Klaus Schulten

Description

Address

  • 3147 Beckman Institute
  • 405 North Mathews Avenue
  • Urbana, Illinois 61801

Biography

Klaus Schulten received his Ph.D. from Harvard University in 1974. He is Swanlund Professor of Physics and is also affiliated with the Department of Chemistry as well as with the Center for Biophysics and Computational Biology. Professor Schulten is a full-time faculty member in the Beckman Institute and directs the Theoretical and Computational Biophysics Group. His professional interests are theoretical physics and theoretical biology. His current research focuses on the structure and function of supramolecular systems in the living cell, and on the development of non-equilibrium statistical mechanical descriptions and efficient computing tools for structural biology.

Honors

University of Illinois Scholar (1996); Fellow of the American Physical Society (1993); Nernst Prize of the Physical Chemistry Society of Germany (1981)

Research

Living systems constitute themselves through self-organized aggregation of their molecular components. Klaus Schulten's research in theoretical and computational biophysics focuses on the formation, structure, and function of the respective biopolymer aggregates, in particular those between oligopeptides forming large bioenergetic proteins, complexes of membranes with proteins, or complexes of DNA with chromosomal and regulatory proteins. The investigations explore the physical mechanisms underlying the transformation of light energy into electrical membrane potentials and the synthesis of ATP in photosynthetic systems, as well as the storage and control of genetic information in all cells.

To address its research problems, the Theoretical and Computational Biophysics Group has integrated its widely distributed molecular graphics package VMD and its simulation package NAMD into a comprehensive tool which permits interactive molecular dynamics to study ligand binding and adhesion forces, as well as the stretching and unfolding of proteins. Moreover, a new collaborative environment for structural biology, BioCoRE, is being developed by the group to enable collaborations within the local facility and across distance regardless of where researchers are located.

The Theoretical and Computational Biophysics Group operates a numerical laboratory with powerful parallel computers and a network of advanced graphics workstations. Furthermore, the group develops a theory of the classical and quantum dynamical motion of biopolymers which utilizes numerical experiments, non-equilibrium statistical mechanics, elasticity theory, and the theory of disordered systems.

The research is supported by NIH, NSF and the Roy J. Carver Charitable Trust.

Publications

  • 2016
    • Goh, B. C.; Perilla, J. R.; Heyrana, K. J.; England, M. R.; Craven, R. C.; Schulten, K., Elucidating the Structure, Dynamics and Functions of an Immature Retrovirus in Atomistic Detail. Biophysical Journal 2016, 110, (3), 383a-383a.
    • Gupta, P.; Liu, B.; Klepacki, D.; Gupta, V.; Schulten, K.; Mankinl, A. S.; Vazquez-Laslop, N., Nascent Peptide Assists the Ribosome in Recognizing Chemically Distinct Small Molecules. Nature Chemical Biology 2016, 12, (3), 153-158, DOI:10.1038/Nchembio.1998.
    • Hardy, D. J.; Wolff, M. A.; Xia, J. L.; Schulten, K.; Skeel, R. D., Multilevel Summation with B-Spline Interpolation for Pairwise Interactions in Molecular Dynamics Simulations. Journal of Chemical Physics 2016, 144, (11), DOI:Artn 114112 10.1063/1.4943868.
    • Heyrana, K. J.; Goh, B. C.; Perilla, J. R.; Nguyen, T. L. N.; England, M. R.; Bewley, M. C.; Schulten, K.; Craven, R. C., Contributions of Charged Residues in Structurally Dynamic Capsid Surface Loops to Rous Sarcoma Virus Assembly. Journal of Virology 2016, 90, (12), 5700-5714, DOI:10.1128/Jvi.00378-16.
    • Islam, S. M.; Florin, G.; Qi, Y.; Shen, R.; Han, W.; Stein, R. A.; Schulten, K.; Mchaourab, H. S.; Im, W.; Roux, B., Structural-Function Study of Membrane Proteins with Restrained-Ensemble and Dummy Spin-Label Molecular Dynamics Simulations. Biophysical Journal 2016, 110, (3), 644a-644a.
    • Islam, S. M.; Florin, G.; Qi, Y.; Shen, R.; Han, W.; Stein, R. A.; Schulten, K.; Mchaourab, H. S.; Im, W.; Roux, B., Structural-Function Study of Membrane Proteins with Restrained-Ensemble and Dummy Spin-Label Molecular Dynamics Simulations. Biophysical Journal 2016, 110, (3), 644a-644a.
    • Lam, K.; Wu, Z.; Schulten, K., Computational Modeling of Sodium Channel Inactivation. Biophysical Journal 2016, 110, (3), 108a-108a.
    • Liu, Y.; Singharoy, A.; Mayne, C. G.; Sengupta, A.; Raghavachari, K.; Schulten, K.; Flood, A. H., Flexibility Coexists with Shape-Persistence in Cyanostar Macrocycles. Journal of the American Chemical Society 2016, 138, (14), 4843-4851, DOI:10.1021/jacs.6b00712.
    • Liu, C.; Perilla, J. R.; Ning, J. Y.; Lu, M. M.; Hou, G. J.; Ramalho, R.; Himes, B. A.; Zhao, G. P.; Bedwell, G. J.; Byeon, I. J.; Ahn, J.; Gronenborn, A. M.; Prevelige, P. E.; Rousso, I.; Aiken, C.; Polenova, T.; Schulten, K.; Zhang, P. J., Cyclophilin a Stabilizes the Hiv-1 Capsid through a Novel Non-Canonical Binding Site. Nature Communications 2016, 7, DOI:ARTN 10714 10.1038/ncomms10714.
    • McGreevy, R.; Teo, I.; Singharoy, A.; Schulten, K., Advances in the Molecular Dynamics Flexible Fitting Method for Cryo-Em Modeling. Methods 2016, 100, 50-60, DOI:10.1016/j.ymeth.2016.01.009.
    • Perilla, J. R.; Hadden, J. A.; Goh, B. C.; Mayne, C. G.; Schulten, K., All-Atom Molecular Dynamics of Virus Capsids as Drug Targets. Journal of Physical Chemistry Letters 2016, 7, (10), 1836-1844, DOI:10.1021/acs.jpclett.6b00517.
    • Qiu, H.; Girdhar, A.; Schulten, K.; Leburton, J. P., Electrically Tunable Quenching of DNA Fluctuations in Biased Solid-State Nanopores. ACS Nano 2016, 10, (4), 4482-4488, DOI:10.1021/acsnano.6b00226.
    • Qiu, H.; Sarathy, A.; Leburton, J. P.; Schulten, K., Stepwise Transport of Stretched Ssdna through Graphene Nanopores. Biophysical Journal 2016, 110, (3), 508a-508a.
    • Radak, B. K.; Singharoy, A.; Schulten, K.; Roux, B., Inclusion of Ph Effects in Molecular Dynamics Simulations of Membranes and Membrane Proteins. Biophysical Journal 2016, 110, (3), 646a-646a.
    • Ribeiro, J. V.; Bernardi, R. C.; Rudack, T.; Stone, J. E.; Phillips, J. C.; Freddolino, P. L.; Schulten, K., Qwikmd - Integrative Molecular Dynamics Toolkit for Novices and Experts. Scientific Reports 2016, 6, DOI:ARTN 26536 10.1038/srep26536.
    • Ribeiro, J. V.; Bernardi, R. C.; Rudack, T.; Schulten, K., Easy and Fast Setup of Molecular Dynamics Simulations: Combining VMD and NAMD for Experimentalists. Biophysical Journal 2016, 110, (3), 641a-641a.
    • Rudack, T.; McGreevy, R.; Siggel, M.; Schulten, K., A Tool to Integrate User Expertise into Building Atomic Level Models for Large Biomolecular Systems. Biophysical Journal 2016, 110, (3), 346a-346a.
    • Sarathy, A.; Qiu, H.; Schulten, K.; Leburton, J. P., Single-Site Resolution Detection of Methylation in DNA with Graphene Nanopores. Biophysical Journal 2016, 110, (3), 654a-654a.
    • Vukovic, L.; Chipot, C.; Makino, D. L.; Conti, E.; Schulten, K., Molecular Mechanism of Processive 3 ' to 5 ' RNA Translocation in the Active Subunit of the RNA Exosome Complex. Journal of the American
    • Shahoei, R.; Trebesch, N.; Singharoy, A.; Schulten, K., Structure and Function of Yidc, an Insertase That Channels Newly Synthesized Proteins into the Cell Membrane. Biophysical Journal 2016, 110, (3), 234a-234a.
    • Wang, Y. H.; Singharoy, A.; Schulten, K.; Tajkhorshid, E., Allosteric Regulation Mechanism of Trimeric Membrane. Biophysical Journal 2016, 110, (3), 383a-383a.
    • Wu, Z.; Schulten, K., Dynamics and Energetics of Snare Zippering in Membrane Fusion. Biophysical Journal 2016, 110, (3), 249a-249a.
    • Zhang, Y.; Schulten, K.; Gruebele, M.; Bansal, P. S.; Wilson, D.; Daly, N. L., Disulfide Bridges: Bringing Together Frustrated Structure in a Bioactive Peptide. Biophysical Journal 2016, 110, (8), 1744-1752, DOI:10.1016/j.bpj.2016.03.027.
    • Zhang, Y.; Bansal, P.; Wilson, D.; Schulten, K.; Daly, N.; Gruebele, M., Disulfide Bridges: Bringing Together Frustrated Structure in a Bioactive Peptide. Biophysical Journal 2016, 110, (3), 210a-210a.
  • 2015
    • Ma, W.; Schulten, K., Mechanism of Substrate Trans Location by a Ring-Shaped ATPase Motor at Millisecond Resolution. Journal of the American Chemical Society 2015, 137, (8), 3031-3040, DOI: 10.1021/Ja512605w.

