Applications > namd

Publications

Users of this package associated the following 81 publications with the XSEDE allocation/account under which they were running this software. Thus the publications may have come before or after the runs of this software, but the authors considered them to be related to the same line of research.

  • Yuzhuo Chu, Jianzhuang Yao, Hong Guo (University of Tennessee, Knoxville), (2012) "QM/MM MD and Free Energy Simulations of G9a-Like Protein (GLP) and Its Mutants: Understanding the Factors that Determine the Product Specificity", PLoS ONE 7 / 5, e37674. http://dx.doi.org/10.1371/journal.pone.0037674
  • Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), Robert Brunner, Eduardo Cruz-Chu, Jeffrey Comer (University of Illinois at Urbana-Champaign), Klaus Schulten, (2009) "Modeling transport through synthetic nanopores", IEEE Nanotechnology Magazine 3 / 1, 20-28. http://dx.doi.org/10.1109/MNANO.2008.931112
  • Kai Zhang, Li Wang, Yanxin Liu, Kwok-Yan Chan, Xiaoyun Pang, Klaus Schulten, Zhiyang Dong, Fei Sun, (June2013) "Flexible interwoven termini determine the thermal stability of thermosomes", Protein & Cell 4 / 6, 432-444. http://dx.doi.org/10.1007/s13238-013-3026-9
  • Bala Murali Venkatesan, James Polans, Jeffrey Comer (University of Illinois at Urbana-Champaign), Supriya Sridhar, David Wendell, Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), Rashid Bashir, (2011) "Lipid bilayer coated Al2O3 nanopore sensors: towards a hybrid biological solid-state nanopore", Biomedical Microdevices 13 / 4, 671-682. http://dx.doi.org/10.1007/s10544-011-9537-3
  • Jianzhuang Yao, Alexander Wlodawer, Hong Guo (University of Tennessee, Knoxville), (2013) "Understanding the Autocatalytic Process of Pro-kumamolisin Activation from Molecular Dynamics and Quantum Mechanical/Molecular Mechanical (QM/MM) Free-Energy Simulations", Chemistry - A European Journal undefined / undefined, n/a-n/a. http://dx.doi.org/10.1002/chem.201301310
  • Yanxin Liu, Jen Hsin, HyeongJun Kim, Paul R. Selvin, Klaus Schulten, (June2011) "Extension of a Three-Helix Bundle Domain of Myosin VI and Key Role of Calmodulins", Biophysical Journal 100 / 12, 2964-2973. http://dx.doi.org/10.1016/j.bpj.2011.05.010
  • Chul-Ho Lee, Theanne Schiros, Elton Jose Dos Santos (Stanford University), Bumjung Kim, Kevin G. Yager, Seok Ju Kang, Sunwoo Lee, Jaeeun Yu, Kenji Watanabe, Takashi Taniguchi, James Hone, Efthimios Kaxiras, Colin Nuckolls, Philip Kim, (January2014) "Epitaxial Growth of Molecular Crystals on van der Waals Substrates for High-Performance Organic Electronics", Advanced Materials undefined / undefined, n/a-n/a. http://dx.doi.org/10.1002/adma.201304973
  • Qiangjun Zhou, Jiangmei Li, Hang Yu, Yujia Zhai, Zhen Gao, Yanxin Liu, Xiaoyun Pang, Lunfeng Zhang, Klaus Schulten, Fei Sun, Chang Chen, (March2014) "Molecular insights into the membrane-associated phosphatidylinositol 4-kinase IIα", Nature Communications 5, 3552. http://dx.doi.org/10.1038/ncomms4552
  • Ji Young Lee, Edward Lyman (University of Delaware), (September2012) "Predictions for Cholesterol Interaction Sites on the A2AAdenosine Receptor", Journal of the American Chemical Society 134 / 40, 16512-16515. http://dx.doi.org/10.1021/ja307532d
  • Y. Wang, Yanxin Liu, H. A. DeBerg, T. Nomura, M. T. Hoffman, P. R. Rohde, K. Schulten, B. Martinac, P. R. Selvin, (February2014) "Single molecule FRET reveals pore size and opening mechanism of a mechano-sensitive ion channel", eLife 3, e01834-e01834. http://dx.doi.org/10.7554/eLife.01834
  • Yanxin Liu, Maxim B. Prigozhin, Klaus Schulten, Martin Gruebele, (March2014) "Observation of Complete Pressure-Jump Protein Refolding in Molecular Dynamics Simulation and Experiment", Journal of the American Chemical Society 136 / 11, 4265-4272. http://dx.doi.org/10.1021/ja412639u
