopher and Xie, Xiang-Qun and Wang, Junmei}, year={2023}, month={Jun} }
 @article{fakharzadeh_zhang_roland_sagui_2022, title={Novel eGZ-motif formed by regularly extruded guanine bases in a left-handed Z-DNA helix as a major motif behind CGG trinucleotide repeats}, ISSN={["1362-4962"]}, DOI={10.1093/nar/gkac339}, abstractNote={Abstract}, journal={NUCLEIC ACIDS RESEARCH}, author={Fakharzadeh, Ashkan and Zhang, Jiahui and Roland, Christopher and Sagui, Celeste}, year={2022}, month={May} }
 @article{zhang_fakharzadeh_roland_sagui_2022, title={RNA as a Major-Groove Ligand: RNA-RNA and RNA-DNA Triplexes Formed by GAA and UUC or TTC Sequences}, volume={7}, ISSN={["2470-1343"]}, DOI={10.1021/acsomega.2c04358}, abstractNote={Friedreich’s ataxia is associated with noncanonical nucleic acid structures that emerge when GAA:TTC repeats in the first intron of the FXN gene expand beyond a critical number of repeats. Specifically, the noncanonical repeats are associated with both triplexes and R-loops. Here, we present an in silico investigation of all possible triplexes that form by attaching a third RNA strand to an RNA:RNA or DNA:DNA duplex, complementing previous DNA-based triplex studies. For both new triplexes results are similar. For a pyridimine UUC+ third strand, the parallel orientation is stable while its antiparallel counterpart is unstable. For a neutral GAA third strand, the parallel conformation is stable. A protonated GA+A third strand is stable in both parallel and antiparallel orientations. We have also investigated Na+ and Mg2+ ion distributions around the triplexes. The presence of Mg2+ ions helps stabilize neutral, antiparallel GAA triplexes. These results (along with previous DNA-based studies) allow for the emergence of a complete picture of the stability and structural characteristics of triplexes based on the GAA and TTC/UUC sequences, thereby contributing to the field of trinucleotide repeats and the associated unusual structures that trigger expansion.}, number={43}, journal={ACS OMEGA}, author={Zhang, Jiahui and Fakharzadeh, Ashkan and Roland, Christopher and Sagui, Celeste}, year={2022}, month={Nov}, pages={38728–38743} }
 @article{zhang_fakharzadeh_pan_roland_sagui_2021, title={Construction of DNA/RNA Triplex Helices Based on GAA/TTC Trinucleotide Repeats}, volume={11}, ISSN={["2331-8325"]}, DOI={10.21769/BioProtoc.4155}, abstractNote={Atypical DNA and RNA secondary structures play a crucial role in simple sequence repeat (SSR) diseases, which are associated with a class of neurological and neuromuscular disorders known as "anticipation diseases," where the age of disease onset decreases and the severity of the disease is increased as the intergenerational expansion of the SSR increases. While the mechanisms underlying these diseases are complex and remain elusive, there is a consensus that stable, non-B-DNA atypical secondary structures play an important - if not causative - role. These structures include single-stranded DNA loops and hairpins, G-quartets, Z-DNA, triplex nucleic acid structures, and others. While all of these structures are of interest, structures based on nucleic acid triplexes have recently garnered increased attention as they have been implicated in gene regulation, gene repair, and gene engineering. Our work here focuses on the construction of DNA triplexes and RNA/DNA hybrids formed from GAA/TTC trinucleotide repeats, which underlie Friedreich's ataxia. While there is some software, such as the Discovery Studio Visualizer, that can aid in the initial construction of DNA triple helices, the only option for the triple helix is constrained to be that of an antiparallel pyrimidine for the third strand. In this protocol, we illustrate how to build up more generalized DNA triplexes and DNA/RNA mixed hybrids. We make use of both the Discovery Studio Visualizer and the AMBER simulation package to construct the initial triplexes. Using the steps outlined here, one can - in principle - build up any triple nucleic acid helix with a desired sequence for large-scale molecular dynamics simulation studies.}, number={18}, journal={BIO-PROTOCOL}, author={Zhang, Jiahui and Fakharzadeh, Ashkan and Pan, Feng and Roland, Christopher and Sagui, Celeste}, year={2021}, month={Sep} }
 @misc{pan_zhang_xu_man_roland_weninger_sagui_2021, title={Molecular conformations and dynamics of nucleotide repeats associated with neurodegenerative diseases: double helices and CAG hairpin loops}, volume={19}, ISSN={["2001-0370"]}, DOI={10.1016/j.csbj.2021.04.037}, abstractNote={Pathogenic DNA secondary structures have been identified as a common and causative factor for expansion in trinucleotide, hexanucleotide, and other simple sequence repeats. These expansions underlie about fifty neurological and neuromuscular disorders known as “anticipation diseases”. Cell toxicity and death have been linked to the pathogenic conformations and functional changes of the RNA transcripts, of DNA itself and, when trinucleotides are present in exons, of the translated proteins. We review some of our results for the conformations and dynamics of pathogenic structures for both RNA and DNA, which include mismatched homoduplexes formed by trinucleotide repeats CAG and GAC; CCG and CGG; CTG(CUG) and GTC(GUC); the dynamics of DNA CAG hairpins; mismatched homoduplexes formed by hexanucleotide repeats (GGGGCC) and (GGCCCC); and G-quadruplexes formed by (GGGGCC) and (GGGCCT). We also discuss the dynamics of strand slippage in DNA hairpins formed by CAG repeats as observed with single-molecule Fluorescence Resonance Energy Transfer. This review focuses on the rich behavior exhibited by the mismatches associated with these simple sequence repeat noncanonical structures.}, journal={COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL}, author={Pan, Feng and Zhang, Yuan and Xu, Pengning and Man, Viet Hoang and Roland, Christopher and Weninger, Keith and Sagui, Celeste}, year={2021}, pages={2819–2832} }
 @article{tran_pan_tran_roland_sagui_2021, title={The F19W mutation reduces the binding affinity of the transmembrane A beta(11-40) trimer to the membrane bilayer}, volume={11}, ISSN={["2046-2069"]}, DOI={10.1039/d0ra08837d}, abstractNote={Dominant conformations of F19W 3Aβ11–40 immersed in transmembrane DPPC lipid bilayer submerged in aqueous solution.}, number={5}, journal={RSC ADVANCES}, author={Tran, Thanh Thuy and Pan, Feng and Tran, Linh and Roland, Christopher and Sagui, Celeste}, year={2021}, month={Jan}, pages={2664–2676} }
 @article{zhang_fakharzadeh_pan_roland_sagui_2020, title={Atypical structures of GAA/TTC trinucleotide repeats underlying Friedreich's ataxia: DNA triplexes and RNA/DNA hybrids}, volume={48}, ISSN={["1362-4962"]}, DOI={10.1093/nar/gkaa665}, abstractNote={Abstract}, number={17}, journal={NUCLEIC ACIDS RESEARCH}, author={Zhang, Jiahui and Fakharzadeh, Ashkan and Pan, Feng and Roland, Christopher and Sagui, Celeste}, year={2020}, month={Sep}, pages={9899–9917} }
 @article{pan_zhang_man_roland_sagui_2018, title={E-motif formed by extrahelical cytosine bases in DNA homoduplexes of trinucleotide and hexanucleotide repeats}, volume={46}, ISSN={["1362-4962"]}, DOI={10.1093/nar/gkx1186}, abstractNote={Abstract Atypical DNA secondary structures play an important role in expandable trinucleotide repeat (TR) and hexanucleotide repeat (HR) diseases. The cytosine mismatches in C-rich homoduplexes and hairpin stems are weakly bonded; experiments show that for certain sequences these may flip out of the helix core, forming an unusual structure termed an ‘e-motif’. We have performed molecular dynamics simulations of C-rich TR and HR DNA homoduplexes in order to characterize the conformations, stability and dynamics of formation of the e-motif, where the mismatched cytosines symmetrically flip out in the minor groove, pointing their base moieties towards the 5′-direction in each strand. TRs have two non-equivalent reading frames, (GCC)n and (CCG)n; while HRs have three: (CCCGGC)n, (CGGCCC)n, (CCCCGG)n. We define three types of pseudo basepair steps related to the mismatches and show that the e-motif is only stable in (GCC)n and (CCCGGC)n homoduplexes due to the favorable stacking of pseudo GpC steps (whose nature depends on whether TRs or HRs are involved) and the formation of hydrogen bonds between the mismatched cytosine at position i and the cytosine (TRs) or guanine (HRs) at position i − 2 along the same strand. We also characterize the extended e-motif, where all mismatched cytosines are extruded, their extra-helical stacking additionally stabilizing the homoduplexes.}, number={2}, journal={NUCLEIC ACIDS RESEARCH}, author={Pan, Feng and Zhang, Yuan and Man, Viet Hoang and Roland, Christopher and Sagui, Celeste}, year={2018}, month={Jan}, pages={942–955} }
 @article{zhang_roland_sagui_2018, title={Structural and Dynamical Characterization of DNA and RNA Quadruplexes Obtained from the GGGGCC and GGGCCT Hexanucleotide Repeats Associated with C9FTD/ALS and SCA36 Diseases}, volume={9}, ISSN={["1948-7193"]}, DOI={10.1021/acschemneuro.7b00476}, abstractNote={A (GGGGCC) hexanucleotide repeat (HR) expansion in the C9ORF72 gene has been considered the major cause behind both frontotemporal dementia and amyotrophic lateral sclerosis, while a (GGGCCT) is associated with spinocerebellar ataxia 36. Recent experiments involving NMR, CD, optical melting and 1D 1H NMR spectroscopy, suggest that the r(GGGGCC) HR can adopt a hairpin structure with G-G mismatches in equilibrium with a G-quadruplex structure. G-Quadruplexes have also been identified for d(GGGGCC). As these experiments lack molecular resolution, we have used molecular dynamics microsecond simulations to obtain a structural characterization of the G-quadruplexes associated with both HRs. All DNA G-quadruplexes, parallel or antiparallel, with or without loops are stable, while only parallel and one antiparallel (stabilized by diagonal loops) RNA G-quadruplexes are stable. It is known that antiparallel G-quadruplexes require alternating guanines to be in a syn conformation that is hindered by the C3'-endo pucker preferred by RNA. Initial RNA antiparallel quadruplexes built with C2'-endo sugars evolve such that the transition (C2'-endo)-to-(C3'-endo) triggers unwinding and buckling of the flat G-tetrads, resulting in the unfolding of the RNA antiparallel quadruplex. Finally, a parallel G-quadruplex stabilizes an adjacent C-tetrad in both DNA and RNA (thus effectively becoming a mixed quadruplex of 5 layers). The C-tetrad is stabilized by the stacking interactions with the preceding G-tetrad, by cyclical hydrogen bonds C(N4)-(O2), and by an ion between the G-tetrad and the C-tetrad. In addition, antiparallel DNA G-quadruplexes also stabilize flat C-layers at the ends of the quadruplexes.}, number={5}, journal={ACS CHEMICAL NEUROSCIENCE}, author={Zhang, Yuan and Roland, Christopher and Sagui, Celeste}, year={2018}, month={May}, pages={1104–1117} }
 @article{pan_man_roland_sagui_2018, title={Structure and Dynamics of DNA and RNA Double Helices Obtained from the CCG and GGC Trinucleotide Repeats}, volume={122}, ISSN={["1520-6106"]}, DOI={10.1021/acs.jpcb.8b01658}, abstractNote={Expansions of both GGC and CCG sequences lead to a number of expandable, trinucleotide repeat (TR) neurodegenerative diseases. Understanding of these diseases involves, among other things, the structural characterization of the atypical DNA and RNA secondary structures. We have performed molecular dynamics simulations of (GCC) n and (GGC) n homoduplexes in order to characterize their conformations, stability, and dynamics. Each TR has two reading frames, which results in eight nonequivalent RNA/DNA homoduplexes, characterized by CpG or GpC steps between the Watson-Crick base pairs. Free energy maps for the eight homoduplexes indicate that the C-mismatches prefer anti-anti conformations, while G-mismatches prefer anti-syn conformations. Comparison between three modifications of the DNA AMBER force field shows good agreement for the mismatch free energy maps. The mismatches in DNA-GCC (but not CCG) are extrahelical, forming an extended e-motif. The mismatched duplexes exhibit characteristic sequence-dependent step twist, with strong variations in the G-rich sequences and the e-motif. The distribution of Na+ is highly localized around the mismatches, especially G-mismatches. In the e-motif, there is strong Na+ binding by two G(N7) atoms belonging to the pseudo GpC step created when cytosines are extruded and by extrahelical cytosines. Finally, we used a novel technique based on fast melting by means of an infrared laser pulse to classify the relative stability of the different DNA-CCG and -GGC homoduplexes.}, number={16}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Pan, Feng and Man, Viet Hoang and Roland, Christopher and Sagui, Celeste}, year={2018}, month={Apr}, pages={4491–4512} }