    • Landry, M. P.; Vukovic, L.; Kruss, S.; Bisker, G.; Landry, A. M.; Islam, S.; Jain, R.; Schulten, K.; Strano, M. S., Comparative Dynamics and Sequence Dependence of DNA and RNA Binding to Single Walled Carbon Nanotubes. Journal of Physical Chemistry C 2015, 119, (18), 10048-10058, DOI: 10.1021/Jp511448e.

    • Hardy, D. J.; Wu, Z.; Phillips, J. C.; Stone, J. E.; Skeel, R. D.; Schulten, K., Multilevel Summation Method for Electrostatic Force Evaluation. Journal of Chemical Theory and Computation 2015, 11, (2), 766-779, DOI: 10.1021/Ct5009075.

    • Girdhar, A.; Sathe, C.; Schulten, K.; Leburton, J. P., Tunable Graphene Quantum Point Contact Transistor for DNA Detection and Characterization. Nanotechnology 2015, 26, (13), DOI:Artn 134005 DOI:10.1088/0957-4484/26/13/134005.

    • Fraiberg, M.; Afanzar, O.; Cassidy, C. K.; Gabashvili, A.; Schulten, K.; Levin, Y.; Eisenbach, M., Chey's Acetylation Sites Responsible for Generating Clockwise Flagellar Rotation in Escherichia Coli. Molecular Microbiology 2015, 95, (2), 231-244, DOI: 10.1111/Mmi.12858.

    • Englander, M. T.; Avins, J. L.; Fleisher, R. C.; Liu, B.; Effraim, P. R.; Wang, J.; Schulten, K.; Leyh, T. S.; Gonzalez, R. L.; Cornish, V. W., The Ribosome Can Discriminate the Chirality of Amino Acids within Its Peptidyl-Transferase Center. Proceedings of the National Academy of Sciences of the United States of America 2015, 112, (19), 6038-6043, DOI: 10.1073/pnas.1424712112.

    • Bernardi, R. C.; Melo, M. C. R.; Schulten, K., Enhanced Sampling Techniques in Molecular Dynamics Simulations of Biological Systems. Biochimica Et Biophysica Acta-General Subjects 2015, 1850, (5), 872-877, DOI: 10.1016/j.bbagen.2014.10.019.

    • Barragan, A. M.; Crofts, A. R.; Schulten, K.; Solov'yov, I. A., Identification of Ubiquinol Binding Motifs at the Q(O)-Site of the Cytochrome Bc(1) Complex. Journal of Physical Chemistry B 2015, 119, (2), 433-447, DOI: 10.1021/Jp510022w.