  • Wei Li Wang, Elton Santos (Stanford University), Bin Jiang, Ekin Cubuk, Colin Ophus, Alba Centeno, Amaia Pesquera, Amaia Zurutuza, Jim Ciston, Robert M Westervelt, Efthimios Kaxiras, (January2014) "Direct Observation of a long-lived single-atom catalyst chiseling atomic structures in graphene", Nano Letters undefined / undefined, 140121142046000. http://dx.doi.org/10.1021/nl403327u
  • Elton Jose Dos Santos (Stanford University), (2013) "Magnetoelectric effect in functionalized few-layer graphene", Physical Review B 87 / 15, . http://dx.doi.org/10.1103/PhysRevB.87.155440
  • Utkur Mirsaidov, Jeffrey Comer (University of Illinois at Urbana-Champaign), Valentin Dimitrov, Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), Gregory Timp, (2010) "Slowing the translocation of double-stranded DNA using a nanopore smaller than the double helix", Nanotechnology 21 / 39, 395501. http://dx.doi.org/10.1088/0957-4484/21/39/395501
  • Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), Robert Brunner, Eduardo Cruz-Chu, Jeffrey Comer (University of Illinois at Urbana-Champaign), Klaus Schulten, (2009) "Modeling transport through synthetic nanopores", IEEE Nanotechnology Magazine 3 / 1, 20-28. http://dx.doi.org/10.1109/MNANO.2008.931112
  • Christopher Maffeo (University of Illinois at Urbana-Champaign), Robert Schöpflin, Hergen Brutzer, René Stehr, Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), Gero Wedemann, Ralf Seidel, (2010) "DNA–DNA Interactions in Tight Supercoils Are Described by a Small Effective Charge Density", Physical Review Letters 105 / 15, 158101. http://dx.doi.org/10.1103/PhysRevLett.105.158101
  • Bala Murali Venkatesan, James Polans, Jeffrey Comer (University of Illinois at Urbana-Champaign), Supriya Sridhar, David Wendell, Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), Rashid Bashir, (2011) "Lipid bilayer coated Al2O3 nanopore sensors: towards a hybrid biological solid-state nanopore", Biomedical Microdevices 13 / 4, 671-682. http://dx.doi.org/10.1007/s10544-011-9537-3
  • Elton Jose Dos Santos (Stanford University), (November2013) "Electrically Driven Tuning of the Dielectric Constant in MoS2Layers", ACS Nano 7 / 12, 10741-10746. http://dx.doi.org/10.1021/nn403738b
  • Elton Jose Dos Santos (Stanford University), (November2013) "Carrier-Mediated Magnetoelectric Coupling in Functionalized Graphene", ACS Nano 7 / 11, 9927-9932. http://dx.doi.org/10.1021/nn4037877
  • Swati Bhattacharya (University of Illinois at Urbana-Champaign), Julien Muzard (Ecole Supérieure de Physique et Chimie Industrielles, ParisTech, Centre National de la Recherche Scientifique, France), Linda Payet (Ecole Supérieure de Physique et Chimie Industrielles, ParisTech, Centre National de la Recherche Scientifique, France), Jerome Mathe (Ecole Supérieure de Physique et Chimie Industrielles, ParisTech, Centre National de la Recherche Scientifique, France), Ulrich Bockelmann (Ecole Supérieure de Physique et Chimie Industrielles, ParisTech, Centre National de la Recherche Scientifique, France), Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), Virgile Viasnoff (Ecole Supérieure de Physique et Chimie Industrielles, ParisTech, Centre National de la Recherche Scientifique, France), (February2011) "Rectification of the Current in α-Hemolysin Pore Depends on the Cation Type: The Alkali Series Probed by Molecular Dynamics Simulations and Experiments", Journal of Physical Chemistry C 115, 4255. http://pubs.acs.org/doi/abs/10.1021/jp111441p