 @article{zhang_roland_sagui_2017, title={Structure and Dynamics of DNA and RNA Double Helices Obtained from the GGGGCC and CCCCGG Hexanucleotide Repeats That Are the Hallmark of C9FTD/ALS Diseases}, volume={8}, ISSN={["1948-7193"]}, DOI={10.1021/acschemneuro.6b00348}, abstractNote={A (GGGGCC) hexanucleotide repeat (HR) expansion in the C9ORF72 gene, and its associated antisense (CCCCGG) expansion, are considered the major cause behind frontotemporal dementia and amyotrophic lateral sclerosis. We have performed molecular dynamics simulations to characterize the conformation and dynamics of the 12 duplexes that result from the three different reading frames in sense and antisense HRs for both DNA and RNA. These duplexes display atypical structures relevant not only for a molecular level understanding of these diseases but also for enlarging the repertoire of nucleic-acid structural motifs. G-rich helices share common features. The inner G-G mismatches stay inside the helix in Gsyn-Ganti conformations and form two hydrogen bonds (HBs) between the Watson-Crick edge of Ganti and the Hoogsteen edge of Gsyn. In addition, Gsyn in RNA forms a base-phosphate HB. Inner G-G mismatches cause local unwinding of the helix. G-rich double helices are more stable than C-rich helices due to better stacking and HBs of G-G mismatches. C-rich helix conformations vary wildly. C mismatches flip out of the helix in DNA but not in RNA. Least (most) stable C-rich RNA and DNA helices have single (double) mismatches separated by two (four) Watson-Crick basepairs. The most stable DNA structure displays an "e-motif" where mismatched bases flip toward the minor groove and point in the 5' direction. There are two RNA conformations, where the orientation and HB pattern of the mismatches is coupled to bending of the helix.}, number={3}, journal={ACS CHEMICAL NEUROSCIENCE}, author={Zhang, Yuan and Roland, Christopher and Sagui, Celeste}, year={2017}, month={Mar}, pages={578–591} }
 @article{pan_man_roland_sagui_2017, title={Structure and Dynamics of DNA and RNA Double Helices of CAG and GAC Trinucleotide Repeats}, volume={113}, ISSN={["1542-0086"]}, DOI={10.1016/j.bpj.2017.05.041}, abstractNote={CAG trinucleotide repeats are known to cause 10 late-onset progressive neurodegenerative disorders as the repeats expand beyond a threshold, whereas GAC repeats are associated with skeletal dysplasias and expand from the normal five to a maximum of seven repeats. The TR secondary structure is believed to play a role in CAG expansions. We have carried out free energy and molecular dynamics studies to determine the preferred conformations of the A-A noncanonical pairs in (CAG)n and (GAC)n trinucleotide repeats (n = 1, 4) and the consequent changes in the overall structure of the RNA and DNA duplexes. We find that the global free energy minimum corresponds to A-A pairs stacked inside the core of the helix with anti-anti conformations in RNA and (high-anti)-(high-anti) conformations in DNA. The next minimum corresponds to anti-syn conformations, whereas syn-syn conformations are higher in energy. Transition rates of the A-A conformations are higher for RNA than DNA. Mechanisms for these various transitions are identified. Additional structural and dynamical aspects of the helical conformations are explored, with a focus on contrasting CAG and GAC duplexes. The neutralizing ion distribution around the noncanonical pairs is described.}, number={1}, journal={BIOPHYSICAL JOURNAL}, author={Pan, Feng and Man, Viet Hoang and Roland, Christopher and Sagui, Celeste}, year={2017}, month={Jul}, pages={19–36} }
 @article{zhang_man_roland_sagui_2016, title={Amyloid Properties of Asparagine and Glutamine in Prion-like Proteins}, volume={7}, ISSN={1948-7193 1948-7193}, url={http://dx.doi.org/10.1021/ACSCHEMNEURO.5B00337}, DOI={10.1021/ACSCHEMNEURO.5B00337}, abstractNote={Sequences rich in glutamine (Q) and asparagine (N) are intrinsically disordered in monomeric form, but can aggregate into highly ordered amyloids, as seen in Q/N-rich prion domains (PrDs). Amyloids are fibrillar protein aggregates rich in β-sheet structures that can self-propagate through protein-conformational chain reactions. Here, we present a comprehensive theoretical study of N/Q-rich peptides, including sequences found in the yeast Sup35 PrD, in parallel and antiparallel β-sheet aggregates, and probe via fully atomistic molecular dynamics simulations all their possible steric-zipper interfaces in order to determine their protofibril structure and their relative stability. Our results show that polyglutamine aggregates are more stable than polyasparagine aggregates. Enthalpic contributions to the free energy favor the formation of polyQ protofibrils, while entropic contributions favor the formation of polyN protofibrils. The considerably larger phase space that disordered polyQ must sample on its way to aggregation probably is at the root of the associated slower kinetics observed experimentally. When other amino acids are present, such as in the Sup35 PrD, their shorter side chains favor steric-zipper formation for N but not Q, as they preclude the in-register association of the long Q side chains.}, number={5}, journal={ACS Chemical Neuroscience}, publisher={American Chemical Society (ACS)}, author={Zhang, Yuan and Man, Viet Hoang and Roland, Christopher and Sagui, Celeste}, year={2016}, month={Mar}, pages={576–587} }
 @article{man_pan_sagui_roland_2016, title={Comparative melting and healing of B-DNA and Z-DNA by an infrared laser pulse}, volume={144}, ISSN={["1089-7690"]}, DOI={10.1063/1.4945340}, abstractNote={We explore the use of a fast laser melting simulation approach combined with atomistic molecular dynamics simulations in order to determine the melting and healing responses of B-DNA and Z-DNA dodecamers with the same d(5′-CGCGCGCGCGCG-3′)2 sequence. The frequency of the laser pulse is specifically tuned to disrupt Watson-Crick hydrogen bonds, thus inducing melting of the DNA duplexes. Subsequently, the structures relax and partially refold, depending on the field strength. In addition to the inherent interest of the nonequilibrium melting process, we propose that fast melting by an infrared laser pulse could be used as a technique for a fast comparison of relative stabilities of same-sequence oligonucleotides with different secondary structures with full atomistic detail of the structures and solvent. This could be particularly useful for nonstandard secondary structures involving non-canonical base pairs, mismatches, etc.}, number={14}, journal={JOURNAL OF CHEMICAL PHYSICS}, author={Man, Viet Hoang and Pan, Feng and Sagui, Celeste and Roland, Christopher}, year={2016}, month={Apr} }
 @article{zhang_hoang man_roland_sagui_2016, title={Contrasting Roles of Asparagine and Glutamine in the Aggregation of Prion-Like Proteins}, volume={110}, ISSN={0006-3495}, url={http://dx.doi.org/10.1016/J.BPJ.2015.11.1191}, DOI={10.1016/J.BPJ.2015.11.1191}, abstractNote={Sequences rich in glutamine (Q) and asparagine (N) are intrinsically disordered in monomeric form, but can aggregate into highly ordered amyloids, as seen in Q/N-rich prion domains (PrDs). Amyloids are fibrillar protein aggregates rich in β-sheet structures that can self-propagate through protein-conformational chain reactions. It has been shown that tuning the amount of Ns and Qs in yeast PrDs results in very different effects: N-rich mutants lead to non-pathological self-seeding amyloids while Q-rich mutants lead to toxic nonamyloid structures. These structural preferences have been explained in terms of an enhanced β- hairpin turn propensity of Ns over Qs. Here, we consider a variety of N/Q-rich peptides, including sequences found in the yeast Sup35 PrD, in parallel and antiparallel β-sheet aggregates, and probe all their possible steric-zipper interfaces to determine their relative stability. Our results show that polyglutamine aggregates are more stable than polyasparagine aggregates. The observation that Q-rich PrD mutants lack amyloid structure can be attributed to three facts. First, although once formed polyglutamine aggregates are more stable, their entropic contribution to the free energy is less favorable: Q-rich sequences have a larger phase space to sample. Second, N-rich sequences favor parallel β sheets, for which the formation of hairpin turns is irrelevant: indeed polyasparagine β-hairpins are more unstable than polyglutamine hairpins. Third, when other amino acids are present, such as in the Sup35 PrD, their shorter side chains favor steric-zipper formation for N but not Q, as they preclude the in-register association of the long Q side chains.}, number={3}, journal={Biophysical Journal}, publisher={Elsevier BV}, author={Zhang, Yuan and Hoang Man, Viet and Roland, Christopher and Sagui, Celeste}, year={2016}, month={Feb}, pages={214a–215a} }
 @article{man_van-oanh_derreumaux_li_roland_sagui_nguyen_2016, title={Picosecond infrared laser-induced all-atom nonequilibrium molecular dynamics simulation of dissociation of viruses}, volume={18}, ISSN={["1463-9084"]}, DOI={10.1039/c5cp07711g}, abstractNote={Laser-induced all-atom nonequilibrium molecular dynamics simulation of virus dissociation.}, number={17}, journal={PHYSICAL CHEMISTRY CHEMICAL PHYSICS}, author={Man, Viet Hoang and Van-Oanh, Nguyen-Thi and Derreumaux, Philippe and Li, Mai Suan and Roland, Christopher and Sagui, Celeste and Nguyen, Phuong H.}, year={2016}, month={May}, pages={11951–11958} }
 @article{pan_man_roland_sagui_2016, title={Stability and Ion Distributions Around Left- and Right-Handed DNA and RNA Duplexes: A Comparative Study}, volume={110}, ISSN={0006-3495}, url={http://dx.doi.org/10.1016/J.BPJ.2015.11.2197}, DOI={10.1016/J.BPJ.2015.11.2197}, abstractNote={The determination of the relative stability of nucleic acids structures is often critical for the understanding of their molecular functions. Theoretically, the relative stability of polynucleotides is determined via free energy or thermal melting simulations. These quantities may, however, be computationally quite intensive and therefore challenging. As an interesting alternative, we explore the use of a non-equilibrium laser melting approach combined with molecular dynamics simulations in order to determine the relative stability of B-DNA and Z-DNA duplexes. Specifically, a fast laser pulse is applied to the d(5’-CGCGCGCGCGCG-3’)2 dodecamer in either form. A laser pulse, whose frequency is tuned to disrupt the Watson-Crick hydrogen bonds, is applied and induces a partial melting of the DNA duplexes. The subsequent structural relaxations and partial refolding is indicative of the greater stability of B-DNA in different aqueous environments. In addition, we have also carried out a detailed investigation of the ion atmosphere around both the B- and Z-DNA/RNA duplexes. This ion atmosphere is an intrinsic part of the structure of the solvated nucleic acids, but is difficult to probe experimentally. The ions investigated include Na+, K+, Mg2+, and Cl- in various concentrations. The simulations results quantitatively describe the characteristics of the ion distributions around the different nucleic acid structures. These, in turn, reflect the effect of the different ion types and the atomistic and structural elements of the nucleic acids, which are described and contrasted.}, number={3}, journal={Biophysical Journal}, publisher={Elsevier BV}, author={Pan, Feng and Man, Viet H. and Roland, Christopher and Sagui, Celeste}, year={2016}, month={Feb}, pages={407a} }