    • Aghtar, M.; Strumpfer, J.; Schulten, K.; Kleinekathofer, U., Environmental Coupling and Population Dynamics in the Pe545 Light­Harvesting Complex. Biophysical Journal 2015, 108, (2), 604a­605a.
    • Barragan, A. M.; Crofts, A.; Schulten, K.; Solov'yov, I., Molecular Aspects of the Q­Cycle: Quinol Binding and Proton­Coupled Electron Transfer. Febs Journal 2015, 282, 404­404.
    • Barragan, A. M.; Singharoy, A.; Crofts, A. R.; Schulten, K.; Solov'yov, I. A., New Perspectives on Quinol Binding Motifs at the BC1 Complex Based on Md Simulations. Biophysical Journal 2015, 108, (2), 602a-603a.
    • Cassidy, C. K.; Himes, B. A.; Alvarez, F. J.; Ma, J.; Zhao, G. P.; Perilla, J. R.; Schulten, K.; Zhang, P. J., Cryoem and Computer Simulations Reveal a Novel Kinase Conformational Switch in Bacterial Chemotaxis Signaling. Elife 2015, 4, DOI:ARTN e08419 10.7554/eLife.08419.
    • Cassidy, C. K.; Himes, B.; Alvarez, F. J. D.; Perilla, J. R.; Ma, J.; Zhao, G. P.; Zhang, P. J.; Schulten, K., Molecular Insights into the Signaling Mechanism of the Histidine Kinase Chea within an Intact Bacterial Chemosensory Array. Biophysical Journal 2015, 108, (2), 317a-317a.
    • Girdhar, A.; Sathe, C.; Schulten, K.; Leburton, J. P., Tunable Graphene Quantum Point Contact Transistor for DNA Detection and Characterization. Nanotechnology 2015, 26, (13), DOI:Artn 134005 10.1088/0957-4484/26/13/134005.
    • Goh, B. C.; Perilla, J. R.; England, M. R.; Heyrana, K. J.; Craven, R. C.; Schulten, K., Atomic Modeling of an Immature Retroviral Lattice using Molecular Dynamics and Mutagenesis. Structure 2015, 23, (8), 1414-1425, DOI:10.1016/j.str.2015.05.017.
    • Goh, B. C.; Rynkiewicz, M. J.; McCormack, F. X.; Seaton, B. A.; Schulten, K., Unraveling the Dual Role of Surfactant Protein a at Atomistic Detail. Biophysical Journal 2015, 108, (2), 255a-256a.
    • Han, W.; Schulten, K., New Insight into Amyloid-Beta Fibril Growth and Its Inhibition: Kinetic Network Analysis of Multi-Scale Molecular Dynamics Simulations. Biophysical Journal 2015, 108, (2), 495a-496a.
    • Himes, B. A.; Cassidy, C. K.; Ma, J.; Alvarez, F. J. D.; Perilla, J. R.; Zhao, G. P.; Schulten, K.; Zhang, P. J., Cryo-Electron Tomography and Computer Simulations Reveal Distinct Chea Kinase Conformation in Bacterial Chemotaxis Signaling Receptor Complex. Biophysical Journal 2015, 108, (2), 418a-418a.
    • Lam, K.; Wu, Z.; Schulten, K., Molecular Basis of Neuronal Signaling. Biophysical Journal 2015, 108, (2), 151a-151a.
    • Lesieur, C.; Schulten, K., Editorial Overview: Theory and Simulation. Current Opinion in Structural Biology 2015, 31, V-VI, DOI:10.1016/j.sbi.2015.05.008.
    • Lu, M. M.; Hou, G. J.; Zhang, H. L.; Suiter, C. L.; Ahn, J.; Byeon, I. J. L.; Perilla, J. R.; Langmead, C. J.; Hung, I.; Gor'kov, P. L.; Gan, Z. H.; Brey, W.; Aiken, C.; Zhang, P. J.; Schulten, K.; Gronenborn, A. M.; Polenova, T., Dynamic Allostery Governs Cyclophilin a-HIV Capsid Interplay. Proceedings of the National Academy of Sciences of the United States of America 2015, 112, (47), 14617-14622, DOI:10.1073/pnas.1516920112.
    • Ma, W.; Schulten, K., RNA Translocation Coupled to Large-Scale Conformational Transitions of a Hexameric Helicase. Biophysical Journal 2015, 108, (2), 212a-212a.
    • Misra, S. K.; Ghoshal, G.; Gartia, M. R.; Wu, Z.; De, A. K.; Ye, M.; Bromfield, C. R.; Williams, E. M.; Singh, K.; Tangella, K. V.; Rund, L.; Schulten, K.; Schook, L. B.; Ray, P. S.; Burdette, E. C.; Pan, D., Trimodal Therapy: Combining Hyperthermia with Repurposed Bexarotene and Ultrasound for Treating Liver Cancer. ACS Nano 2015, 9, (11), 10695-10718, DOI:10.1021/acsnano.5b05974.
    • Perilla, J. R.; Goh, B. C.; Cassidy, C. K.; Liu, B.; Bernardi, R. C.; Rudack, T.; Yu, H.; Wu, Z.; Schulten, K., Molecular Dynamics Simulations of Large Macromolecular Complexes. Current Opinion in Structural Biology 2015, 31, 64-74, DOI:10.1016/j.sbi.2015.03.007.
    • Perilla, J. R.; Schulten, K., Atomistic Characterization of the HIV Capsid from Molecular Dynamics Simulations. Biophysical Journal 2015, 108, (2), 209a-209a.
    • Qiu, H.; Sarathy, A.; Leburton, J. P.; Schulten, K., Intrinsic Stepwise Translocation of Stretched Ssdna in Graphene Nanopores. Nano Letters 2015, 15, (12), 8322-8330, DOI:10.1021/acs.nanolett.5b03963.
    • Rudack, T.; Zhang, Y.; Vucovic, L.; Han, W.; Schulten, K., Computational Study of Ubiquitin Recruitment and Transport of the 26s Proteasome. Biophysical Journal 2015, 108, (2), 318a-318a.
    • Schoeler, C.; Bernardi, R. C.; Malinowska, K. H.; Durner, E.; Ott, W.; Bayer, E. A.; Schulten, K.; Nash, M. A.; Gaub, H. E., Mapping Mechanical Force Propagation through Biomolecular Complexes. Nano Letters 2015, 15, (11), 7370-7376, DOI:10.1021/acs.nanolett.5b02727.
    • Schulten, K., Discoveries in Biophysics through the Computational Microscope. Biophysical Journal 2015, 108, (2), 209a-209a.
    • Shen, R.; Han, W.; Fiorin, G.; Islam, S. M.; Schulten, K.; Roux, B., Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-Interacting Molecular Fragments. Plos Computational Biology 2015, 11, (10), DOI:ARTN e1004368 10.1371/journal.pcbi.1004368.
    • Singharoy, A.; Wickles, S.; Beckmann, R.; Schulten, K., A Structural Model of the Ribosome-Bound Protein Insertase Yidc Reveals Lateral Translocation of the Nascent Chain. Biophysical Journal 2015, 108, (2), 390a-390a.
    • Singharoy, A.; Chandler, D.; Durrant, J.; Sener, M.; Amaro, R.; Schulten, K., The Do's and Do Not's of a 100 Million Atom Molecular Dynamics Simulation. Biophysical Journal 2015, 108, (2), 158a-158a.
    • Singharoy, A.; Schulten, K., Towards the Simulation of a Complete ATP Synthase: Unravelling the Structural Basis of the Enzyme's Reversible Action. Biophysical Journal 2015, 108, (2), 319a-319a.
    • Sinigharoy, A.; Venkatakrishnan, B.; Liu, Y.; Mayne, C. G.; Lee, S.; Chen, C. H.; Zlotnick, A.; Schulten, K.; Flood, A. H., Macromolecular Crystallography for Synthetic Abiological Molecules: Combining Xmdff and Phenix for Structure Determination of Cyanostar Macrocycles. Journal of the American Chemical Society 2015, 137, (27), 8810-8818, DOI:10.1021/jacs.5b04407.
    • Vukovic, L.; Makino, D. L.; Chipot, C.; Conti, E.; Schulten, K., Molecular Mechanism of Processive 3 ' to 5 ' RNA Translocation in the RNA Exosome Complex. Biophysical Journal 2015, 108, (2), 400a-400a.
    • Wang, X. L.; Vukovic, L.; Koh, H. R.; Schulten, K.; Myong, S., Dynamic Profiling of Double-Stranded RNA Binding Proteins. Nucleic Acids Research 2015, 43, (15), 7566-7576, DOI:10.1093/nar/gkv726.
    • Wirth, A. J.; Liu, Y. X.; Prigozhin, M. B.; Schulten, K.; Gruebele, M., Comparing Fast Pressure Jump and Temperature Jump Protein Folding Experiments and Simulations. Journal of the American Chemical Society 2015, 137, (22), 7152-7159, DOI:10.1021/jacs.5b02474.
    • Wu, Z.; Hardy, D. J.; Phillips, J. C.; Stone, J. E.; Skeel, R. D.; Schulten, K., Multilevel Summation Method for Electrostatic Force Evaluation. Biophysical Journal 2015, 108, (2), 183a-183a.
    • Wu, Z.; Yu, H.; Arkhipov, A.; Yin, Y.; Schulten, K., How Synaptotagmin I, N-Bar and F-Bar Domains Generate Membrane Curvature. Biophysical Journal 2015, 108, (2), 555a-555a.
    • Yu, H.; Han, W.; Ma, W.; Schulten, K., Transient Beta-Hairpin Formation in Alpha-Synuclein Monomer Revealed by Coarse-Grained Molecular Dynamics Simulation. Journal of Chemical Physics 2015, 143, (24), DOI:Artn 243142 10.1063/1.4936910.
    • Zhang, P. J.; Liu, C.; Perilla, J. R.; Byeon, I. J.; Ning, J. Y.; Ahn, J.; Aiken, C.; Gronenborn, A. M.; Polenova, T.; Schulten, K., Cyclophilin a Stabilizes the Mature HIV-1 Capsid through a Novel Non-Canonical Binding Site. Biophysical Journal 2015, 108, (2), 190a-190a.
  • 2014
    • Chandler, D. E.; Strumpfer, J.; Sener, M.; Scheuring, S.; Schulten, K., Light Harvesting by Lamellar Chromatophores in Rhodospirillum Photometricum. Biophysical Journal 2014, 106, (11), 2503-2510.

    • Comer, J.; Schulten, K.; Chipot, C., Calculation of Lipid-Bilayer Permeabilities Using an Average Force. Journal of Chemical Theory and Computation 2014, 10, (2), 554-564, DOI: 10.1021/ct400925s.

    • Gamini, R.; Han, W.; Stone, J. E.; Schulten, K., Assembly of Nsp1 Nucleoporins Provides Insight into Nuclear Pore Complex Gating. Plos Computational Biology 2014, 10, e1003488.

    • Jiang, W.; Phillips, J. C.; Huang, L.; Fajer, M.; Meng, Y. L.; Gumbart, J. C.; Luo, Y.; Schulten, K.; Roux, B., Generalized Scalable Multiple Copy Algorithms for Molecular Dynamics Simulations in Namd. Computer Physics Communications 2014, 185, (3), 908-916, DOI: 10.1016/j.cpc.2013.12.014.