  • Meni Wanunu (Departments of Physics and Chemistry/Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States), Swati Bhattacharya (University of Illinois at Urbana-Champaign), Yun Xie (Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States), Yitzhak Tor (Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States), Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), Marija Drndik (Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania), (November2011) "Nanopore Analysis of Individual RNA/Antibiotic Complexes", ACS Nano 5, 9345. http://pubs.acs.org/doi/abs/10.1021/nn203764j#cor1
  • Xueqing Zou, Yanxin Liu, Zhongzhou Chen, Gloria Ines Cárdenas-Jirón, Klaus Schulten, (August2010) "Flow-Induced β-Hairpin Folding of the Glycoprotein Ibα β-Switch", Biophysical Journal 99 / 4, 1182-1191. http://dx.doi.org/10.1016/j.bpj.2010.05.035
  • Swati Bhattacharya (University of Illinois at Urbana-Champaign), Ian M. Derrington (Department of Physics, University of Washington Seattle, 3910 15th Avenue, Seattle, Washington, 98195, United States ), Mikhail Pavlenok (Department of Microbiology, University of Alabama at Birmingham, 609 Bevill Biomedical Research Building, 845 19th Street South, Birmingham, Alabama 35294, United States), Michael Niederweis (Department of Microbiology, University of Alabama at Birmingham, 609 Bevill Biomedical Research Building, 845 19th Street South, Birmingham, Alabama 35294, United States), Jens H. Gundlach (Department of Physics, University of Washington Seattle, 3910 15th Avenue, Seattle, Washington, 98195, United States ), Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), (2012) "Molecular Dynamics Study of MspA Arginine Mutants Predicts Slow DNA Translocations and Ion Current Blockades Indicative of DNA Sequence", ACS Nano 6 / 8, 6960-6968. http://dx.doi.org/10.1021/nn3019943
  • Christopher Maffeo (University of Illinois at Urbana-Champaign), Binquan Luan (University of Illinois at Urbana-Champaign), Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), (2012) "End-to-end attraction of duplex DNA", Nucleic Acids Research 40 / 9, 3812-3821. http://dx.doi.org/10.1093/nar/gkr1220
  • David Wells (University of Illinois at Urbana-Champaign), Volha Abramkina, Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), (2007) "Exploring transmembrane transport through α-hemolysin with grid-steered molecular dynamics", The Journal of Chemical Physics 127 / 12, 125101. http://dx.doi.org/10.1063/1.2770738
  • Justin A Lemkul, Alexey Savelyev, Alexander D MacKerell, (June2014) "Induced Polarization Influences the Fundamental Forces in DNA Base Flipping", The Journal of Physical Chemistry Letters 5 / 12, 2077-2083. http://dx.doi.org/10.1021/jz5009517
  • Rogan Carr (University of Illinois at Urbana-Champaign), Jeffrey Comer (University of Illinois at Urbana-Champaign), Mark D. Ginsberg, Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), (2011) "Modeling Pressure-Driven Transport of Proteins Through a Nanochannel", IEEE Transactions on Nanotechnology 10 / 1, 75-82. http://dx.doi.org/10.1109/TNANO.2010.2062530
  • Jeffrey Comer, Aleksei Aksimentiev, (January2012) "Predicting the DNA Sequence Dependence of Nanopore Ion Current Using Atomic-Resolution Brownian Dynamics", The Journal of Physical Chemistry C 116 / 5, 3376-3393. http://dx.doi.org/10.1021/jp210641j
  • Jejoong Yoo, Aleksei Aksimentiev, (2012) "Improved Parametrization of Li+, Na+, K+, and Mg2+Ions for All-Atom Molecular Dynamics Simulations of Nucleic Acid Systems", The Journal of Physical Chemistry Letters 3 / 1, 45-50. http://dx.doi.org/10.1021/jz201501a
  • Christopher G. Myers, Bernard Montgomery Pettitt (University of Texas Medical Branch), (March2013) "Communication: Origin of the contributions to DNA structure in phages", The Journal of Chemical Physics 138 / 7, 071103. http://dx.doi.org/10.1063/1.4791708