 @article{man_roland_sagui_2016, title={Structural Determinants of Polyqlutamine Protofibrils and Crystallites}, volume={110}, ISSN={0006-3495}, url={http://dx.doi.org/10.1016/J.BPJ.2015.11.1192}, DOI={10.1016/J.BPJ.2015.11.1192}, abstractNote={Nine inherited neurodegenerative diseases are associated with the expansion of the CAG codon. Once the translated polyglutamine expansion becomes longer than ∼36 residues, it triggers the formation of intraneural protein aggregates that often display the signature of cross-β amyloid fibrils. Here, we use fully atomistic molecular dynamics simulations with explicit solvent and state-of-the-art force field to probe the structural stability and conformational dynamics of both previously proposed and new polyglutamine aggregate models, for a cumulative time of over 23 μs. We estimate the relative stability of parallel and antiparallel β sheets, and characterize possible steric interfaces between neighboring sheets and the effects of different alignments of the side-chain carboxamide dipoles. The results indicate that (i) different initial oligomer structures converge to crystals consistent with available diffraction data, after undergoing cooperative side-chain rotational transitions and quarter-stagger displacements on a microsecond time scale, (ii) structures previously deemed stable on a hundred nanosecond time scale are unstable over the microsecond time scale, and (iii) conversely, structures previously deemed unstable did not account for the correct side-chain packing and once the correct symmetry is considered the structures become stable for over a microsecond, due to tightly interdigitated side chains, which lock into highly regular polar zippers with inter-side-chain and backbone−side-chain hydrogen bonds. With these insights, we built Q40 monomeric models with different combinations of arc and hairpin turns and tested them for stability. The stable monomers were further probed as a function of repeat length. Our results are consistent with the aggregation threshold. These results explain and reconcile previously reported experimental and model discrepancies about polyglutamine aggregate structures.}, number={3}, journal={Biophysical Journal}, publisher={Elsevier BV}, author={Man, Viet H. and Roland, Christopher and Sagui, Celeste}, year={2016}, month={Feb}, pages={215a} }
 @article{moradi_sagui_roland_2015, title={Calculating transition and reaction rates with nonequilibrium work measurements}, volume={640}, ISSN={["1742-6596"]}, DOI={10.1088/1742-6596/640/1/012014}, abstractNote={By combining elements of the nonequilibrium work theorem with Transition Path Theory (TPT), we have developed a formalism for investigating transition pathways and probabilities that may effectively be implemented by means of Steered Molecular Dynamics (SMD) simulations. The workings of this formalism are illustrated by means a simple example based on a diproline peptide.}, journal={XXVI IUPAP CONFERENCE ON COMPUTATIONAL PHYSICS (CCP2014)}, author={Moradi, Mahmoud and Sagui, Celeste and Roland, Christopher}, year={2015} }
 @article{viet_derreumaux_li_roland_sagui_nguyen_2015, title={Picosecond dissociation of amyloid fibrils with infrared laser: A nonequilibrium simulation study}, volume={143}, ISSN={["1089-7690"]}, DOI={10.1063/1.4933207}, abstractNote={Recently, mid-infrared free-electron laser technology has been developed to dissociate amyloid fibrils. Here, we present a theoretical framework for this type of experiment based on laser-induced nonequilibrium all-atom molecular dynamics simulations. We show that the fibril is destroyed due to the strong resonance between its amide I vibrational modes and the laser field. The effects of laser irradiation are determined by a balance between fibril formation and dissociation. While the overall rearrangements of the fibril finish over short time scales, the interaction between the peptides and the solvent continues over much longer times indicating that the waters play an important role in the dissociation process. Our results thus provide new insights into amyloid fibril dissociation by laser techniques and open up new venues to investigate the complex phenomena associated with amyloidogenesis.}, number={15}, journal={JOURNAL OF CHEMICAL PHYSICS}, author={Viet, Man Hoang and Derreumaux, Philippe and Li, Mai Suan and Roland, Christopher and Sagui, Celeste and Nguyen, Phuong H.}, year={2015}, month={Oct} }
 @article{viet_truong_derreumaux_li_roland_sagui_nguyen_2015, title={Picosecond melting of peptide nanotubes using an infrared laser: a nonequilibrium simulation study}, volume={17}, ISSN={["1463-9084"]}, DOI={10.1039/c5cp04401d}, abstractNote={Resonance between carboxylate bond vibrations and laser frequency results in melting of nanotube.}, number={41}, journal={PHYSICAL CHEMISTRY CHEMICAL PHYSICS}, author={Viet, Man Hoang and Truong, Phan Minh and Derreumaux, Philippe and Li, Mai Suan and Roland, Christopher and Sagui, Celeste and Nguyen, Phuong H.}, year={2015}, pages={27275–27280} }
 @article{man_roland_sagui_2015, title={Structural Determinants of Polyglutamine Protofibrils and Crystallites}, volume={6}, ISSN={["1948-7193"]}, DOI={10.1021/cn500358g}, abstractNote={Nine inherited neurodegenerative diseases are associated with the expansion of the CAG codon. Once the translated polyglutamine expansion becomes longer than ~36 residues, it triggers the formation of intraneural protein aggregates that often display the signature of cross-β amyloid fibrils. Here, we use fully atomistic molecular dynamics simulations to probe the structural stability and conformational dynamics of both previously proposed and new polyglutamine aggregate models. We test the relative stability of parallel and antiparallel β sheets, and characterize possible steric interfaces between neighboring sheets and the effects of different alignments of the side-chain carboxamide dipoles. Results indicate that (i) different initial oligomer structures converge to crystals consistent with available diffraction data, after undergoing cooperative side-chain rotational transitions and quarter-stagger displacements on a microsecond time scale, (ii) structures previously deemed stable on a hundred nanosecond time scale are unstable over the microsecond time scale, and (iii) conversely, structures previously deemed unstable did not account for the correct side-chain packing and once the correct symmetry is considered the structures become stable for over a microsecond, due to tightly interdigitated side chains, which lock into highly regular polar zippers with inter-side-chain and backbone-side-chain hydrogen bonds. With these insights, we built Q40 monomeric models with different combinations of arc and hairpin turns and tested them for stability. The stable monomers were further probed as a function of repeat length. Our results are consistent with the aggregation threshold. These results explain and reconcile previously reported experimental and model discrepancies about polyglutamine aggregate structures.}, number={4}, journal={ACS CHEMICAL NEUROSCIENCE}, author={Man, Viet Hoang and Roland, Christopher and Sagui, Celeste}, year={2015}, month={Apr}, pages={632–645} }
 @article{moradi_babin_roland_sagui_2015, title={The Adaptively Biased Molecular Dynamics method revisited: New capabilities and an application}, volume={640}, ISSN={["1742-6596"]}, DOI={10.1088/1742-6596/640/1/012020}, abstractNote={The free energy is perhaps one of the most important quantity required for describing biomolecular systems at equilibrium. Unfortunately, accurate and reliable free energies are notoriously difficult to calculate. To address this issue, we previously developed the Adaptively Biased Molecular Dynamics (ABMD) method for accurate calculation of rugged free energy surfaces (FES). Here, we briefly review the workings of the ABMD method with an emphasis on recent software additions, along with a short summary of a selected ABMD application based on the B-to-Z DNA transition. The ABMD method, along with current extensions, is currently implemented in the AMBER (ver.10-14) software package.}, journal={XXVI IUPAP CONFERENCE ON COMPUTATIONAL PHYSICS (CCP2014)}, author={Moradi, Mahmoud and Babin, Volodymyr and Roland, Christopher and Sagui, Celeste}, year={2015} }
 @article{moradi_sagui_roland_2014, title={Investigating rare events with nonequilibrium work measurements. I. Nonequilibrium transition path probabilities}, volume={140}, ISSN={0021-9606 1089-7690}, url={http://dx.doi.org/10.1063/1.4861055}, DOI={10.1063/1.4861055}, abstractNote={We have developed a formalism for investigating transition pathways and transition probabilities for rare events in biomolecular systems. In this paper, we set the theoretical framework for employing nonequilibrium work relations to estimate the relative reaction rates associated with different classes of transition pathways. Particularly, we derive an extension of Crook's transient fluctuation theorem, which relates the relative transition rates of driven systems in the forward and reverse directions, and allows for the calculation of these relative rates using work measurements (e.g., in Steered Molecular Dynamics). The formalism presented here can be combined with Transition Path Theory to relate the equilibrium and driven transition rates. The usefulness of this framework is illustrated by means of a Gaussian model and a driven proline dimer.}, number={3}, journal={The Journal of Chemical Physics}, publisher={AIP Publishing}, author={Moradi, Mahmoud and Sagui, Celeste and Roland, Christopher}, year={2014}, month={Jan}, pages={034114} }
 @article{moradi_sagui_roland_2014, title={Investigating rare events with nonequilibrium work measurements. I. Nonequilibrium transition path probabilities (vol 140, 034114, 2014)}, volume={140}, ISSN={["1089-7690"]}, DOI={10.1063/1.4865580}, abstractNote={First Page}, number={6}, journal={JOURNAL OF CHEMICAL PHYSICS}, author={Moradi, Mahmoud and Sagui, Celeste and Roland, Christopher}, year={2014}, month={Feb} }
 @article{moradi_sagui_roland_2014, title={Investigating rare events with nonequilibrium work measurements. II. Transition and reaction rates}, volume={140}, ISSN={0021-9606 1089-7690}, url={http://dx.doi.org/10.1063/1.4861056}, DOI={10.1063/1.4861056}, abstractNote={We present a formalism for investigating transition pathways and transition probabilities for rare events in biomolecular systems. The formalism is based on combining Transition Path Theory with the results of nonequilibrium work relations, and shows that the equilibrium and nonequilibrium transition rates are in fact related. Aside from its fundamental importance, this allows for the calculation of relative equilibrium reaction rates with driven nonequilibrium simulations such as Steered Molecular Dynamics. The workings of the formalism are illustrated with a few typical numerical examples.}, number={3}, journal={The Journal of Chemical Physics}, publisher={AIP Publishing}, author={Moradi, Mahmoud and Sagui, Celeste and Roland, Christopher}, year={2014}, month={Jan}, pages={034115} }
 @article{moradi_sagui_roland_2014, title={Investigating rare events with nonequilibrium work measurements. II. Transition and reaction rates (vol 140, 034115, 2014)}, volume={140}, ISSN={["1089-7690"]}, DOI={10.1063/1.4865582}, abstractNote={First Page}, number={6}, journal={JOURNAL OF CHEMICAL PHYSICS}, author={Moradi, Mahmoud and Sagui, Celeste and Roland, Christopher}, year={2014}, month={Feb} }
 @article{moradi_babin_sagui_roland_2011, title={A Statistical Analysis of the PPII Propensity of Amino Acid Guests in Proline-Rich Peptides}, volume={100}, ISSN={0006-3495}, url={http://dx.doi.org/10.1016/j.bpj.2010.12.3742}, DOI={10.1016/j.bpj.2010.12.3742}, abstractNote={There has been considerable debate about the intrinsic PPII propensity of amino-acid residues in denatured polypeptides. Experimentally, the propensity scale is based on the behavior of guest amino-acid residues placed in the middle of polyproline hosts. We have used classical molecular dynamics simulations, with state-of-the-art force fields to carry out a comprehensive analysis of the conformational equilibria of the proline-based host oligopeptides with single guests. The tracked structural characteristics include the PPII content, the cis/trans isomerization of the prolyl bonds, the puckering of the pyrrolidine rings of the proline residues, and the secondary structural motifs. We find no evidence for an intrinsic PPII propensity in any of the guest amino acids other than proline. Instead, the PPII content as derived from experiments may be explained in terms of: 1), a local correlation between the dihedral angles of the guest amino acid and the proline residue immediately preceding it; and 2), a nonlocal correlation between the cis/trans states of the peptide bonds. In terms of the latter, we find that the presence of a guest (other than proline, tyrosine, or tryptophan) increases the trans content of most of the prolyl bonds, which results in an effective increase of the peptide PPII content. With respect to the local dihedral correlations, we find that these are well described in terms of the so-called odds-ratio statistic. Expressed in terms of free energy language, the PPII content based on the odds-ratio of the relevant residues correlate well with the experimentally measured PPII content.}, number={4}, journal={Biophysical Journal}, publisher={Elsevier BV}, author={Moradi, Mahmoud and Babin, Volodymyr and Sagui, Celeste and Roland, Christopher}, year={2011}, month={Feb}, pages={1083–1093} }
