Applications > charmrun

Publications

Users of this package associated the following 66 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.

  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • David Mowrey (University of Pittsburgh), Esmael J. Haddadian, Lu Tian Liu, Dan Willenbring, Yan Xu, Pei Tang, (May2010) "Unresponsive Correlated Motion in α7 nAChR to Halothane Binding Explains Its Functional Insensitivity to Volatile Anesthetics", The Journal of Physical Chemistry B 114 / 22, 7649-7655. http://dx.doi.org/10.1021/jp1009675
  • David Mowrey (University of Pittsburgh), Mary Hongying Cheng, Lu Tian Liu, Dan Willenbring, Xinghua Lu, Troy Wymore, Yan Xu, Pei Tang, (January2013) "Asymmetric Ligand Binding Facilitates Conformational Transitions in Pentameric Ligand-Gated Ion Channels", Journal of the American Chemical Society 135 / 6, 2172-2180. http://dx.doi.org/10.1021/ja307275v
  • 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
  • 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
  • Yuri A. Nedialkov, Kristopher Opron (Michigan State University), Fadi Assaf, Irina Artsimovitch, Maria L. Kireeva, Mikhail Kashlev, Robert Cukier (Michigan State University), Evgeny Nudler, Zachary Burton (Michigan State University), (November2012) "The RNA polymerase bridge helix YFI motif in catalysis, fidelity and translocation", Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms undefined / undefined, . http://dx.doi.org/10.1016/j.bbagrm.2012.11.005
  • Joseph R Peterson (University of Illinois at Urbana-Champaign), Michael Hallock (University of Illinois at Urbana-Champaign), John Cole (University of Illinois at Urbana-Champaign), Zaida Luthey-Schulten, (2013) "A Problem Solving Environment for Stochastic Biological Simulations", Python for High Performance and Scientific Computing (PyHPC 2013) Workshop Denver, CO , . http://www.dlr.de/sc/en/Portaldata/15/Resources/dokumente/PyHPC2013/submissions/pyhpc2013_submission_8.pdf
  • Jonathan Lai (University of Illinois at Urbana-Champaign), Ke Chen (University of Illinois at Urbana-Champaign), Zaida Luthey-Schulten, (2013) "Structural Intermediates and Folding Events in the Early Assembly of the Ribosomal Small Subunit", The Journal of Physical Chemistry B 117 / 42, 13335-13345. http://dx.doi.org/10.1021/jp404106r
  • Michael Hallock (University of Illinois at Urbana-Champaign), John E. Stone, Elijah Roberts (University of Illinois at Urbana-Champaign), Corey Fry, Zaida Luthey-Schulten, (2014) "Simulation of reaction diffusion processes over biologically relevant size and time scales using multi-GPU workstations", Parallel Computing 40 / 5-6, 86-99. http://dx.doi.org/10.1016/j.parco.2014.03.009
  • 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
  • Li Li (University of Illinois at Urbana-Champaign), Susan A. Martinis, Zaida Luthey-Schulten, (2013) "Capture and Quality Control Mechanisms for Adenosine-5′-triphosphate Binding", Journal of the American Chemical Society 135 / 16, 6047-6055. http://dx.doi.org/10.1021/ja308044w
  • 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
  • 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
  • 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
  • Ji Young Lee, Edward Lyman (University of Delaware), (May2012) "Agonist Dynamics and Conformational Selection during Microsecond Simulations of the A2A Adenosine Receptor", Biophysical Journal 102 / 9, 2114-2120. http://dx.doi.org/10.1016/j.bpj.2012.03.061
  • 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
  • Maria L Kireeva, Kristopher Opron (Michigan State University), Steve A Seibold, C�line Domecq, Robert Cukier (Michigan State University), Benoit Coulombe, Mikhail Kashlev, Zachary Burton (Michigan State University), (June2012) "Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase", BMC Biophysics 5 / 1, 11. http://dx.doi.org/10.1186/2046-1682-5-11
  • 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.
  • 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
  • Rogan Carr (University of Illinois at Urbana-Champaign), Ira A. Weinstock, Asipu Sivaprasadarao, Achim Müller, Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), (2008) "Synthetic Ion Channels via Self-Assembly: A Route for Embedding Porous Polyoxometalate Nanocapsules in Lipid Bilayer Membranes", Nano Letters 8 / 11, 3916-3921. http://dx.doi.org/10.1021/nl802366k
  • Xue Wang, Fengting Xu, Jiasen Liu, Bingquan Gao, Yanxin Liu, Yujia Zhai, Jun Ma, Kai Zhang, Timothy S. Baker, Klaus Schulten, Dong Zheng, Hai Pang, Fei Sun, (January2013) "Atomic Model of Rabbit Hemorrhagic Disease Virus by Cryo-Electron Microscopy and Crystallography", PLoS Pathogens 9 / 1, e1003132. http://dx.doi.org/10.1371/journal.ppat.1003132
  • Yanxin Liu, Johan Strümpfer, Peter L. Freddolino, Martin Gruebele, Klaus Schulten, (May2012) "Structural Characterization of λ-Repressor Folding from All-Atom Molecular Dynamics Simulations", The Journal of Physical Chemistry Letters 3 / 9, 1117-1123. http://dx.doi.org/10.1021/jz300017c
  • Adarsh D. Radadia, Courtney J. Stavis, Rogan Carr (University of Illinois at Urbana-Champaign), Hongjun Zeng, William P. King, John A. Carlisle, Aleksei Aksimentiev (University of Illinois at Urbana-Champaign), Robert J. Hamers, Rashid Bashir, (2011) "Control of Nanoscale Environment to Improve Stability of Immobilized Proteins on Diamond Surfaces", Advanced Functional Materials 21 / 6, 1040-1050. http://dx.doi.org/10.1002/adfm.201002251