  • Jianzhuang Yao, Yuzhuo Chu, Ran An, Hong Guo (University of Tennessee, Knoxville), (2012) "Understanding Product Specificity of Protein Lysine Methyltransferases from QM/MM Molecular Dynamics and Free Energy Simulations: The Effects of Mutation on SET7/9 beyond the Tyr/Phe Switch", Journal of Chemical Information and Modeling 52 / 2, 449-456. http://dx.doi.org/10.1021/ci200364m
  • M. B. Prigozhin, Yanxin Liu, A. J. Wirth, S. Kapoor, R. Winter, K. Schulten, M. Gruebele, (May2013) "Misplaced helix slows down ultrafast pressure-jump protein folding", Proceedings of the National Academy of Sciences 110 / 20, 8087-8092. http://dx.doi.org/10.1073/pnas.1219163110
  • David Wells (University of Illinois at Urbana-Champaign), Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), (2010) "Mechanical Properties of a Complete Microtubule Revealed through Molecular Dynamics Simulation", Biophysical Journal 99 / 2, 629-637. http://dx.doi.org/10.1016/j.bpj.2010.04.038
  • Thomas Furlani (SUNY at Buffalo), Matthew D. Jones, Steve Gallo (SUNY at Buffalo), Andrew E. Bruno, Charng-Da Lu, Amin Ghadersohi, Ryan J. Gentner, Abani Patra, Robert L. DeLeon, Gregor von Laszewski, Fugang Wang, Ann Zimmerman, (2012) "Performance metrics and auditing framework using application kernels for high-performance computer systems", Concurrency and Computation: Practice and Experience 25 / 7, 918-931. http://dx.doi.org/10.1002/cpe.2871
  • James C. Browne, Thomas Furlani (SUNY at Buffalo), Robert T. McLay, Robert L. DeLeon, Charng-Da Lu, Matthew D. Jones, Steve Gallo (SUNY at Buffalo), Amin Ghadersohi, Abani K. Patra, William Barth (University of Texas at Austin), John Hammond, (November2013) "Enabling comprehensive data-driven system management for large computational facilities", Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis on - SC '13 Denver, CO, USA , 1-11. http://dx.doi.org/10.1145/2503210.2503230
  • Cheng Zhang (UTMB), Bernard Pettitt (UTMB), (April2014) "Computation of high-order virial coefficients in high-dimensional hard-sphere fluids by Mayer sampling", Molecular Physics 112/9-10, 1427-1447. http://www.tandfonline.com/doi/abs/10.1080/00268976.2014.904945
  • HyeongJun Kim, Jen Hsin, Yanxin Liu, Paul R. Selvin, Klaus Schulten, (November2010) "Formation of Salt Bridges Mediates Internal Dimerization of Myosin VI Medial Tail Domain", Structure 18 / 11, 1443-1449. http://dx.doi.org/10.1016/j.str.2010.09.011
  • B. Dorvel, G. Sigalov, Q. Zhao, Jeffrey Comer (University of Illinois at Urbana-Champaign), V. Dimitrov, U. Mirsaidov, Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), G. Timp, (2009) "Analyzing the forces binding a restriction endonuclease to DNA using a synthetic nanopore", Nucleic Acids Research 37 / 12, 4170-4179. http://dx.doi.org/10.1093/nar/gkp317
  • Jeffrey Comer (University of Illinois at Urbana-Champaign), Valentin Dimitrov, Qian Zhao, Gregory Timp, Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), (2009) "Microscopic Mechanics of Hairpin DNA Translocation through Synthetic Nanopores", Biophysical Journal 96 / 2, 593-608. http://dx.doi.org/10.1016/j.bpj.2008.09.023
  • Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), Robert Brunner, Eduardo Cruz-Chu, Jeffrey Comer (University of Illinois at Urbana-Champaign), Klaus Schulten, (2009) "Modeling transport through synthetic nanopores", IEEE Nanotechnology Magazine 3 / 1, 20-28. http://dx.doi.org/10.1109/MNANO.2008.931112
  • Luca Larini (University of California-Santa Barbara), Lanyuan Lu (University of Utah), Gregory Voth (University of Chicago), (April2010) "The multiscale coarse-graining method. VI. Implementation of three-body coarse-grained potentials", The Journal of Chemical Physics 132 / 16, 164107. http://dx.doi.org/10.1063/1.3394863