    • Li, Q. F.; Wanderling, S.; Paduch, M.; Medovoy, D.; Singharoy, A.; McGreevy, R.; Villalba-Galea, C. A.; Hulse, R. E.; Roux, B.; Schulten, K.; Kossiakoff, A.; Perozo, E., Structural Mechanism of Voltage-Dependent Gating in an Isolated Voltage-Sensing Domain. Nature Structural & Molecular Biology 2014, 21, (3), 244-252, DOI: 10.1038/nsmb.2768.

    • Liu, Y. X.; Prigozhin, M. B.; Schulten, K.; Gruebele, M., Observation of Complete Pressure-Jump Protein Refolding in Molecular Dynamics Simulation and Experiment. Journal of the American Chemical Society 2014, 136, (11), 4265-4272, DOI: 10.1021/ja412639u.

    • Qi, Y. F.; Cheng, X.; Han, W.; Jo, S.; Schulten, K.; Im, W., Charmm-Gui Pace Cg Builder for Solution, Micelle, and Bilayer Coarse-Grained Simulations. Journal of Chemical Information and Modeling 2014, 54, (3), 1003-1009, DOI: 10.1021/ci500007n.

    • Solov'yov, I. A.; Domratcheva, T.; Schulten, K., Separation of Photo-Induced Radical Pair in Cryptochrome to a Functionally Critical Distance. Scientific Reports 2014, 4, DOI: 10.1038/srep03845.

    • Wang, Y.; Liu, Y. X.; DeBerg, H. A.; Nomura, T.; Hoffman, M. T.; Rohde, P. R.; Schulten, K.; Martinac, B.; Selvin, P. R., Single Molecule Fret Reveals Pore Size and Opening Mechanism of a Mechano-Sensitive Ion Channel. Elife 2014, 3, DOI: 10.7554/eLife.01834.

    • Zhou, Q. J.; Li, J. M.; Yu, H.; Zhai, Y. J.; Gao, Z.; Liu, Y. X.; Pang, X. Y.; Zhang, L. F.; Schulten, K.; Sun, F.; Chen, C., Molecular Insights into the Membrane-Associated Phosphatidylinositol 4-Kinase Ii Alpha. Nature Communications 2014, 5, DOI: 10.1038/ncomms4552.

    • Wu, Z.; Schulten, K., Synaptotagmin's Role in Neurotransmitter Release Likely Involves Ca2+-Induced Conformational Transition. Biophysical Journal 2014, 107, (5), 1156-1166, DOI: 10.1016/j.bpj.2014.07.041

    • Wickles, S.; Singharoy, A.; Andreani, J.; Seemayer, S.; Bischoff, L.; Berninghausen, O.; Soeding, J.; Schulten, K.; van der Sluis, E. O.; Beckmann, R., A Structural Model of the Active Ribosome-Bound Membrane Protein Insertase YidC. Elife 2014, 3, DOI:ARTN e03035 DOI 10.7554/eLife.03035.

    • Stone, J. E.; McGreevy, R.; Isralewitz, B.; Schulten, K., Gpu-Accelerated Analysis and Visualization of Large Structures Solved by Molecular Dynamics Flexible Fitting. Faraday Discussions 2014, 169, 265-283, DOI: 10.1039/C4fd00005f.

    • Stone, J. E.; Isralewitz, B.; Schulten, K., Early Experiences Scaling VMD Molecular Visualization and Analysis Jobs on Blue Waters. 2013 Extreme Scaling Workshop (Xsw 2013) 2014 43-50, DOI: 10.1109/Xsw.2013.10.

    • Sothiselvam, S.; Liu, B.; Han, W.; Ramu, H.; Klepacki, D.; Atkinson, G. C.; Brauer, A.; Remm, M.; Tenson, T.; Schulten, K.; Vazquez-Laslop, N.; Mankin, A. S., Macrolide Antibiotics Allosterically Predispose the Ribosome for Translation Arrest. Proceedings of the National Academy of Sciences of the United States of America 2014, 111, (27), 9804-9809, DOI: 10.1073/pnas.1403586111.

    • Solov'yov, I. A.; Ritz, T.; Schulten, K.; Hore, P. J., A Chemical Compass for Bird Navigation. Quantum Effects in Biology 2014 218-236, DOI:Book_Doi 10.1017/Cbo9780511863189.

    • Schulten, K.; Hayashi, S., Quantum Biology of Retinal. Quantum Effects in Biology 2014 237-263, DOI:Book_Doi 10.1017/Cbo9780511863189.

    • Schoeler, C.; Malinowska, K. H.; Bernardi, R. C.; Milles, L. F.; Jobst, M. A.; Durner, E.; Ott, W.; Fried, D. B.; Bayer, E. A.; Schulten, K.; Gaub, H. E.; Nash, M. A., Ultrastable Cellulosome-Adhesion Complex Tightens under Load. Nature Communications 2014, 5, DOI:Artn 5635 DOI:10.1038/Ncomms6635.

    • Sathe, C.; Girdhar, A.; Leburton, J. P.; Schulten, K., Electronic Detection of dsDNA Transition from Helical to Zipper Conformation Using Graphene Nanopores. Nanotechnology 2014, 25, (44), DOI:Artn 445105 DOI:10.1088/0957-4484/25/44/445105.

    • McGreevy, R.; Singharoy, A.; Li, Q. F.; Zhang, J. F.; Xu, D.; Perozo, E.; Schulten, K., Xmdff: Molecular Dynamics Flexible Fitting of Low-Resolution X-Ray Structures. Acta Crystallographica Section D-Biological Crystallography 2014, 70, 2344-2355, DOI: 10.1107/S1399004714013856.

    • Kosztin, I.; Schulten, K., Structure, Function, and Quantum Dynamics of Pigment-Protein Complexes. Quantum Effects in Biology 2014 123-143, DOI:Book_DOI:10.1017/Cbo9780511863189.

    • Han, W.; Schulten, K., Fibril Elongation by a Beta(17-42): Kinetic Network Analysis of Hybrid-Resolution Molecular Dynamics Simulations. Journal of the American Chemical Society 2014, 136, (35), 12450-12460, DOI: 10.1021/Ja507002p.

    • Girdhar, A.; Sathe, C.; Schulten, K.; Leburton, J. P., Gate-Modulated Graphene Quantum Point Contact Device for DNA Sensing. Journal of Computational Electronics 2014, 13, (4), 839-846, DOI: 10.1007/s10825-014-0596-6.

    • Comer, J.; Schulten, K.; Chipot, C., Diffusive Models of Membrane Permeation with Explicit Orientational Freedom. Journal of Chemical Theory and Computation 2014, 10, (7), 2710-2718, DOI: 10.1021/Ct500209j.

    • Comer, J.; Phillips, J. C.; Schulten, K.; Chipot, C., Multiple-Replica Strategies for Free-Energy Calculations in NAMD: Multiple-Walker Adaptive Biasing Force and Walker Selection Rules. Journal of Chemical Theory and Computation 2014, 10, (12), 5276-5285, DOI: 10.1021/Ct500874p.

    • Cartron, M. L.; Olsen, J. D.; Sener, M.; Jackson, P. J.; Brindley, A. A.; Qian, P.; Dickman, M. J.; Leggett, G. J.; Schulten, K.; Hunter, C. N., Integration of Energy and Electron Transfer Processes in the Photosynthetic Membrane of Rhodobacter Sphaeroides. Biochimica Et Biophysica Acta-Bioenergetics 2014, 1837, (10), 1769-1780, DOI: 10.1016/j.bbabio.2014.02.003.

    • Cai, E.; Ge, P. H.; Lee, S. H.; Jeyifous, O.; Wang, Y.; Liu, Y. X.; Wilson, K. M.; Lim, S. J.; Baird, M. A.; Stone, J. E.; Lee, K. Y.; Davidson, M. W.; Chung, H. J.; Schulten, K.; Smith, A. M.; Green, W. N.; Selvin, P. R., Stable Small Quantum Dots for Synaptic Receptor Tracking on Live Neurons. Angewandte Chemie-International Edition 2014, 53, (46), 12484-12488, DOI: 10.1002/anie.201405735.