 @article{moradi_sagui_roland_2011, title={Calculating relative transition rates with driven nonequilibrium simulations}, volume={518}, ISSN={["1873-4448"]}, DOI={10.1016/j.cplett.2011.10.054}, abstractNote={A formalism is presented for investigating transition pathways and transition probabilities for rare events in complex systems. Specifically, we show how driven simulations may be used to calculate relative reaction rates between stable states by means of nonequilibrium work measurements. Our relation between equilibrium and nonequilibrium rates may further be optimized by means of bidirectional estimators. A simple proline system is used to numerically illustrate the results.}, journal={CHEMICAL PHYSICS LETTERS}, author={Moradi, Mahmoud and Sagui, Celeste and Roland, Christopher}, year={2011}, month={Dec}, pages={109–113} }
 @article{moradi_babin_sagui_roland_2011, title={PPII Propensity of Multiple-Guest Amino Acids in a Proline-Rich Environment}, volume={115}, ISSN={1520-6106 1520-5207}, url={http://dx.doi.org/10.1021/jp203874f}, DOI={10.1021/jp203874f}, abstractNote={There has been considerable debate about the intrinsic PPII propensity of amino acid residues in denatured polypeptides. Experimentally, this scale is based on the behavior of guest amino acid residues placed in the middle of proline-based hosts. We have used classical molecular dynamics simulations combined with replica-exchange methods to carry out a comprehensive analysis of the conformational equilibria of proline-based host oligopeptides with multiple guest amino acids including alanine, glutamine, valine, and asparagine. The tracked structural characteristics include the secondary structural motifs based on the Ramachandran angles and the cis/trans isomerization of the prolyl bonds. In agreement with our recent study of single amino acid guests, we did not observe an intrinsic PPII propensity in any of the guest amino acids in a multiple-guest setting. Instead, the experimental results can be explained in terms of (i) the steric restrictions imposed on the C-terminal guest amino acid that is immediately followed by a proline residue and (ii) an increase in the trans content of the prolyl bonds due to the presence of guest residues. In terms of the latter, we found that the more guests added to the system, the larger the increase in the trans content of the prolyl bonds, which results in an effective increase in the PPII content of the peptide.}, number={26}, journal={The Journal of Physical Chemistry B}, publisher={American Chemical Society (ACS)}, author={Moradi, Mahmoud and Babin, Volodymyr and Sagui, Celeste and Roland, Christopher}, year={2011}, month={Jul}, pages={8645–8656} }
 @article{babin_roland_sagui_2011, title={The α-sheet: A missing-in-action secondary structure?}, volume={79}, ISSN={0887-3585}, url={http://dx.doi.org/10.1002/prot.22935}, DOI={10.1002/prot.22935}, abstractNote={Abstract}, number={3}, journal={Proteins: Structure, Function, and Bioinformatics}, publisher={Wiley}, author={Babin, Volodymyr and Roland, Christopher and Sagui, Celeste}, year={2011}, month={Jan}, pages={937–946} }
 @article{moradi_babin_roland_sagui_2010, title={A classical molecular dynamics investigation of the free energy and structure of short polyproline conformers}, volume={133}, ISSN={["0021-9606"]}, DOI={10.1063/1.3481087}, abstractNote={Folded polyproline peptides can exist as either left-(PPII) or right-handed (PPI) helices, depending on their environment. In this work, we have characterized the conformations and the free energy landscapes of Ace–(Pro)n–Nme, n=2,3,…,9, and 13 peptides both in vacuo and in an implicit solvent environment. In order to enhance the sampling provided by regular molecular dynamics simulations, we have used the recently developed adaptively biased molecular dynamics method—which provides an accurate description of the free energy landscapes in terms of a set of relevant collective variables—combined with Hamiltonian and temperature replica exchange molecular dynamics methods. The collective variables, which are chosen so as to reflect the stable structures and the “slow modes” of the polyproline system, were based primarily on properties of length and of the cis/trans isomerization associated with the prolyl bonds. Results indicate that the space of peptide structures is characterized not just by pure PPII and PPI structures, but rather by a broad distribution of stable minima with similar free energies. These results are in agreement with recent experimental work. In addition, we have used steered molecular dynamics methods in order to quantitatively estimate the free energy difference of PPI and PPII for peptides of the length n=2,…,5 in vacuo and implicit water and qualitatively investigate transition pathways and mechanisms for the PPII to PPI transitions. A zipper-like mechanism, starting from either the center of the peptide or the amidated end, appear to be the most likely mechanisms for the PPII→PPI transition for the longer peptides.}, number={12}, journal={JOURNAL OF CHEMICAL PHYSICS}, author={Moradi, Mahmoud and Babin, Volodymyr and Roland, Christopher and Sagui, Celeste}, year={2010}, month={Sep} }
 @article{lee_sagui_roland_2010, title={Dimerization free energy of vancomycin-group antibiotics and the cooperative effect: A density functional approach}, volume={110}, ISSN={0020-7608}, url={http://dx.doi.org/10.1002/qua.22926}, DOI={10.1002/qua.22926}, abstractNote={Abstract}, number={15}, journal={International Journal of Quantum Chemistry}, publisher={Wiley}, author={Lee, Jung-Goo and Sagui, Celeste and Roland, Christopher}, year={2010}, month={Sep}, pages={2894–2902} }
 @article{moradi_lee_babin_roland_sagui_2010, title={Free energy and structure of polyproline peptides: An ab initio and classical molecular dynamics investigation}, volume={110}, ISSN={0020-7608}, url={http://dx.doi.org/10.1002/qua.22875}, DOI={10.1002/qua.22875}, abstractNote={Abstract}, number={15}, journal={International Journal of Quantum Chemistry}, publisher={Wiley}, author={Moradi, Mahmoud and Lee, Jung-Goo and Babin, Volodymyr and Roland, Christopher and Sagui, Celeste}, year={2010}, month={Aug}, pages={2865–2879} }
 @article{babin_karpusenka_moradi_roland_sagui_2009, title={Adaptively Biased Molecular Dynamics: An Umbrella Sampling Method With a Time-Dependent Potential}, volume={109}, ISSN={["1097-461X"]}, DOI={10.1002/qua.22413}, abstractNote={Abstract}, number={15}, journal={INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY}, author={Babin, Volodymyr and Karpusenka, Vadzim and Moradi, Mahmoud and Roland, Christopher and Sagui, Celeste}, year={2009}, month={Dec}, pages={3666–3678} }
 @article{moradi_babin_roland_darden_sagui_2009, title={Conformations and free energy landscapes of polyproline peptides}, volume={106}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.0906500106}, abstractNote={The structure of the proline amino acid allows folded polyproline peptides to exist as both left- (PPII) and right-handed (PPI) helices. We have characterized the free energy landscapes of hexamer, nanomer, and tridecamer polyproline peptides in gas phase and implicit water as well as explicit hexane and 1-propanol for the nanomer. To enhance the sampling provided by regular molecular dynamics, we used the recently developed adaptively biased molecular dynamics method, which describes Landau free energy maps in terms of relevant collective variables. These maps, as a function of the collective variables of handedness, radius of gyration, and three others based on the peptide torsion angle ω, were used to determine the relative stability of the different structures, along with an estimate of the transition pathways connecting the different minima. Results show the existence of several metastable isomers and therefore provide a complementary view to experimental conclusions based on photo-induced electron transfer experiments with regard to the existence of stable heterogeneous subpopulations in PPII polyproline.}, number={49}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Moradi, Mahmoud and Babin, Volodymyr and Roland, Christopher and Darden, Thomas A. and Sagui, Celeste}, year={2009}, month={Dec}, pages={20746–20751} }
 @article{babin_roland_sagui_2008, title={Adaptively biased molecular dynamics for free energy calculations}, volume={128}, DOI={10.1063/1.2844595}, abstractNote={We present an adaptively biased molecular dynamics (ABMD) method for the computation of the free energy surface of a reaction coordinate using nonequilibrium dynamics. The ABMD method belongs to the general category of umbrella sampling methods with an evolving biasing potential and is inspired by the metadynamics method. The ABMD method has several useful features, including a small number of control parameters and an O(t) numerical cost with molecular dynamics time t. The ABMD method naturally allows for extensions based on multiple walkers and replica exchange, where different replicas can have different temperatures and/or collective variables. This is beneficial not only in terms of the speed and accuracy of a calculation, but also in terms of the amount of useful information that may be obtained from a given simulation. The workings of the ABMD method are illustrated via a study of the folding of the Ace-GGPGGG-Nme peptide in a gaseous and solvated environment.}, number={13}, journal={Journal of Chemical Physics}, author={Babin, V. and Roland, C. and Sagui, C.}, year={2008} }
 @article{luo_qian_sagui_roland_2008, title={Amino acid adsorption on the Si(100) surface: The case of glycine}, volume={112}, ISSN={["1932-7455"]}, DOI={10.1021/jp0775193}, abstractNote={Using first principles total energy methods, we have investigated the adsorption of glycinethe simplest amino acidon the Si(100)- c(4 × 2)surface, with a focus on the associated energetics, charge transfer, electronic properties, and structural characteristics. We find that glycine adsorbs primarily on the “down” atoms of a Si dimer, with adsorption of the amino group being slightly favored over the absorption of the carboxylic acid group. Glycine on Si(100) may also involve the removal of a H atom from the chemical group most directly absorbed. In addition, there is evidence for a [2 + 2] cycloaddition reaction when both “CO” atoms absorb, as well as the more drastic breakup of the glycine molecule and the formation of a ketenimine molecule under high-energy conditions.}, number={7}, journal={JOURNAL OF PHYSICAL CHEMISTRY C}, author={Luo, Xuan and Qian, Gefei and Sagui, Celeste and Roland, Christopher}, year={2008}, month={Feb}, pages={2640–2648} }
 @article{lee_lee_roland_2008, title={Structural determination of large molecules through the reassembly of optimized fragments}, volume={27}, ISSN={["1873-4243"]}, DOI={10.1016/j.jmgm.2008.06.004}, abstractNote={The accurate determination of the optimized structures of large molecules is, computationally quite expensive. As an alternate to the conventional approaches to structural optimization, we have explored the accuracy and speed-up obtained when variants of the fragmentation optimization and recombination method (FORM) are used. Specifically, the method was applied to eight prototypical molecules -n-decane, hexa-alanine, a long conjugate hydrocarbon molecule, a large polar conjugated molecule, large (5,5) armchair single-walled carbon nanotubes, a salen-aluminum complex and a multiply H-bonded system (two conformers of vancomycin aglycon with Di-N-acetyl-l-Lys-d-Ala-d-Ala - without optimizing the structure of the whole molecules. We find that FORM can predict the structure of these molecules with an acceptable accuracy, all at a computational cost that is 2-11 times less than conventional quantum mechanical methods at the Hartree-Fock (HF), density functional theory (DFT) and MP2 level of accuracy. FORM may therefore represent a viable approach for the fast structural predictions of large molecules.}, number={3}, journal={JOURNAL OF MOLECULAR GRAPHICS & MODELLING}, author={Lee, Jung-Goo and Lee, Yoon Sup and Roland, Christopher}, year={2008}, month={Oct}, pages={364–375} }
 @article{sabir_lu_roland_bernholc_2007, title={Ab initio simulations of H-2 in Li-doped carbon nanotube systems}, volume={19}, number={8}, journal={Journal of Physics. Condensed Matter}, author={Sabir, A. K. and Lu, W. C. and Roland, C. and Bernholc, J.}, year={2007} }