  • David Wells (University of Illinois at Urbana-Champaign), Maxim Belkin (University of Illinois at Urbana-Champaign), Jeffrey Comer (University of Illinois at Urbana-Champaign), Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), (July2012) "Assessing Graphene Nanopores for Sequencing DNA", Nano Letters 12 / 8, 4117-4123. http://dx.doi.org/10.1021/nl301655d
  • U. Hömmerich, A.G. Bluiett, Ivy Jones (Hampton University), S.B. Trivedi, R.T. Shah, (January2006) "Crystal growth and infrared spectroscopy of Cr:Cd1−xZnxTe and Cr:Cd1−xMgxTe", Journal of Crystal Growth 287 / 2, 243-247. http://dx.doi.org/10.1016/j.jcrysgro.2005.11.015
  • Ivy Jones (Hampton University), (May2008) "Effect of polyhedral-oligomeric-sil-sesquioxanes on thermal and mechanical behavior of SC-15 epoxy", eXPRESS Polymer Letters 2 / 7, 494-501. http://dx.doi.org/10.3144/expresspolymlett.2008.59
  • U. Hömmerich, Ivy Jones (Hampton University), Ei Ei Nyein, S.B. Trivedi, (January2006) "Comparison of the optical properties of diffusion-doped polycrystalline Cr:ZnSe and Cr:CdTe windows", Journal of Crystal Growth 287 / 2, 450-453. http://dx.doi.org/10.1016/j.jcrysgro.2005.11.064
  • Christopher Maffeo (University of Illinois at Urbana-Champaign), Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), (2009) "Structure, Dynamics, and Ion Conductance of the Phospholamban Pentamer", Biophysical Journal 96 / 12, 4853-4865. http://dx.doi.org/10.1016/j.bpj.2009.03.053
  • Jing Huang (University of Maryland, Baltimore), Alexander D. MacKerell, (2013) "CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data", Journal of Computational Chemistry 34 / 25, 2135-2145. http://dx.doi.org/10.1002/jcc.23354
  • Chuanying Chen (University of Texas Medical Branch), Bernard Pettitt (University of Texas Medical Branch), (2011) "The Binding Process of a Nonspecific Enzyme with DNA", Biophysical Journal 101 / 5, 1139-1147. http://dx.doi.org/10.1016/j.bpj.2011.07.016
  • Hironori Kokubo (University of Houston-Downtown), Char Hu (University of Houston-Downtown), Bernard Pettitt (University of Texas Medical Branch), (2011) "Peptide Conformational Preferences in Osmolyte Solutions: Transfer Free Energies of Decaalanine", Journal of the American Chemical Society 133 / 6, 1849-1858. http://dx.doi.org/10.1021/ja1078128
  • John S Perkyns (University of Texas Medical Branch), Gillian C Lynch (University of Texas Medical Branch), Jesse J Howard (University of Houston-Downtown), B Montgomery Pettitt (University of Texas Medical Branch), (2010) "Protein solvation from theory and simulation: Exact treatment of Coulomb interactions in three-dimensional theories", The Journal of Chemical Physics 132 / 6, 064106. http://dx.doi.org/10.1063/1.3299277
  • C. Stavis, T. L. Clare, J. E. Butler, A. D. Radadia, Rogan Carr (University of Illinois at Urbana-Champaign), H. Zeng, W. P. King, J. A. Carlisle, Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), R. Bashir, R. J. Hamers, (2010) "Surface Chemistry Special Feature: Surface functionalization of thin-film diamond for highly stable and selective biological interfaces", Proceedings of the National Academy of Sciences 108 / 3, 983-988. http://dx.doi.org/10.1073/pnas.1006660107
  • Ekin D. Cubuk, Wei L. Wang, Kejie Zhao (Massachusetts Institute of Technology), Joost J. Vlassak, Zhigang Suo, Efthimios Kaxiras, (March2013) "Morphological Evolution of Si Nanowires upon Lithiation: A First-Principles Multiscale Model", Nano Letters 13 / 5, 2011-2015. http://dx.doi.org/10.1021/nl400132q