    • Blanchard, A. E.; Arcario, M. J.; Schulten, K.; Tajkhorshid, E., A Highly Tilted Membrane Configuration for the Prefusion State of Synaptobrevin. Biophysical Journal 2014, 107, (9), 2112-2121, DOI: 10.1016/j.bpj.2014.09.013.

    • Aghtar, M.; Strumpfer, J.; Olbrich, C.; Schulten, K.; Kleinekathofer, U., Different Types of Vibrations Interacting with Electronic Excitations in Phycoerythrin 545 and Fenna-Matthews-Olson Antenna Systems. Journal of Physical Chemistry Letters 2014, 5, (18), 3131-3137, DOI: 10.1021/Jz501351p.

  • 2013
    • Lai, Y.; Diao, J. J.; Liu, Y. X.; Ishitsuka, Y.; Su, Z. L.; Schulten, K.; Ha, T.; Shin, Y. K., Fusion Pore Formation and Expansion Induced by Ca2+ and Synaptotagmin 1. Proceedings of the National Academy of Sciences of the United States of America , 2013 110, (4), 1333-1338.

    • Aghtar, M.; Strumpfer, J.; Othrich, C.; Schulten, K.; Kleinekathofer, U., The FMO Complex in a Glycerol-Water Mixture. Journal of Physical Chemistry B 2013, 117, (24), 7157-7163, DOI: 10.1021/jp311380k.

    • Crofts, A. R.; Hong, S. J.; Wilson, C.; Burton, R.; Victoria, D.; Harrison, C.; Schulten, K., The Mechanism of Ubihydroquinone Oxidation at the Q0-Site of the Cytochrome bc1 Complex. Biochimica Et Biophysica Acta-Bioenergetics 2013, 1827, (11-12), 1362-1377, DOI: 10.1016/j.bbabio.2013.01.009.

    • Freddolino, P. L.; Gardner, K. H.; Schulten, K., Signaling Mechanisms of Lov Domains: New Insights from Molecular Dynamics Studies. Photochemical & Photobiological Sciences 2013, 12, (7), 1158-1170, DOI: 10.1039/c3pp25400c.

    • Girdhar, A.; Sathe, C.; Schulten, K.; Leburton, J. P., Graphene Quantum Point Contact Transistor for DNA Sensing. Proceedings of the National Academy of Sciences of the United States of America 2013, 110, (42), 16748-16753, DOI: 10.1073/pnas.1308885110.

    • Goh, B. C.; Rynkiewicz, M. J.; Cafarella, T. R.; White, M. R.; Hartshorn, K. L.; Allen, K.; Crouch, E. C.; Calin, O.; Seeberger, P. H.; Schulten, K.; Seaton, B. A., Molecular Mechanisms of Inhibition of Influenza by Surfactant Protein D Revealed by Large-Scale Molecular Dynamics Simulation. Biochemistry 2013, 52, (47), 8527-8538, DOI: 10.1021/bi4010683.

    • Gumbart, J. C.; Teo, I.; Roux, B.; Schulten, K., Reconciling the Roles of Kinetic and Thermodynamic Factors in Membrane-Protein Insertion. Journal of the American Chemical Society 2013, 135, (6), 2291-2297.

    • Han, W.; Schulten, K., Characterization of Folding Mechanisms of Trp-Cage and WW-Domain by Network Analysis of Simulations with a Hybrid-Resolution Model. Journal of Physical Chemistry B 2013, 117, (42), 13367-13377, DOI: 10.1021/jp404331d.

    • Landry, M. P.; Zou, X. Q.; Wang, L.; Huang, W. M.; Schulten, K.; Chemla, Y. R., DNA Target Sequence Identification Mechanism for Dimer-Active Protein Complexes. Nucleic Acids Research 2013, 41, (4), 2416-2427.

    • Li, W.; Atkinson, G. C.; Thakor, N. S.; Allas, U.; Lu, C. C.; Chan, K. Y.; Tenson, T.; Schulten, K.; Wilson, K. S.; Hauryliuk, V.; Frank, J., Mechanism of Tetracycline Resistance by Ribosomal Protection Protein Tet(O). Nature Communications 2013, 4.

    • Mayne, C. G.; Saam, J.; Schulten, K.; Tajkhorshid, E.; Gumbart, J. C., Rapid Parameterization of Small Molecules Using the Force Field Toolkit. Journal of Computational Chemistry 2013, 34, (32), 2757-2770, DOI: 10.1002/jcc.23422.

    • Prigozhin, M. B.; Liu, Y. X.; Wirth, A. J.; Kapoor, S.; Winter, R.; Schulten, K.; Gruebele, M., Misplaced Helix Slows Down Ultrafast Pressure-Jump Protein Folding. Proceedings of the National Academy of Sciences of the United States of America 2013, 110, (20), 8087-8092, DOI: 10.1073/pnas.1219163110.

    • Severin, P. M. D.; Zou, X. Q.; Schulten, K.; Gaub, H. E., Effects of Cytosine Hydroxymethylation on DNA Strand Separation. Biophysical Journal 2013, 104, (1), 208-215.

    • Shim, J.; Humphreys, G. I.; Venkatesan, B. M.; Munz, J. M.; Zou, X. Q.; Sathe, C.; Schulten, K.; Kosari, F.; Nardulli, A. M.; Vasmatzis, G.; Bashir, R., Detection and Quantification of Methylation in DNA Using Solid-State Nanopores. Scientific Reports 2013, 3.

    • Solov'yov, I. A.; Chang, P.; Schulten, K., Vibrationally Assisted Electron Transfer Mechanism of Olfaction: Myth or Reality? Physical Chemistry - Chemical Physics 2013, 14, 1386-1387.

    • Stone, J. E.; Isralewitz, B.; Schulten, K. Early Experiences Scaling VMD Molecular Visualization and Analysis Jobs on Blue Waters, Proceedings of the XSEDE Extreme Scaling Workshop,  Boulder, CO, August 2013.

    • Stone, J. E.; Vandivort, K. L.; Schulten, K. Gpu-Accelerated Molecular Visualization on Petascale Supercomputing Platforms, Proceedings of the 8th International Workshop on Ultrascale Visualization, UltraVis '13,  Denver, CO, Nov 17, 2013, Vol. 6, 1-8.

    • Teo, I.; Schulten, K., A Computational Kinetic Model of Diffusion for Molecular Systems. Journal of Chemical Physics 2013, 139, (12), DOI: 10.1063/1.4820876.

    • Vukovic, L.; Koh, H. R.; Myong, S.; Schulten, K., Substrate Recognition and Specificity of Double-Stranded RNA Binding Proteins. Biochemistry 2013, 53, (21), 3457-3466.

    • Wang, X.; Xu, F. T.; Liu, J. S.; Gao, B. Q.; Liu, Y. X.; Zhai, Y. J.; Ma, J.; Zhang, K.; Baker, T. S.; Schulten, K.; Zheng, D.; Pang, H.; Sun, F., Atomic Model of Rabbit Hemorrhagic Disease Virus by Cryo-Electron Microscopy and Crystallography. Plos Pathogens 2013, 9, (1).

    • Yu, H.; Schulten, K., Membrane Sculpting by F-Bar Domains Studied by Molecular Dynamics Simulations. Plos Computational Biology 2013, 9, (1).

    • Zhang, K.; Wang, L.; Liu, Y. X.; Chan, K. Y.; Pang, X. Y.; Schulten, K.; Dong, Z. Y.; Sun, F., Flexible Interwoven Termini Determine the Thermal Stability of Thermosomes. Protein & Cell 2013, 4, (6), 432-444, DOI: 10.1007/s13238-013-3026-9.

