Applications > env

Publications

Users of this package associated the following 37 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), 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
  • 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
  • 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
  • David Wright (University College, London), S. Kashif Sadiq, Gianni De Fabritiis, Peter V. Coveney, (July2012) "Thumbs Down for HIV: Domain Level Rearrangements Do Occur in the NNRTI-Bound HIV-1 Reverse Transcriptase", Journal of the American Chemical Society 134 / 31, 12885-12888. http://dx.doi.org/10.1021/ja301565k
  • 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
  • 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
  • Benjamin A. Hall, David Wright (University College, London), Shantenu Jha, Peter V. Coveney, (August2012) "Quantized Water Access to the HIV-1 Protease Active Site as a Proposed Mechanism for Cooperative Mutations in Drug Affinity", Biochemistry 51 / 33, 6487-6489. http://dx.doi.org/10.1021/bi300432u
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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, 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
  • 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
  • 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
  • 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
  • S. Wan, David Wright (University College, London), P. V. Coveney, (August2012) "Mechanism of Drug Efficacy within the Epidermal Growth Factor Receptor Revealed by Microsecond Molecular Dynamics Simulation", Molecular Cancer Therapeutics undefined / undefined, . http://dx.doi.org/10.1158/1535-7163.MCT-12-0644-T
  • David Wright (University College, London), Benjamin A. Hall, Paul Kellam, Peter V. Coveney, (June2012) "Global Conformational Dynamics of HIV-1 Reverse Transcriptase Bound to Non-Nucleoside Inhibitors", Biology 1 / 2, 222-244. http://dx.doi.org/10.3390/biology1020222
  • 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
  • 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
  • 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
  • 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