  • Binquan Luan, Rogan Carr, Martin Caffrey, Aleksei Aksimentiev, (2010) "The effect of calcium on the conformation of cobalamin transporter BtuB", Proteins: Structure, Function, and Bioinformatics 78 / 5, 1153-1162. http://dx.doi.org/10.1002/prot.22635
  • Y. Lai, J. Diao, Yanxin Liu (University of Illinois at Urbana-Champaign), Y. Ishitsuka, Z. Su, Klaus Schulten (University of Illinois at Urbana-Champaign), T. Ha, Y.-K. Shin, (January2013) "Fusion pore formation and expansion induced by Ca2+ and synaptotagmin 1", Proceedings of the National Academy of Sciences 110 / 4, 1333-1338. http://dx.doi.org/10.1073/pnas.1218818110
  • Danielle McHarris (Utica College), Daniel Barr (Utica College), (August2012) "Sequence-Specific DNA-Binding Behavior of GCN4", 244th ACS National Meeting Philadelphia, PA , . http://abstracts.acs.org/chem/244nm/program/view.php?obj_id=152217&terms=
  • Sara Nichols (University of California-San Diego), Carlos Hernandez (Stanford University), Yi Wang (University of California-San Diego), James McCammon (University of California-San Diego), (June2013) "Structure-based network analysis of an evolved G protein-coupled receptor homodimer interface", Protein Science 22 / 6, 745-754. http://dx.doi.org/10.1002/pro.2258
  • Suliman Salman (Utica College), Daniel Barr (Utica College), (August2012) "Peptides derived from the recognition helices of the gal and lac repressor proteins demonstrate sequence-specific DNA-binding", 244th ACS National Meeting Philadelphia, PA , .
  • Jejoong Yoo (University of Illinois at Urbana-Champaign), Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), (2012) "Improved Parametrization of Li+, Na+, K+, and Mg2+Ions for All-Atom Molecular Dynamics Simulations of Nucleic Acid Systems", The Journal of Physical Chemistry Letters 3 / 1, 45-50. http://dx.doi.org/10.1021/jz201501a
  • Winston Timp, Jeffrey Comer (University of Illinois at Urbana-Champaign), Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), (May2012) "DNA Base-Calling from a Nanopore Using a Viterbi Algorithm", Biophysical Journal 102 / 10, L37-L39. http://dx.doi.org/10.1016/j.bpj.2012.04.009
  • Q. Zhao, J. Comer, V. Dimitrov, S. Yemenicioglu, Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), G. Timp, (2008) "Stretching and unzipping nucleic acid hairpins using a synthetic nanopore", Nucleic Acids Research 36 / 5, 1532-1541. http://dx.doi.org/10.1093/nar/gkm1017
  • Jeffrey Comer (University of Illinois at Urbana-Champaign), Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), (January2012) "Predicting the DNA Sequence Dependence of Nanopore Ion Current Using Atomic-Resolution Brownian Dynamics", The Journal of Physical Chemistry C 116 / 5, 3376-3393. http://dx.doi.org/10.1021/jp210641j
  • Stefan W. Kowalczyk, David Wells (University of Illinois at Urbana-Champaign), Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), Cees Dekker, (January2012) "Slowing down DNA Translocation through a Nanopore in Lithium Chloride", Nano Letters 12 / 2, 1038-1044. http://dx.doi.org/10.1021/nl204273h
  • Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), Robert Brunner, Jordi Cohen, Jeffrey Comer (University of Illinois at Urbana-Champaign), Eduardo Cruz-Chu, David Hardy, Aruna Rajan, Amy Shih, Grigori Sigalov, Ying Yin, Klaus Schulten (University of Illinois at Urbana-Champaign), (2008) "Nanostructure Design", , 181-234. http://dx.doi.org/10.1007/978-1-59745-480-3_11
  • Grigori Sigalov, Jeffrey Comer (University of Illinois at Urbana-Champaign), Gregory Timp, Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), (2008) "Detection of DNA Sequences Using an Alternating Electric Field in a Nanopore Capacitor", Nano Letters 8 / 1, 56-63. http://dx.doi.org/10.1021/nl071890k