    • Zhao, G. P.; Perilla, J. R.; Yufenyuy, E. L.; Meng, X.; Chen, B.; Ning, J. Y.; Ahn, J.; Gronenborn, A. M.; Schulten, K.; Aiken, C.; Zhang, P. J., Mature HIV-1 Capsid Structure by Cryo-Electron Microscopy and All-Atom Molecular Dynamics. Nature 2013, 497, (7451), 643-646, DOI: 10.1038/nature12162.

  • 2012
    • Chan, K. Y.; Trabuco, L. G.; Schreiner, E.; Schulten, K., Cryo-Em Modeling by the Molecular Dynamics Flexible Fitting Method. Biopolymers 2012, 97, 678-686.

    • Khalili-Araghi, F.; Tajkhorshid, E.; Roux, B.; Schulten, K., Molecular Dynamics Investigation of the Omega-Current in the Kv1.2 Voltage Sensor Domains. Biophysical Journal 2012, 102, (2), 258-267.

    • Lee, W.; Strümpfer, J.; Bennett, V.; Schulten, K.; Marszalek, P. E., Mutation of Conserved Histidines Alters the Tertiary Structure and Nanomechanics of Consensus Ankyrin Repeats. Journal of Biological Chemistry 2012, 287, 19115-19121.

    • Liu, Y. X.; Strumpfer, J.; Freddolino, P. L.; Gruebele, M.; Schulten, K., Structural Characterization of Lambda-Repressor Folding from All-Atom Molecular Dynamics Simulations. Journal of Physical Chemistry Letters 2012, 3, (9), 1117-1123.

    • Solov'yov, I. A.; Schulten, K., Reaction Kinetics and Mechanism of Magnetic Field Effects in Cryptochrome. Journal of Physical Chemistry B 2012, 116, (3), 1089-1099.

    • Strumpfer, J.; Sener, M.; Schulten, K., How Quantum Coherence Assists Photosynthetic Light-Harvesting. Journal of Physical Chemistry Letters 2012, 3, (4), 536-542.

    • Zou, X. Q.; Ma, W.; Solov'yov, I. A.; Chipot, C.; Schulten, K., Recognition of Methylated DNA through Methyl-Cpg Binding Domain Proteins. Nucleic Acids Research 2012, 40, (6), 2747-2758.

    • Chen, Y.; Cruz-Chu, E. R.; Woodard, J. C.; Gartia, M. R.; Schulten, K.; Liu, L., Electrically Induced Conformational Change of Peptides on Metallic Nanosurfaces. ACS Nano 2012, 6, (10), 8847-8856.

    • Gumbart, J.; Schreiner, E.; Wilson, D. N.; Beckmann, R.; Schulten, K., Mechanisms of SecM-Mediated Stalling in the Ribosome. Biophysical Journal 2012, 103, (2), 331-341.

    • Han, W.; Schulten, K., Further Optimization of a Hybrid United-Atom and Coarse-Grained Force Field for Folding Simulations: Improved Backbone Hydration and Interactions between Charged Side Chains. Journal of Chemical Theory and Computation 2012, 8, (11), 4413-4424.

    • Solov'yov, I. A.; Domratcheva, T.; Shahi, A. R. M.; Schulten, K., Decrypting Cryptochrome: Revealing the Molecular Identity of the Photoactivation Reaction. Journal of the American Chemical Society 2012, 134, (43), 18046-18052.

    • Strumpfer, J.; Schulten, K., Excited State Dynamics in Photosynthetic Reaction Center and Light Harvesting Complex 1. Journal of Chemical Physics 2012, 137, (6).

    • Vargas, E.; Yarov-Yarovoy, V.; Khalili-Araghi, F.; Catterall, W. A.; Klein, M. L.; Tarek, M.; Lindahl, E.; Schulten, K.; Perozo, E.; Bezanilla, F.; Roux, B., An Emerging Consensus on Voltage-Dependent Gating from Computational Modeling and Molecular Dynamics Simulations. Journal of General Physiology 2012, 140, (6), 587-594.

    • Vergara-Jaque, A.; Poblete, H.; Lee, E. H.; Schulten, K.; Gonzalez-Nilo, F.; Chipot, C., Molecular Basis of Drug Resistance in A/H1N1 Virus. Journal of Chemical Information and Modeling 2012, 52, (10), 2650-2656.

    • von Castelmur, E.; Struempfer, J.; Franke, B.; Bogomolovas, J.; Barbieri, S.; Qadota, H.; Konarev, P. V.; Svergun, D. I.; Labeit, S.; Benian, G. M.; Schulten, K.; Mayans, O., Identification of an N-Terminal Inhibitory Extension as the Primary Mechanosensory Regulator of Twitchin Kinase. Proceedings of the National Academy of Sciences of the United States of America 2012, 109, (34), 13608-13613.

    • Aghtar, M.; Liebers, J.; Strümpfer, J.; Schulten, K.; Kleinekathöfer, U., Juxtaposing Density Matrix and Classical Path-Based Wave Packet Dynamics. Journal of Chemical Physics 2012, 136, 214101.

    • Agirrezabala, X.; Liao, H. Y.; Schreiner, E.; Fu, J.; Ortiz-Meoz, R. F.; Schulten, K.; Green, R.; Frank, J., Structural Characterization of mRNA-tRNA Translocation Intermediates. Proceedings of the National Academy of Sciences of the United States of America 2012, 109, (16), 6094-6099.

  • 2011
    • Chan, K. Y.; Gumbart, J.; McGreevy, R.; Watermeyer, J. M.; Sewell, B. T.; Schulten, K., Symmetry-Restrained Flexible Fitting for Symmetric EM Maps. Structure 2011, 19, (9), 1211-1218.

    • Trabuco, L. G.; SchreineR, E.; Gumbart, J.; Hsin, J.; Villa, E.; Schulten, K., Applications of the molecular dynamics flexible fitting method. Journal of Structural Biology 2011, 173, (3), 420-427. 

    • Wang, Y.; Harrison, C. B.; Schulten, K.; McCammon, J. A., Implementation of accelerated molecular dynamics in NAMD. Computer Science Discovery 2011, 4, 015002 (11 pages). 

    • Str¨umpfer, J.; Hsin, J.; Sener, M.; Chandler, D.; Schulten, K., Introduction to a quantum biological device, the light harvesting apparatus in purple photosynthetic bacteria. In Molecular Machines, Roux, B., Ed. World Scientific Press: 2011; Vol. 2, pp 19-48. 

    • Strumpfer, J.; Schulten, K., The effect of correlated bath fluctuations on exciton transfer. Journal of Chemical Physics 2011, 134, (9). 

    • Tanner, D. E.; Ma, W.; Chen, Z.; Schulten, K., Theoretical and computational investigation of flagellin translocation and bacterial flagellum growth. Biophysical Journal 2011, 100, 2548-2556. 

    • Li, W.; Trabuco, L. G.; Schulten, K.; Frank, J., Molecular dynamics of EF-G during translocation. Proteins-Structure Function and Bioinformatics 2011, 79, (5), 1478-1486.

    • Olbrich, C.; Strumpfer, J.; Schulten, K.; Kleinekathofer, U., Quest for Spatially Correlated Fluctuations in the FMO Light-Harvesting Complex. Journal of Physical Chemistry B 2011, 115, (4), 758-764.

    • Sener, M.; Strumpfer, J.; Hsin, J.; Chandler, D.; Scheuring, S.; Hunter, C. N.; Schulten, K., Forster Energy Transfer Theory as Reflected in the Structures of Photosynthetic Light-Harvesting Systems. Chemphyschem 2011, 12, (3), 518-531. 

    • Song, S. H.; Freddolino, P. L.; Nash, A. I.; Carroll, E. C.; Schulten, K.; Gardner, K. H.; Larsen, D. S., Modulating LOV Domain Photodynamics with a Residue Alteration outside the Chromophore Binding Site. Biochemistry 2011, 50, (13), 2411-2423. 

    • Stone, J. E.; Hardy, D. J.; Isralwitz, B.; Schulten, K., GPU algorithms for molecular modeling. In Scientific Computing with Multicore and Accelerators, Dongarra, J.; Bader, D. A.; Kurzak, J., Eds. Chapman & Hall/CRC Press: 2011; Vol. 16, pp 351-371. 