 @article{sabir_lu_roland_bernholc_2007, title={Ab initio simulations of H2 in Li-doped carbon nanotube systems}, volume={19}, ISSN={0953-8984 1361-648X}, url={http://dx.doi.org/10.1088/0953-8984/19/8/086226}, DOI={10.1088/0953-8984/19/8/086226}, abstractNote={Because of their unique structure, it has been proposed that carbon nanotube ropes may well provide an ideal container for the storage of molecular hydrogen. Indeed, there has been some experimental evidence of enhanced hydrogen uptake in doped Li and other alkali metal systems (Chen et al 1999 Science 285 91). We have therefore addressed this issue of hydrogen storage in Li-doped graphite and carbon nanotube systems theoretically with ab initio simulations. Our results find no evidence for such enhanced storage, based on the induced structural changes. In addition, we have also investigated the diffusion barriers for hydrogen to enter into nanotube interiors, both in the presence and absence of topological defects. Even if nanotube interiors are made accessible, the hydrogen uptake remains modest, i.e., less than 3.5 wt%. Mechanically or chemically processing nanotubes is therefore not likely to lead to greatly increased hydrogen storage. Even with its limitation, because of the use of the LDA and GGA approaches, the current investigation must be regarded as a means in the search for proper media that can successfully enhance hydrogen storage.}, number={8}, journal={Journal of Physics: Condensed Matter}, publisher={IOP Publishing}, author={Sabir, A K and Lu, Wenchang and Roland, Christopher and Bernholc, Jerzy}, year={2007}, month={Feb}, pages={086226} }
 @article{odbadrakh_luo_lee_sagui_roland_2007, title={Theoretical investigation of the interaction of glycine with diamond C(100) and C(111) (2x1) surfaces}, volume={111}, ISSN={["1932-7455"]}, DOI={10.1021/jp073042j}, abstractNote={With density functional theory-based simulations, we have investigated the binding of the amino acid glycine on two of the most prominent diamond surfaces, that is, C(100) and C(111) (2 × 1), with a focus on the associated energetics, charge transfer, electronic, and structural characteristics. With regards to the dimerized C(100) surface, interaction is mostly via the amino group of the glycine molecule (both with and without H-atom abstraction) or the hydroxyl group with the loss of an associated H-atom. Barriers for these and other reactions were estimated with quantum chemistry methods. In contrast, the C(111) (2 × 1) surface was found to be mostly inert with respect to interactions with the glycine molecule.}, number={34}, journal={JOURNAL OF PHYSICAL CHEMISTRY C}, author={Odbadrakh, Khorgolkhuu and Luo, Xuan and Lee, Jung-Goo and Sagui, Celeste and Roland, Christopher}, year={2007}, month={Aug}, pages={12760–12767} }
 @article{odbadrakh_pomorski_roland_2006, title={Ab initio band bending, metal-induced gap states, and Schottky barriers of a carbon and a boron nitride nanotube device}, volume={73}, ISSN={["2469-9969"]}, DOI={10.1103/physrevb.73.233402}, abstractNote={We have characterized the fully self-consistent electronic properties of a prototypical metal/nanotube interface using a combined nonequilibrium Green's function and density-functional-theory-based formalism, under different conditions of gate and bias voltages. Both carbon and boron nitride nanotubes between Al electrodes were considered. The electronic properties of the interface are dominated both by a dipole and by metal-induced gap states formed through the transfer of charge between the metal and the nanotube. In addition, first-principles estimates\char22{}within the local density approximation\char22{}of the Schottky barrier heights are given.}, number={23}, journal={PHYSICAL REVIEW B}, author={Odbadrakh, Khorgolkhuu and Pomorski, Pawel and Roland, Christopher}, year={2006}, month={Jun} }
 @article{lee_asciutto_babin_sagui_darden_roland_2006, title={Deprotonation of solvated formic acid: Car-Parrinello and metadynamics simulations}, volume={110}, ISSN={["1520-5207"]}, DOI={10.1021/jp055809i}, abstractNote={The deprotonation of solvated formic acid was investigated theoretically with ab initio simulations. With the Car-Parrinello method, deprotonation and reprotonation by means of a proton wire were observed. The microscopics of these reactions were analyzed, and reveal the key role played by nearby water molecules in catalyzing the reactions. A constrained molecular dynamics calculation was carried out to estimate the dissociation free energy. Deprotonation of formic acid was further investigated with the recently developed metadynamics method using the formic acid oxygen coordination numbers as the collective variables. The determined free-energy landscape gives barriers similar to that obtained with the constrained free-energy calculation.}, number={5}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Lee, JG and Asciutto, E and Babin, V and Sagui, C and Darden, T and Roland, C}, year={2006}, month={Feb}, pages={2325–2331} }
 @article{babin_roland_darden_sagui_2006, title={The free energy landscape of small peptides as obtained from metadynamics with umbrella sampling corrections}, volume={125}, ISSN={["1089-7690"]}, DOI={10.1063/1.2393236}, abstractNote={There is considerable interest in developing methodologies for the accurate evaluation of free energies, especially in the context of biomolecular simulations. Here, we report on a reexamination of the recently developed metadynamics method, which is explicitly designed to probe “rare events” and areas of phase space that are typically difficult to access with a molecular dynamics simulation. Specifically, we show that the accuracy of the free energy landscape calculated with the metadynamics method may be considerably improved when combined with umbrella sampling techniques. As test cases, we have studied the folding free energy landscape of two prototypical peptides: Ace-(Gly)2-Pro-(Gly)3-Nme in vacuo and trialanine solvated by both implicit and explicit water. The method has been implemented in the classical biomolecular code AMBER and is to be distributed in the next scheduled release of the code.}, number={20}, journal={JOURNAL OF CHEMICAL PHYSICS}, author={Babin, Volodymyr and Roland, Christopher and Darden, Thomas A. and Sagui, Celeste}, year={2006}, month={Nov} }
 @article{sagui_asciutto_roland_2005, title={New and exotic self-organized patterns for modulated nanoscale systems}, volume={5}, ISSN={["1530-6992"]}, DOI={10.1021/nl048224t}, abstractNote={The self-assembled domain patterns of modulated systems are the result of competing short-range attractive and long-range repulsive interactions found in diverse physical and chemical systems. From an application point of view, there is considerable interest in these domain patterns, as they form templates suitable for the fabrication of nanostructures. In this work we have generated a variety of new and exotic patterns, which represent either metastable or glassy states. These patterns arise as a compromise between the required equilibrium modulation period and the strain resulting from topologically constrained trajectories in phase space that effectively preclude the equilibrium configuration.}, number={2}, journal={NANO LETTERS}, author={Sagui, C and Asciutto, E and Roland, C}, year={2005}, month={Feb}, pages={389–395} }
 @article{lee_sagui_roland_2005, title={Quantum simulations of the structure and binding of glycopeptide antibiotic aglycons to cell wall analogues}, volume={109}, ISSN={["1520-5207"]}, DOI={10.1021/jp0548117}, abstractNote={The recent rise of vancomycin-resistant enterococci (VRE) and vancomycin-resistant Staphylococcus aureus (VRSA) has given new impetus to the study of the binding between glycopeptide antibiotics and bacterial cell wall termini. Here, we report on an extensive first principles investigation of the binding of vancomycin, avoparcin, teicoplanin, and ristocetin aglycons with dipetides, Ac-d-Ala-X, where X = d-Lac and d-Ser (characteristic of VREs) and X = d-Ala, Gly (characteristic of non-VREs), and a model "methylated d-Ala" CH(2)CH(CH(3))COO(-), in liquid as well as gas phase. The gas-phase ordering of the binding, from strongest to weakest, is Gly, d-Ala, d-Ser, CH(2)CH(CH(3))COO(-), and d-Lac. Calculations show that the order of the Gly and d-Ala binding is reversed in solution. The results are in good agreement with recent experimental findings.}, number={43}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Lee, JG and Sagui, C and Roland, C}, year={2005}, month={Nov}, pages={20588–20596} }
 @article{asciutto_roland_sagui_2005, title={Self-assembled patterns and strain-induced instabilities for modulated systems}, volume={72}, ISSN={["1550-2376"]}, DOI={10.1103/physreve.72.021504}, abstractNote={The self-assembled domain patterns of modulated systems are characteristic of a wide variety of chemical and physical systems, and are the result of competing interactions. From a technological point of view, there is considerable interest in these domain patterns, as they form suitable templates for the fabrication of nanostructures. We have analyzed the domains and instabilities that form in modulated systems, and show that a large variety of patterns--based on long-lived metastable or glassy states--may be formed as a compromise between the required equilibrium modulation period and the strain present in the system. The strain results from topologically constrained trajectories in phase space, that effectively preclude the equilibrium configuration.}, number={2}, journal={PHYSICAL REVIEW E}, author={Asciutto, E and Roland, C and Sagui, C}, year={2005}, month={Aug} }
 @article{sagui_pomorski_darden_roland_2004, title={Ab initio calculation of electrostatic multipoles with Wannier functions for large-scale biomolecular simulations}, volume={120}, ISSN={["1089-7690"]}, DOI={10.1063/1.1644800}, abstractNote={It has long been known that accurate electrostatics is a key issue for improving current force fields for large-scale biomolecular simulations. Typically, this calls for an improved and more accurate description of the molecular electrostatic potential, which eliminates the artifacts associated with current point charge-based descriptions. In turn, this involves the partitioning of the extended molecular charge distribution, so that charges and multipole moments can be assigned to different atoms. As an alternate to current approaches, we have investigated a charge partitioning scheme that is based on the maximally localized Wannier functions. This has the advantage of partitioning the charge, and placing it around the molecule in a chemically meaningful manner. Moreover, higher order multipoles may all be calculated without any undue numerical difficulties. Tests on isolated molecules and water dimers, show that the molecular electrostatic potentials generated by such a Wannier-function based approach are in excellent agreement with the density functional-based calculations.}, number={9}, journal={JOURNAL OF CHEMICAL PHYSICS}, author={Sagui, C and Pomorski, P and Darden, TA and Roland, C}, year={2004}, month={Mar}, pages={4530–4544} }
 @article{pomorski_pastewka_roland_guo_wang_2004, title={Capacitance, induced charges, and bound states of biased carbon nanotube systems}, volume={69}, ISSN={["2469-9969"]}, DOI={10.1103/physrevb.69.115418}, abstractNote={Although it has long been known that the classical notions of capacitance need modification at the nanoscale, in order to account for important quantum effects, very few first-principles investigations of these properties exist for any real material systems. Here we present the results of a large-scale ab initio investigation of the capacitance properties of carbon nanotube systems. The simulations are based on a recently developed real-space nonequilibrium Green's-function approach, with special attention being paid to the treatment of the bound states present in the system. In addition, use has been made of a symmetry decomposition scheme for the charge density. This is needed both to speed up the calculations and in order to study the origins of the induced charges. Specific systems investigated include two and three nested nanotube shells, the insertion of a capped nanotube into another, a connected (12,0)/(6,6) nanotube junction, and the properties of a nanotube acting as a probe over a flat aluminum surface. First-principles estimates of the capacitance matrix coefficients for all these systems are provided, along with a discussion of the quantum corrections. For the case of the nanotube junction, the numerical value of the capacitance is sufficiently high, as to be useful for future device applications.}, number={11}, journal={PHYSICAL REVIEW B}, author={Pomorski, P and Pastewka, L and Roland, C and Guo, H and Wang, J}, year={2004}, month={Mar} }
 @article{lee_sagui_roland_2004, title={First principles investigation of vancomycin and teicoplanin binding to bacterial cell wall termini}, volume={126}, ISSN={["0002-7863"]}, DOI={10.1021/ja048645c}, abstractNote={The recent rise of vancomycin-resistant enterococci (VRE) has given new impetus to the study of the binding between glycopeptide antibiotics and bacterial cell wall termini. Here, we report on an extensive first principles investigation of the binding of vancomycin and teicoplanin with d-Ala-d-Lac (characteristic of VREs) and d-Ala-d-Ala (characteristic of non-VREs). Binding of both antibiotics to d-Ala-d-Ala was found to be stronger by about 3-5 kcal/mol and due primarily to the oxygen-oxygen lone-pair repulsion characteristic of the antibiotic/d-Ala-d-Lac complex. These results are in good agreement with recent experimental findings.}, number={27}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Lee, JG and Sagui, C and Roland, C}, year={2004}, month={Jul}, pages={8384–8385} }