  • Jianzhuang Yao, Qin Xu, Hong Guo (University of Tennessee, Knoxville), (2013) "QM/MM and free-energy simulations of deacylation reaction catalysed by sedolisin, a serine-carboxyl peptidase", Molecular Simulation 39 / 3, 206-213. http://dx.doi.org/10.1080/08927022.2012.714467
  • U Hommerich, Ivy Jones (Hampton University), EiEi Nyein, S.B. Trivedi, (2005) "Chromium Diffusion Doping of Commercial ZnSe and CdTe Windows for Mid-Infrared Solid-State Laser Applications", 2005 MRS Spring Meeting San Francisco, California 864/Symposium E - Semiconductor Defect Engineering - Materials, Synthesis Structures and Devices, . http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=8009067
  • Peter L. Freddolino, Christopher B. Harrison, Yanxin Liu, Klaus Schulten, (October2010) "Challenges in protein-folding simulations", Nature Physics 6 / 10, 751-758. http://dx.doi.org/10.1038/nphys1713
  • Elton Jose Dos Santos (Stanford University), Efthimios Kaxiras, (2013) "Electric-Field Dependence of the Effective Dielectric Constant in Graphene", Nano Letters 13 / 3, 898-902. http://dx.doi.org/10.1021/nl303611v
  • Boon Chong Goh (University of Illinois at Urbana-Champaign), Michael J Rynkiewicz, Tanya R Cafarella, Mitchell R White, Kevan L Hartshorn, Kimberly Allen, Erika C Crouch, Oliviana Calin, Peter H Seeberger, Klaus Schulten, Barbara A Seaton, (November2013) "Molecular Mechanisms of Inhibition of Influenza by Surfactant Protein D Revealed by Large-Scale Molecular Dynamics Simulation", Biochemistry 52 / 47, 8527-8538. http://dx.doi.org/10.1021/bi4010683
  • Malakhat Turabekova (Jackson State University), Bakhtiyor Rasulev (Jackson State University), Mellisa Theodore (Johns-Hopkins University), Joany Jackman (Johns-Hopkins University), Danuta Leszczynska (Jackson State University), Jerzy Leszczynski (Jackson State University), (January2014) "Immunotoxicity of nanoparticles: Computational study suggests that CNTs and C60 fullerenes might be recognized as pathogens by Toll-like receptors", Nanoscale undefined / undefined, . http://dx.doi.org/10.1039/C3NR05772K
  • Mauro Lapelosa (Drexel University), Cameron Abrams (Drexel University), (February2013) "A Computational Study of Water and CO Migration Sites and Channels Inside Myoglobin", Journal of Chemical Theory and Computation , 1265-1271.
  • Lucky Ahmed, Bakhtiyor Rasulev (Jackson State University), Malakhat Turabekova, Danuta Leszczynska, Jerzy Leszczynski (Jackson State University), (September2013) "Receptor- and ligand-based study of fullerene analogues: comprehensive computational approach including quantum-chemical, QSAR and molecular docking simulations", Organic & Biomolecular Chemistry 11 / 35, 5798. http://dx.doi.org/10.1039/c3ob40878g
  • Rogan Carr (University of Illinois at Urbana-Champaign), Jeffrey Comer (University of Illinois at Urbana-Champaign), Mark D. Ginsberg, Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), (2011) "Modeling Pressure-Driven Transport of Proteins Through a Nanochannel", IEEE Transactions on Nanotechnology 10 / 1, 75-82. http://dx.doi.org/10.1109/TNANO.2010.2062530
  • Svetla Stoilova-McPhie, Gillian C Lynch (University of Texas Medical Branch), Steven Ludtke, Bernard Montgomery Pettitt (University of Texas Medical Branch), (2013) "Domain organization of membrane-bound factor VIII", Biopolymers undefined / undefined, n/a-n/a. http://dx.doi.org/10.1002/bip.22199
  • Loredana Mereuta, Mahua Roy, Alina Asandei, Jong Kook Lee, Yoonkyung Park, Ioan Andricioaei, Tudor Luchian, (2014) "Slowing down single-molecule trafficking through a protein nanopore reveals intermediates for peptide translocation", Scientific Reports 4 / undefined, . http://dx.doi.org/10.1038/srep03885
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