    • Stone, J. E.; Hardy, D. J.; Saam, J.; Vandivort, K. L.; Schulten, K., GPU-accelerated computation and interactive display of molecular orbitals. In GPU Computing Gems, Hwu, W., Ed. Morgan Kaufmann Publishers: 2011; Vol. 1, pp 5-18. 

    • Agirrezabala, X.; Schreiner, E.; Trabuco, L. G.; Lei, J. L.; Ortiz-Meoz, R. F.; Schulten, K.; Green, R.; Frank, J., Structural insights into cognate versus near-cognate discrimination during decoding. EMBO Journal 2011, 30, (8), 1497-1507.

    • Chen, W.; Lou, J. Z.; Hsin, J.; Schulten, K.; Harvey, S. C.; Zhu, C., Molecular Dynamics Simulations of Forced Unbending of Integrin alpha(V)beta(3). PLOS Computational Biology 2011, 7, (2). 

    • Frauenfeld, J.; Gumbart, J.; van der Sluis, E. O.; Funes, S.; Gartmann, M.; Beatrix, B.; Mielke, T.; Berninghausen, O.; Becker, T.; Schulten, K.; Beckmann, R., Cryo-EM structure of the ribosome-SecYE complex in the membrane environment. Nature Structural & Molecular Biology 2011, 18, (5), 614-U127. 

    • Gumbart, J.; Chipot, C.; Schulten, K., Free Energy of Nascent-Chain Folding in the Translocon. Journal of the American Chemical Society 2011, 133, (19), 7602-7607.

    • Gumbart, J.; Chipot, C.; Schulten, K., Free-energy cost for translocon-assisted insertion of membrane proteins. Proceedings of the National Academy of Sciences of the United States of America 2011, 108, (9), 3596-3601. 

    • Hardy, D. J.; Stone, J. E.; Vandirot, K. L.; Gohara, D.; Rodrigues, C.; Schulten, K., Fast molecular electrostatics algorithms on GPUs. In GPU Computing Gems, Hwu, W., Ed. Morgan Kaufmann Publichers: 2011; Vol. 4, pp 43-58.

    • Hsin, J.; Schulten, K., Improved Resolution of Tertiary Structure Elasticity in Muscle Protein. Biophysical Journal 2011, 100, (4), L22-L24.

    • Hsin, J.; Strueumpfer, J.; Lee, E. H.; Schulten, K., Molecular origin of the hierarchical elasticity of titin: simulation, experiment and theory. Annual Review of Biophysics 2011, 40, 187-203.

    • Jiang, W.; Hardy, D. J.; Phillips, J. C.; MacKerell, A. D.; Schulten, K.; Roux, B., High-Performance Scalable Molecular Dynamics Simulations of a Polarizable Force Field Based on Classical Drude Oscillators in NAMD. Journal of Physical Chemistry Letters 2011, 2, (2), 87-92.

    • Kaminski, C. F.; Sackmann, E.; Schulten, K., Theodor Forster: A Giant of Modern Photochemistry. Chemphyschem 2011, 12, (3), 423-424.

    • Tanner, D. E.; Chan, K. Y.; Phillips, J. C.; Schulten, K., Parallel Generalized Born Implicit Solvent Calculations with NAMD. Journal of Chemical Theory and Computation 2011, 7, (11), 3635-3642.

    • Timp, G.; Mirsaidov, U.; Timp, W.; Shim, J.; Wang, D. Q.; Dimitrov, V.; Scrimgeour, J.; Lin, C. C.; Comer, J.; Ho, A. H.; Zou, X. Q.; Aksimentiev, A.; Schulten, K. Third Generation DNA Sequencing with a Nanopore, 2011, 287-311.

    • Stone, J. E.; Vandivort, K. L.; Schulten, K., Immersive out-of-Core Visualization of Large-Size and Long-Timescale Molecular Dynamics Trajectories. Lecture Notes in Computer Science 2011, 6939, 1-12.

    • Olbrich, C.; Jansen, T. L. C.; Liebers, J.; Aghtar, M.; Strumpfer, J.; Schulten, K.; Knoester, J.; Kleinekathofer, U., From Atomistic Modeling to Excitation Transfer and Two-Dimensional Spectra of the FMO Light-Harvesting Complex. Journal of Physical Chemistry B 2011, 115, (26), 8609-8621.

    • Olbrich, C.; Strumpfer, J.; Schulten, K.; Kleinekathofer, U., Theory and Simulation of the Environmental Effects on Fmo Electronic Transitions. Journal of Physical Chemistry Letters 2011, 2, (14), 1771-1776.

    • Sathe, C.; Zou, X. Q.; Leburton, J. P.; Schulten, K., Computational Investigation of DNA Detection Using Graphene Nanopores. ACS Nano 2011, 5, (11), 8842-8851.

    • Severin, P. M. D.; Zou, X. Q.; Gaub, H. E.; Schulten, K., Cytosine Methylation Alters DNA Mechanical Properties. Nucleic Acids Research 2011, 39, (20), 8740-8751.

    • Gamini, R.; Sotomayor, M.; Chipot, C.; Schulten, K., Cytoplasmic Domain Filter Function in the Mechanosensitive Channel of Small Conductance. Biophysical Journal 2011, 101, (1), 80-89.

    • Hsin, J.; LaPointe, L. M.; Kazy, A.; Chipot, C.; Senes, A.; Schulten, K., Oligomerization State of Photosynthetic Core Complexes Is Correlated with the Dimerization Affinity of a Transmembrane Helix. Journal of the American Chemical Society 2011, 133, (35), 14071-14081.

    • Hsin, J.; Strumpfer, J.; Lee, E. H.; Schulten, K., Molecular Origin of the Hierarchical Elasticity of Titin: Simulation, Experiment, and Theory, In Annual Review of Biophysics; Rees, D. C., Dill, K. A., Williamson, J. R., Eds. 2011; Vol. 40, 187-203.

  • 2010
    • Yin, Y.; Arkhipov, A.; Schulten, K., Multi-scale simulations of membrane sculpting by NBAR domains. In Philip Biggin and Mark Sansom, editors, Molecular Simulations and Biomembranes:  From Biophysics to Function. Royal Society of Chemistry 2010, 6, 146-176.

    • Kijac, A.; Shih, A. Y.; Nieuwkoop, A. J.; Schulten, K.; Sligar, S. G.; Rienstra, C. M., Lipid-Protein Correlations in Nanoscale Phospholipid Bilayers Determined by Solid-State Nuclear Magnetic Resonance. Biochemistry 2010, 49, (43), 9190-9198.

    • Kim, H.; Hsin, J.; Liu, Y. X.; Selvin, P. R.; Schulten, K., Formation of Salt Bridges Mediates Internal Dimerization of Myosin VI Medial Tail Domain. Structure 2010, 18, (11), 1443-1449.

    • Le, L.; Lee, E. H.; Hardy, D. J.; Truong, T. N.; Schulten, K., Molecular Dynamics Simulations Suggest that Electrostatic Funnel Directs Binding of Tamiflu to Influenza N1 Neuraminidases. PLOS Computational Biology 2010, 6, (9).

    • Hsin, J.; Struempfer, J.; Sener, M.; Qian, P.; Hunter, C. N.; Schulten, K., Energy transfer dynamics in an RC-LH1-PufX tubular photosynthetic membrane. New Journal of Physics 2010, 12. 

    • Freddolino, P. L.; Harrison, C. B.; Liu, Y. X.; Schulten, K., Challenges in protein-folding simulations. Nature Physics 2010, 6, (10), 751-758. 

    • Cruz-Chu, E. R.; Schulten, K., Computational Microscopy of the Role of Protonable Surface Residues in Nanoprecipitation Oscillations. ACS Nano 2010, 4, (8), 4463-4474. 