 @article{pomorski_roland_guo_2004, title={Quantum transport through short semiconducting nanotubes: A complex band structure analysis}, volume={70}, ISSN={["2469-9969"]}, DOI={10.1103/physrevb.70.115408}, abstractNote={With a recently developed ab initio nonequilibrium Green's function formalism, we have examined the problem of quantum transport through prototypical, short, semiconducting nanotube devices. Metallic behavior is predicted for very short nanotubes, which crosses over to semiconducting behavior as the tube length is increased. This behavior finds its origins in the evanescent modes that are present in these finite-sized systems, which cannot be ignored. A complex band structure analysis makes the contributions of these modes particularly transparent.}, number={11}, journal={PHYSICAL REVIEW B}, author={Pomorski, P and Roland, C and Guo, H}, year={2004}, month={Sep} }
 @article{pomorski_roland_guo_wang_2003, title={First-principles investigation of carbon nanotube capacitance}, volume={67}, ISSN={["1098-0121"]}, DOI={10.1103/physrevb.67.161404}, abstractNote={With ab initio simulations based on a real-space nonequilibrium Green's function formalism, we have investigated the charging of carbon nanotube systems. The charging effects are described by capacitance coefficients, for which we provide a first-principles estimate. Specifically, the capacitance matrix of nested armchair nanotubes, the insertion of one nanotube into another, and a junction of two metallic nanotubes with a large conductance gap were calculated with a focus on investigating the bias-induced charges. For the case of the nanotube junction, the numerical value of the capacitance is sufficiently high, as to be useful for future device applications.}, number={16}, journal={PHYSICAL REVIEW B}, author={Pomorski, P and Roland, C and Guo, H and Wang, J}, year={2003}, month={Apr} }
 @article{meunier_kephart_roland_bernholc_2002, title={Ab initio investigations of lithium diffusion in carbon nanotube systems}, volume={88}, ISSN={["1079-7114"]}, DOI={10.1103/physrevlett.88.075506}, abstractNote={Li-nanotube systems can substantially improve the capacity of Li-ion batteries by utilizing both nanotube exteriors and interiors. Our ab initio simulations show that while Li motion through the sidewalls is forbidden, Li ions can enter tubes through topological defects containing at least nine-sided rings, or through the ends of open-ended nanotubes. Once inside, their motion is not diffusion limited. These results suggest that "damaging" nanotube ropes by either chemical or mechanical means will yield superior material for electrochemical storage.}, number={7}, journal={PHYSICAL REVIEW LETTERS}, author={Meunier, V and Kephart, J and Roland, C and Bernholc, J}, year={2002}, month={Feb} }
 @article{roland_meunier_larade_guo_2002, title={Charge transport through small silicon clusters}, volume={66}, ISSN={["2469-9969"]}, DOI={10.1103/physrevb.66.035332}, abstractNote={With a recently developed ab initio nonequilibrium Green's-function formalism, we have investigated the transport behavior of small Si n , n= 1-10, 13, and 20 nanoclusters between atomistic Al and Au leads. All of the clusters display metallic I-V characteristics, with typical conductances ranging between two and three (units of G o = 2e 2 /h). The transport properties of these cluster junctions may be understood in terms of both the band structure of the electrodes, and the molecular electronic states of the clusters as modified by the lead environment. In addition, the quantum transport properties of Si nanoclusters doped with a Na atom are also analyzed.}, number={3}, journal={PHYSICAL REVIEW B}, author={Roland, C and Meunier, V and Larade, B and Guo, H}, year={2002}, month={Jul} }
 @article{meunier_roland_bernholc_nardelli_2002, title={Electronic and field emission properties of boron nitride/carbon nanotube superlattices}, volume={81}, ISSN={["1077-3118"]}, DOI={10.1063/1.1491013}, abstractNote={BN/C nanotube superlattices are quasi one-dimensional heterostructures that show unique physical properties derived from their peculiar geometry. Using state-of-the-art ab initio calculations, we show that BN/C systems can be used for effective band-offset nanodevice engineering, polarization-based devices, and robust field emitters with an efficiency enhanced by up to two orders of magnitude over carbon nanotube systems.}, number={1}, journal={APPLIED PHYSICS LETTERS}, author={Meunier, V and Roland, C and Bernholc, J and Nardelli, MB}, year={2002}, month={Jul}, pages={46–48} }
 @misc{bernholc_brenner_nardelli_meunier_roland_2002, title={Mechanical and electrical properties of nanotubes}, volume={32}, ISSN={["1531-7331"]}, DOI={10.1146/annurev.matsci.32.112601.134925}, abstractNote={▪ Abstract  We review the recent progress in our understanding of the mechanical and electrical properties of carbon nanotubes, emphasizing the theoretical aspects. Nanotubes are the strongest materials known, but the ultimate limits of their strength have yet to be reached experimentally. Modeling of nanotube-reinforced composites indicates that the addition of small numbers of nanotubes may lead to a dramatic increase in the modulus, with only minimal crosslinking. Deformations in nanotube structures lead to novel structural transformations, some of which have clear electrical signatures that can be utilized in nanoscale sensors and devices. Chemical reactivity of nanotube walls is facilitated by strain, which can be used in processing and functionalization. Scanning tunneling microscopy and spectroscopy have provided a wealth of information about the structure and electronic properties of nanotubes, especially when coupled with appropriate theoretical models. Nanotubes are exceptional ballistic conductors, which can be used in a variety of nanodevices that can operate at room temperature. The quantum transport through nanotube structures is reviewed at some depth, and the critical roles played by band structure, one-dimensional confinement, and coupling to nanoscale contacts are emphasized. Because disorder or point defect–induced scattering is effectively averaged over the circumference of the nanotube, electrons can propagate ballistically over hundreds of nanometers. However, severe deformations or highly resistive contacts isolate nanotube segments and lead to the formation of quantum dots, which exhibit Coulomb blockade effects, even at room temperature. Metal-nanotube and nanotube-nanotube contacts range from highly transmissive to very resistive, depending on the symmetry of two structures, the charge transfer, and the detailed rehybridization of the wave functions. The progress in terms of nanotube applications has been extraordinarily rapid, as evidenced by the development of several nanotube-based prototypical devices, including memory and logic circuits, chemical sensors, electron emitters and electromechanical actuators.}, number={2002}, journal={ANNUAL REVIEW OF MATERIALS RESEARCH}, author={Bernholc, J and Brenner, D and Nardelli, MB and Meunier, V and Roland, C}, year={2002}, pages={347-+} }
 @article{grunert_hemmerich_2002, title={Sub-Doppler magneto-optical trap for calcium}, volume={65}, ISSN={["1094-1622"]}, DOI={10.1103/physrevb.65.041401}, abstractNote={We have calculated the $I\ensuremath{-}V$ characteristics of short chains of ${\mathrm{C}}_{20}$ molecular cages between $\mathrm{Al}$ and $\mathrm{Au}$ leads with an ab initio formalism. The results indicate that a linear chain of such molecules acts primarily as metallic nanowires. The transmission, however, depends sensitively both on the orientation and distance between the individual ${\mathrm{C}}_{20}$ molecules. Transport through the molecular chains is accompanied by a significant amount of charge transfer, which remains localized at the electrode/molecular interface.}, number={4}, journal={PHYSICAL REVIEW A}, author={Grunert, J and Hemmerich, A}, year={2002}, month={Apr} }
 @article{wei_wang_guo_roland_2001, title={Carbon nanotube parametric electron pump: A molecular device}, volume={64}, ISSN={["1550-235X"]}, DOI={10.1103/physrevb.64.115321}, abstractNote={We have analyzed the device properties of a single-wall metallic carbon nanotube operated as a parametric electron pump. It is found that a dc current can be pumped out from this molecular device by a cyclic variation of two gate voltages near the nanotube, in the absence of any bias voltage. Due to the particular electronic properties of the nanotube, the pumped current is found to show a remarkable parity effect near the resonant levels, with a rather sensitive dependence on the control parameters of the device such as deformation strength, the amplitude and the phase difference of the gate voltage.}, number={11}, journal={PHYSICAL REVIEW B}, author={Wei, YD and Wang, J and Guo, H and Roland, C}, year={2001}, month={Sep} }
 @article{mehrez_guo_wang_roland_2001, title={Carbon nanotubes in the Coulomb blockade regime}, volume={63}, ISSN={["1550-235X"]}, DOI={10.1103/physrevb.63.245410}, abstractNote={Quantum transport through finite-length single wall carbon nanotubes was investigated theoretically in the Coulomb blockade regime. The spin-degenerate state of the nanotube is found to play a crucial role, and is responsible for the experimentally observed alternation in the heights of the conductance spectrum as electrons are added to the nanotubes. We also show that the relaxation of the energy eigenstates, which takes place as the electrons tunnel to and from the nanotubes, is responsible for the current saturation as a function of bias voltage polarity.}, number={24}, journal={PHYSICAL REVIEW B}, author={Mehrez, H and Guo, H and Wang, J and Roland, C}, year={2001}, month={Jun} }
 @article{somoza_sagui_roland_2001, title={Liquid-crystal phases of capped carbon nanotubes}, volume={63}, ISSN={["1550-235X"]}, DOI={10.1103/physrevb.63.081403}, abstractNote={sociated with the electronic properties of carbon nanotubes. Depending on their helicity, single-wall nanotubes are either metallic or semiconducting, and therefore have the potential of forming the basis of a future all-carbon, nanotube-based microelectronics. 2 It is also clear that finite-sized carbon nanotubes are variable-length rods, which by virtue of their shape and size can act as liquid crystals. 3 To examine the possibility of nanotubes forming tailored liquid crystals for application purposes, we investigated the phase diagrams of capped nanotubes as a function of nanotube length and diameter in two limits: in the presence of the attractive van der Waals forces, and in the hard-rod limit characteristic of nanotubes in which such interactions are completely screened. Our results show that when attractive interactions are present, the columnar phase preempts all others at room temperatures.}, number={8}, journal={PHYSICAL REVIEW B}, author={Somoza, AM and Sagui, C and Roland, C}, year={2001}, month={Feb} }
 @article{wei_wang_guo_mehrez_roland_2001, title={Resonant Andreev reflections in superconductor-carbon-nanotube devices}, volume={63}, ISSN={["1550-235X"]}, DOI={10.1103/physrevb.63.195412}, abstractNote={Resonant Andreev reflection through superconductor-carbon-nanotube devices was investigated theoretically with a focus on the superconducting proximity effect. Consistent with a recent experiment, we find that for high transparency devices on-resonance, the Andreev current is characterized by a large value and a resistance dip; low-transparency off-resonance devices give the opposite result. We also give evidence that the observed low-temperature transport anomaly may be a natural result of Andreev reflection process.}, number={19}, journal={PHYSICAL REVIEW B}, author={Wei, YD and Wang, J and Guo, H and Mehrez, H and Roland, C}, year={2001}, month={May} }
 @article{orlikowski_mehrez_taylor_guo_wang_roland_2001, title={Resonant transmission through finite-sized carbon nanotubes}, volume={63}, ISSN={["2469-9969"]}, DOI={10.1103/physrevb.63.155412}, abstractNote={We have investigated theoretically the conductance through finite-sized carbon nanotubes coupled to featureless leads in the context of standard tight-binding models. Conduction takes place via resonant tunneling, and the resultant spectrum of peaks may be understood in terms of the band structure of the nanotubes. Specific nanotubes display both on- and off-resonance behavior as a function of nanotube length depending upon whether or not the bands cross at a nonzero k value. We have also investigated the approach to the infinite limit in detail, and, in general, find that the finite-size effects can persist out to hundreds of nanometers. Since the manipulation of nanotubes into devices is likely to induce defects, we have investigated their effects on the conduction. The effects of bending and two broad classes of defects, i.e., defect in the absence and/or presence of addimers, were considered. In general, the presence of defects leads both to a reduction and shifting of the resonant peaks at the Fermi level. However, in the infinite limit, low concentrations of defects have only a relatively modest effect on the transport properties. Finally, we have investigated the effects of an externally imposed magnetic field oriented perpendicular to the nanotube axis. The magnetic field shifts the levels, thereby turning on- and off-resonant devices into each other. All of the effects discussed here are testable experimentally.}, number={15}, journal={PHYSICAL REVIEW B}, author={Orlikowski, D and Mehrez, H and Taylor, J and Guo, H and Wang, J and Roland, C}, year={2001}, month={Apr} }
 @article{meunier_nardelli_roland_bernholc_2001, title={Structural and electronic properties of carbon nanotube tapers}, volume={64}, ISSN={["2469-9969"]}, DOI={10.1103/physrevb.64.195419}, abstractNote={Since their initial discovery in 1990 by Iijima, 1 carbon nanotubes have come under ever increasing scientific scrutiny. They not only have outstanding mechanical and electrical properties, but also show considerable technological potential as field emitters and electrochemical storage devices. 2 In the emerging field of nanotechnology, carbon nanotubes are playing a crucial role by providing a suitable ‘‘test bed’’ or ‘‘laboratory’’ for materials properties at the nanometer length scale. Single-wall carbon nanotubes are formed when a graphene sheet is curled up into a cylinder and the carbon atoms are joined seamlessly to each other. Nanotubes are therefore characterized by their length, diameter, and helicity. The latter is a measure of the orientation of the graphene sheet as it is folded to form nanotubes. Following the notation of Hamada et al., 3 the structure of a nanotube is described by a pair of integers ( l,m), which give the coordinates of its circumference vector in the basis of the primitive lattice vector of graphene. The helicity is important because it determines both the mechanical and electrical properties of}, number={19}, journal={PHYSICAL REVIEW B}, author={Meunier, V and Nardelli, MB and Roland, C and Bernholc, J}, year={2001}, month={Nov} }
 @article{mehrez_taylor_guo_wang_roland_2000, title={Carbon nanotube based magnetic tunnel junctions}, volume={84}, ISSN={["0031-9007"]}, DOI={10.1103/PhysRevLett.84.2682}, abstractNote={Spin-coherent quantum transport in carbon nanotube magnetic tunnel junctions is investigated theoretically. A spin-valve effect is found for metallic, armchair tubes, with a magnetoconductance ratio ranging up to 20%. Because of the finite length of the nanotube junctions, transport is dominated by resonant transmission. The magnetic tunnel junctions are found to have distinctly different transport behavior depending on whether or not the length of the tubes is commensurate with a 3N+1 rule, with N the number of basic carbon repeat units along the nanotube length.}, number={12}, journal={PHYSICAL REVIEW LETTERS}, author={Mehrez, H and Taylor, J and Guo, H and Wang, J and Roland, C}, year={2000}, month={Mar}, pages={2682–2685} }
 @article{roland_nardelli_wang_guo_2000, title={Dynamic conductance of carbon nanotubes}, volume={84}, ISSN={["0031-9007"]}, DOI={10.1103/PhysRevLett.84.2921}, abstractNote={The dynamic conductance of carbon nanotubes was investigated using the nonequilibrium Green's function formalism within the context of a tight-binding model. Specifically, we have studied the ac response of tubes of different helicities, both with and without defects, and an electronic heterojunction. Because of the induced displacement currents, the dynamic conductance of the nanotubes differs significantly from the dc conductance displaying both capacitive and inductive responses. The important role of photon-assisted transport through nanotubes is revealed and its implications for experiments discussed.}, number={13}, journal={PHYSICAL REVIEW LETTERS}, author={Roland, C and Nardelli, MB and Wang, J and Guo, H}, year={2000}, month={Mar}, pages={2921–2924} }
 @article{bernholc_briggs_bungaro_nardelli_fattebert_rapcewicz_roland_schmidt_zhao_2000, title={Large-scale applications of real-space multigrid methods to surfaces, nanotubes, and quantum transport}, volume={217}, ISSN={["1521-3951"]}, DOI={10.1002/(sici)1521-3951(200001)217:1<685::aid-pssb685>3.0.co;2-3}, abstractNote={The development and applications of real-space multigrid methods are discussed. Multigrid techniques provide preconditioning and convergence acceleration at all length scales, and therefore lead to particularly efficient algorithms. When using localization regions and optimized, non-orthogonal orbitals, calculations involving over 1000 atoms become practical on massively parallel computers. The applications discussed in this chapter include: (i) dopant incorporation and ordering effects during surface incorporation of boron, which lead to the formation of ordered domains at half-monolayer coverage; (ii) incorporation of Mg into GaN during growth, and in particular the conditions that would lead to maximum p-type doping; (iii) optical fingerprints of surface structures for use in real-time feedback control of growth: and (iv) mechanisms of stress release and quantum transport properties of carbon nanotubes.}, number={1}, journal={PHYSICA STATUS SOLIDI B-BASIC SOLID STATE PHYSICS}, author={Bernholc, J and Briggs, EL and Bungaro, C and Nardelli, MB and Fattebert, JL and Rapcewicz, K and Roland, C and Schmidt, WG and Zhao, Q}, year={2000}, month={Jan}, pages={685–701} }
 @article{nardelli_fattebert_orlikowski_roland_zhao_bernholc_2000, title={Mechanical properties, defects and electronic behavior of carbon nanotubes}, volume={38}, ISSN={["1873-3891"]}, DOI={10.1016/S0008-6223(99)00291-2}, abstractNote={Using state-of-the-art classical and quantum simulations, we have studied the mechanical and electronic response of carbon nanotubes to external deformations, such as strain and bending. In strained nanotubes the spontaneous formation of double pentagon–heptagon defect pairs is observed. Tubes containing these defects are energetically preferred to uniformly stretched tubes at strains greater than 5%. These defects act as nucleation centers for the formation of dislocations in the originally ideal graphitic network and constitute the onset of further deformations of the carbon nanotube. In particular, plastic or brittle behaviors can occur depending upon the external conditions and tube symmetry. We have also investigated the effects that the presence of addimers has on strained carbon nanotubes. The main result is the formation of a new class of defects that wrap themselves about the circumference of the nanotube. These defects are shown to modify the geometrical structure and to induce the formation of nanotube-based quantum dots. Finally, we computed transport properties for various ideal and mechanically deformed carbon nanotubes. High defect densities are shown to greatly affect transport in individual nanotubes, while small diameter bent armchair nanotubes mantam thier basic electrical properties even in presence of large deformations with no defects involved.}, number={11-12}, journal={CARBON}, author={Nardelli, MB and Fattebert, JL and Orlikowski, D and Roland, C and Zhao, Q and Bernholc, J}, year={2000}, pages={1703–1711} }
 @article{orlikowski_nardelli_bernholc_roland_2000, title={Theoretical STM signatures and transport properties of native defects in carbon nanotubes}, volume={61}, ISSN={["2469-9969"]}, DOI={10.1103/physrevb.61.14194}, abstractNote={We have investigated theoretically the STM images and conductance signatures of defective carbon nanotubes. The defects considered are those that form on nanotubes under tension, both in the absence and presence of additional carbon atoms. The most prominent features observed in the STM images are a set of bright rings, whose positions correlate with the location of the pentagons within the defect. These features are useful, as they enable the ready identification of many of the defects. By contrast, most of the defects have only a relatively modest effect on the transport properties of the nanotubes. While there is a general decrease in the conductance of the nanotube due to scattering effects, there appears to be no unique feature that can be associated with any of the defects investigated. This unfortunately precludes the use of transport measurements as a means of defect identification. The STM images and conductances of nanotube heterojunctions, as well as tubes under different bias voltages, have also been explored.}, number={20}, journal={PHYSICAL REVIEW B}, author={Orlikowski, D and Nardelli, MB and Bernholc, J and Roland, C}, year={2000}, month={May}, pages={14194–14203} }
 @article{roland_bernholc_brabec_nardelli_maiti_2000, title={Theoretical investigations of carbon nanotube growth}, volume={25}, ISSN={["0892-7022"]}, DOI={10.1080/08927020008044108}, abstractNote={Abstract The growth of carbon nanotubes was investigated using a variety of complementary simulation techniques. Currently, a number of experimental methods are used to synthesize carbon nanotubes suggesting that different mechanisms play a role in their formation. However, it has been shown that growth of nanotubes takes place primarily at the open-ended tips of nanotubes. Ab initio simulations show that the high electric fields present at the nanotube tips in carbon arc discharges cannot be responsible for keeping the tubes open. Rather, the opening and closing of tubes is controlled by the formation of curvature-inducing defects such as adjacent pentagon pairs. On narrow tubes, the formation of such defects is favored leading to the rapid closure of the tubes. By contrast, the formation of hexagons, which lead to straight open-ended growth is favored on large-diameter tubes, with an estimated crossover radius of about 3 nm. Large-scale molecular dynamics and kinetic Monte Carle simulations have been used to verify these ideas. We have also explored the role of the so-called lip–lip interactions during growth. Such an interaction is important in producing multiwalled nanotubes, where the interaction between two open nanotube tips leads to the formation of a network of bonds. Simulations show that such an interaction is indeed significant, but does not provide the additional stabilization required for straight, open-ended, multiwalled nanotube growth. Finally, we consider the formation of nanotubes in the presence of large and small catalytic particles. In the former case, growth is believed to take place via a root-growth mechanism, while the direct adsorption and extrusion of carbon from the vapor dominates the latter. Both mechanisms lead to the formation of small-diameter, single-wall nanotubes.}, number={1-2}, journal={MOLECULAR SIMULATION}, author={Roland, C and Bernholc, J and Brabec, C and Nardelli, MB and Maiti, A}, year={2000}, pages={1–12} }
 @article{roland_nardelli_guo_mehrez_taylor_wang_wei_2000, title={Theoretical investigations of quantum transport through carbon nanotube devices}, volume={7}, DOI={10.1016/S0218-625X(00)00077-4}, abstractNote={By combining a nonequilibrium Green's function analysis with a standard tight-binding model, we have investigated quantum transport through carbon nanotube devices. For finite-sized nanotubes, transport is dominated by resonant tunneling, with the conductance being strongly dependent on the length of the nanotubes. Turning to nanotube devices, we have investigated spin-coherent transport in ferromagnetic–nanotube–ferromagnetic devices and nanotube-superconducting devices. The former shows a significant spin valve effect, while the latter is dominated by resonant Andreev reflections. In addition, we discuss AC transport through carbon nanotubes and the role of photon-assisted tunneling.}, number={5-6}, journal={Surface Review and Letters}, author={Roland, C. and Nardelli, M. B. and Guo, H. and Mehrez, H. and Taylor, J. and Wang, J. and Wei, Y.}, year={2000}, pages={637–642} }
 @article{orlikowski_sagui_somoza_roland_2000, title={Two- and three-dimensional simulations of the phase separation of elastically coherent binary alloys subject to external stresses}, volume={62}, ISSN={["2469-9969"]}, DOI={10.1103/physrevb.62.3160}, abstractNote={The effects of externally imposed stresses on the phase separation process of elastically coherent binary-alloy systems were investigated numerically with large-scale Langevin simulations. Both two- and three-dimensional systems were considered. The intrinsic crystallographic symmetries of the system compete with the external strains in the determination of both the shapes and the orientation of the precipitates. These can go all the way from the configurations predicted by a stress-free equilibrium criterion at small stresses, to lamellar and cylindrical configurations (or stripe configurations in two dimensions) at high stresses. Between these two extremes, there are new shapes and a continuous spectrum of orientation angles. This competition can also induce late-time, large-scale splitting of the domains. The stress effect is larger when the precipitates form the majority phase, and considerably smaller when they are in the minority.}, number={5}, journal={PHYSICAL REVIEW B}, author={Orlikowski, D and Sagui, C and Somoza, AM and Roland, C}, year={2000}, month={Aug}, pages={3160–3168} }
 @article{orlikowski_nardelli_bernholc_roland_1999, title={Ad-dimers on strained carbon nanotubes: A new route for quantum dot formation?}, volume={83}, ISSN={["0031-9007"]}, DOI={10.1103/PhysRevLett.83.4132}, abstractNote={Among the many remarkable properties of single-walled carbon nanotubes, it is their mechanical and electronic properties that stand out [1]. The excellent resistance of carbon nanotubes to bending [2 –7] should lead to future applications of the tubes as a high-strength, lightweight material. Turning to their electronic properties, we find that, at ambient temperatures, single-walled carbon nanotubes may be either metallic or semiconducting, depending upon their helicity [8– 12]. It has been shown [13] that tubes with different helicities may be joined together with one or more pentagon-heptagon (5-7) defects to form different electronic heterojunctions, thereby opening up the intriguing possibility of forming all-carbon based microelectronic devices [14,15]. Some of these remarkable theoretical predictions have recently been confirmed by scanning tunneling microscopy (STM) experiments [16]. However, if the dream of producing an all-carbon-based microelectronics is ever to be realized, then different methods will be needed to produce a variety of devices. Here, we present the results of a large-scale study of the mechanical transformations of strained nanotubes in the presence of ad-dimers and show that this combination may well turn out to be a natural route for the formation of all-carbon nanotube-based quantum dots. Ad-dimers are likely to be present in small amounts on as-grown carbon nanotubes, or they may be deposited there with a STM tip or other methods. The formation of quantum dots with ad-dimers is particularly favorable for the n ,0 zigzag tubes. Specifically, we show that ad-dimers induce plastic behavior on tubes that are otherwise brittle. Before discussing the simulations, we briefly review the}, number={20}, journal={PHYSICAL REVIEW LETTERS}, author={Orlikowski, D and Nardelli, MB and Bernholc, J and Roland, C}, year={1999}, month={Nov}, pages={4132–4135} }
 @article{orlikowski_sagui_somoza_roland_1999, title={Large-scale simulations of phase separation of elastically coherent binary alloy systems}, volume={59}, ISSN={["2469-9969"]}, DOI={10.1103/physrevb.59.8646}, abstractNote={The effects of long-range elastic fields on the phase separation process of both two- and three-dimensional binary alloy systems was investigated with large-scale Langevin simulations. The elastic effects incorporated in the model are the result of anisotropy and dilational misfits introduced via inhomogeneities in the elastic constants of the constituents. The domain morphology obtained is readily understandable in terms of selection criteria for the shape and/or orientation of the domains based on the different shear moduli that are present in the system. Furthermore, the coarsening behavior of the domains is discussed in terms of the generated chemical potential barriers surrounding the precipitates. Other aspects of the coarsening process such as dynamic scaling of the correlation functions and local inverse coarsening are also discussed.}, number={13}, journal={PHYSICAL REVIEW B}, author={Orlikowski, D and Sagui, C and Somoza, A and Roland, C}, year={1999}, month={Apr}, pages={8646–8659} }
 @article{nardelli_brabec_maiti_roland_bernholc_1998, title={Lip-lip interactions and the growth of multiwalled carbon nanotubes}, volume={80}, DOI={10.1103/physrevlett.80.313}, abstractNote={Using a realistic many-body potential, we have simulated the properties of double-walled carbon nanotubes with the aim of investigating the role of lip-lip interactions on nanotube growth. Surprisingly, the lip-lip interaction by itself does not stabilize open-ended growth, but rather facilitates tube closure by mediating the transfer of atoms between inner and outer shells. A simulation of growth on a wide double-wall nanotube leads to considerable deviations from the ideal structure, in contrast to corresponding simulations for single-wall tubes, which result in nearly perfect structures. [S0031-9007(97)04989-2]}, number={2}, journal={Physical Review Letters}, author={Nardelli, M. B. and Brabec, C. and Maiti, A. and Roland, C. and Bernholc, Jerzy}, year={1998}, pages={313–316} }
 @article{nardelli_roland_bernholc_1998, title={Theoretical bounds for multiwalled carbon nanotube growth}, volume={296}, ISSN={["0009-2614"]}, DOI={10.1016/S0009-2614(98)01068-9}, abstractNote={The role of the lip–lip interaction on the non-catalytic growth of multiwalled carbon nanotube is explored with classical molecular dynamics simulations. The simulations show that the lip–lip interaction actually provides a natural mechanism for the closing of the different nanotube shells, irrespective of the number of shells making up the nanotube. Based on an extensive annealing study, we estimate the mean time to closure and an upper bound length for nanotubes that can be formed, as a function of nanotube diameter and temperature. The extrapolated results are in good agreement with the existing experimental data.}, number={5-6}, journal={CHEMICAL PHYSICS LETTERS}, author={Nardelli, MB and Roland, C and Bernholc, J}, year={1998}, month={Nov}, pages={471–476} }
 @article{bernholc_brabec_nardelli_maiti_roland_yakobson_1998, title={Theory of growth and mechanical properties of nanotubes}, volume={67}, ISSN={["1432-0630"]}, DOI={10.1007/s003390050735}, number={1}, journal={APPLIED PHYSICS A-MATERIALS SCIENCE & PROCESSING}, author={Bernholc, J and Brabec, C and Nardelli, MB and Maiti, A and Roland, C and Yakobson, BI}, year={1998}, month={Jul}, pages={39–46} }
 @article{gilmer_huang_roland_1998, title={Thin film deposition: fundamentals and modeling}, volume={12}, ISSN={["1879-0801"]}, DOI={10.1016/S0927-0256(98)00022-6}, abstractNote={We review some of the principles of thin film growth. We begin with a description of the growth modes of films and relate the different structures to the thermodynamic driving forces and to kinetics. The influence of misfit strain, surface free energies, and interface energies are discussed in detail. In particular, we treat the instability of a moving crystal-vapor surface resulting from stress, and the stabilizing influence of step energies in the case where the surface is coincident with a low-index orientation below its surface roughening transition temperature. The introduction of defects by strain, high growth rates, and shadowing instabilities are described. A Monte Carlo model of Al is developed; the model parameters are derived from molecular dynamics calculations of atomic level energetics and kinetics. Anisotropies in surface energies and surface mobilities are found to be large, and have a strong influence on film structures. An extension of the model to polycrystalline films is included. Some of the issues involved in metallization of silicon devices are discussed using results from this model.}, number={4}, journal={COMPUTATIONAL MATERIALS SCIENCE}, author={Gilmer, GH and Huang, HC and Roland, C}, year={1998}, month={Nov}, pages={354–380} }
 @article{sagui_orlikowski_somoza_roland_1998, title={Three-dimensional simulations of Ostwald ripening with elastic effects}, volume={58}, ISSN={["2470-0053"]}, DOI={10.1103/physreve.58.r4092}, abstractNote={The process of phase separation for quenched, three-dimensional binary alloy systems with coupled elastic fields was investigated with Langevin simulations. The elastic effects are the result of a dilational misfit introduced via inhomogeneities in the elastic constants of the system. A selection criterion for the shape and/or orientation of the domains, based on the different shear moduli, is presented. In addition, the coarsening behavior of the domains is discussed in terms of chemical potential barriers surrounding the precipitates.}, number={4}, journal={PHYSICAL REVIEW E}, author={Sagui, C and Orlikowski, D and Somoza, AM and Roland, C}, year={1998}, month={Oct}, pages={R4092–R4095} }
 @article{roland_wensell_hong_tsong_1997, title={Control of Si(100) sublimation with dopants}, volume={78}, ISSN={["1079-7114"]}, DOI={10.1103/PhysRevLett.78.2608}, abstractNote={The sublimation of the Si(100)-( $2\ifmmode\times\else\texttimes\fi{}1$) surface under a tensile strain, induced by dopant segregation, was investigated with low-energy electron microscopy. At a given temperature, samples containing relatively large concentrations of dopants exhibit a step-flow behavior during sublimation. By contrast, the formation and proliferation of terrace vacancies, followed by a disintegration of the surface steps, dominates the sublimation of the lightly doped samples. Molecular dynamics simulations indicate that this striking difference in behavior is due to a strain-induced increase in the formation energy of dimer vacancies on the surface.}, number={13}, journal={PHYSICAL REVIEW LETTERS}, author={Roland, CM and Wensell, MG and Hong, Y and Tsong, IST}, year={1997}, month={Mar}, pages={2608–2611} }
 @misc{bernholc_roland_yakobson_1997, title={Nanotubes}, volume={2}, ISSN={["1879-0348"]}, DOI={10.1016/s1359-0286(97)80014-9}, abstractNote={The field of nanotubes is undergoing an explosive growth, fueled by brakethroughs in synthesis and the promise of unique applications. Highly unusual properties and devices have been predicted and/or observed, including extremely high strength and flexibility, nanoscale electronic devices consisting entirely of carbon, and strong capillary effects leading to the production of exceptionally thin wires, cold cathode field emission and other effects.}, number={6}, journal={CURRENT OPINION IN SOLID STATE & MATERIALS SCIENCE}, author={Bernholc, J and Roland, C and Yakobson, BI}, year={1997}, month={Dec}, pages={706–715} }
 @article{bernholc_briggs_sullivan_brabec_nardelli_rapcewicz_roland_wensell_1997, title={Real space multigrid methods for large scale electronic structure problems}, volume={65}, DOI={10.1002/(SICI)1097-461X(1997)65:5<531::AID-QUA18>3.0.CO;2-5}, abstractNote={We describe the development and applications of a new electronic structure method that uses a real-space grid as a basis. Multigrid techniques provide preconditioning and convergence acceleration at all length scales and therefore lead to particularly efficient algorithms. The salient points of our implementation include: (i) new compact discretization schemes in real space for systems with cubic, orthorhombic, and hexagonal symmetry and (ii) new multilevel algorithms for the iterative solution of Kohn–Sham and Poisson equations. The accuracy of the discretizations was tested by direct comparison with plane-wave calculations, when possible, and the results were in excellent agreement in all cases. These techniques are very suitable for use on massively parallel computers and in O(N) methods. Tests on the Cray-T3D have shown nearly linear scaling of the execution time up to the maximum number of processors (512). The above methodology was tested on a large number of systems, such as the C60 molecule, diamond, Si and GaN supercells, and quantum molecular dynamics simulations for Si. Large-scale applications include a simulation of surface melting of Si and investigations of electronic and structural properties of surfaces, interfaces, and biomolecules. © 1997 John Wiley & Sons, Inc. Int J Quant Chem 65: 531–543, 1997}, number={5}, journal={International Journal of Quantum Chemistry}, author={Bernholc, Jerzy and Briggs, E. L. and Sullivan, D. J. and Brabec, C. J. and Nardelli, M. B. and Rapcewicz, K. and Roland, C. and Wensell, M.}, year={1997}, pages={531–543} }