    • Sener, M.; Strumpfer, J.; Timney, J. A.; Freiberg, A.; Hunter, C. N.; Schulten, K., Photosynthetic vesicle architecture and constraints on efficient energy harvesting. Biophysical Journal 2010, 99, 67-75.

    • Trabuco, L. G.; Harrison, C. B.; Schreiner, E.; Schulten, K., Recognition of the Regulatory Nascent Chain TnaC by the Ribosome. Structure 2010, 18, (5), 627-637.

    • Stone, J. E.; Hardy, D. J.; Ufimtsev, I. S.; Schulten, K., GPU-accelerated molecular modeling coming of age. Journal of Molecular Graphics & Modelling 2010, 29, (2), 116-125. 

    • Stone, J. E.; Kohlmeyer, A.; Vandivort, K. L.; Schulten, K., Immersive molecular visualization and interactive modeling with commidity hardware. Lecture Notes in Computer Science 2010, 6454, 382-393. 

    • Roos, W. H.; Gibbons, M. M.; Arkhipov, A.; Uetrecht, C.; Watts, N. R.; Wingfield, P. T.; Steven, A. C.; Heck, A. J. R.; Schulten, K.; Klug, W. S.; Wuite, G. J. L., Squeezing Protein Shells: How Continuum Elastic Models, Molecular Dynamics Simulations, and Experiments Coalesce at the Nanoscale. Biophysical Journal 2010, 99, (4), 1175-1181. 

    • Saam, J.; Rosini, E.; Molla, G.; Schulten, K.; Pollegioni, L.; Ghisla, S., O-2 Reactivity of Flavoproteins Dynamic Access of Dioxygen to the Active Site and Role of a H+ Relay System in D-Amino Acid Oxidase. Journal of Biological Chemistry 2010, 285, (32), 24439-24446. 

    • Trabuco, L. G.; Schreiner, E.; Eargle, J.; Cornish, P.; Ha, T.; Luthey-Schulten, Z.; Schulten, K., The Role of L1 Stalk-tRNA Interaction in the Ribosome Elongation Cycle. Journal of Molecular Biology 2010, 402, (4), 741-760. 

    • Zou, X. Q.; Liu, Y. X.; Chen, Z. Z.; Cardenas-Jiron, G. I.; Schulten, K., Flow-Induced beta-Hairpin Folding of the Glycoprotein Ib alpha beta-Switch. Biophysical Journal 2010, 99, (4), 1182-1191. 

    • Hsin, J.; Chandler, D. E.; Gumbart, J.; Harrison, C. B.; Sener, M.; Strumpfer, J.; Schulten, K., Self-Assembly of Photosynthetic Membranes. Chemphyschem 2010, 11, (6), 1154-1159.

    • Khalili-Araghi, F.; Jogini, V.; Yarov-Yarovoy, V.; Tajkhorshid, E.; Roux, B.; Schulten, K., Calculation of the Gating Charge for the Kv1.2 Voltage-Activated Potassium Channel. Biophysical Journal 2010, 98, (10), 2189-2198.

    • Lee, E. H.; Hsin, J.; von Castelmur, E.; Mayans, O.; Schulten, K., Tertiary and Secondary Structure Elasticity of a Six-Ig Titin Chain. Biophysical Journal 2010, 98, (6), 1085-1095.

    • Miao, L.; Schulten, K., Probing a Structural Model of the Nuclear Pore Complex Channel through Molecular Dynamics. Biophysical Journal 2010, 98, (8), 1658-1667.

    • Rajan, A.; Freddolino, P. L.; Schulten, K., Going beyond Clustering in MD Trajectory Analysis: An Application to Villin Headpiece Folding. Plos One 2010, 5, (4).

    • Solov’yov, I. A.; Mouritsen, H.; Schulten, K., Acuity of a cryptochrome and vision based magnetoreception system in birds. Biophysical Journal 2010, 99, (1), 40-49.

    • Solov’yov, I. A.; Schulten, K.; Greiner, W., How birds and other animals orient in the Earth magnetic field. Physik Journal 2010, 9, 23-28.

  • 2009
    • Solov'yov, I. A.; Schulten, K., Magnetoreception through Cryptochrome May Involve Superoxide. Biophysical Journal 2009, 96, (12), 4804-4813.

    • Strumpfer, J.; Schulten, K., Light harvesting complex II B850 excitation dynamics. Journal of Chemical Physics 2009, 131, (22), doi:10.1063/1.3271348.

    • Seidelt, B.; Innis, C. A.; Wilson, D. N.; Gartmann, M.; Armache, J. P.; Villa, E.; Trabuco, L. G.; Becker, T.; Mielke, T.; Schulten, K.; Steitz, T. A.; Beckmann, R., Structural Insight into Nascent Polypeptide Chain-Mediated Translational Stalling. Science 2009, 326, (5958), 1412-1415.

    • Knapp, J. E.; Pahl, R.; Cohen, J.; Nichols, J. C.; Schulten, K.; Gibson, Q. H.; Srajer, V.; Royer, W. E., Ligand Migration and Cavities within Scapharca Dimeric Hbl: Studies by Time-Resolved Crystallography, Xe Binding, and Computational Analysis. Structure 2009, 17, (11), 1494-1504.

    • Le, L.; Lee, E. H.; Schulten, K.; Truong, T. T., Molecular modeling of swine influenza A/H1N1, Spanish H1N1, and avian H5N1 flu N1 neuraminidases bound to Tamiflu and Relenza. PLoS Currents: Influenza 2009, RRN1015.

    • Lee, E. H.; Hsin, J.; Sotomayor, M.; Comellas, G.; Schulten, K., Discovery Through the Computational Microscope. Structure 2009, 17, (10), 1295-1306.

    • Hsin, J.; Chipot, C.; Schulten, K., A Glycophorin A-Like Framework for the Dimerization of Photosynthetic Core Complexes. Journal of the American Chemical Society 2009, 131, (47), 17096-17098.

    • Hsin, J.; Gumbart, J.; Trabuco, L. G.; Villa, E.; Qian, P.; Hunter, C. N.; Schulten, K., Protein-Induced Membrane Curvature Investigated through Molecular Dynamics Flexible Fitting. Biophysical Journal 2009, 97, (1), 321-329.

    • Villa, E.; Sengupta, J.; Trabuco, L. G.; LeBarron, J.; Baxter, W. T.; Shaikh, T. R.; Grassucci, R. A.; Nissen, P.; Ehrenberg, M.; Schulten, K.; Frank, J., Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis. Proceedings of the National Academy of Sciences of the United States of America 2009, 106, (4), 1063-1068.

    • Cruz-Chu, E. R.; Aksimentiev, A.; Schulten, K., Ionic Current Rectification through Silica Nanopores. Journal of Physical Chemistry C 2009, 113, (5), 1850-1862.

    • Freddolino, P. L.; Park, S.; Roux, B.; Schulten, K., Force Field Bias in Protein Folding Simulations. Biophysical Journal 2009, 96, (9), 3772-3780.

    • Hardy, D. J.; Stone, J. E.; Schulten, K., Multilevel summation of electrostatic potentials using graphics processing units. Parallel Computing 2009, 35, (3), 164-177.

    • Hayashi, S.; Tajkhorshid, E.; Schulten, K., Photochemical Reaction Dynamics of the Primary Event of Vision Studied by Means of a Hybrid Molecular Simulation. Biophysical Journal 2009, 96, (2), 403-416.

    • Khalili-Araghi, F.; Gumbart, J.; Wen, P. C.; Sotomayor, M.; Tajkhorshid, E.; Schulten, K., Molecular dynamics simulations of membrane channels and transporters. Current Opinion in Structural Biology 2009, 19, (2), 128-137.

    • Maruthamuthu, V.; Schulten, K.; Leckband, D., Elasticity and Rupture of a Multi-Domain Neural Cell Adhesion Molecule Complex. Biophysical Journal 2009, 96, (8), 3005-3014.

    • Miao, L. L.; Schulten, K., Transport-Related Structures and Processes of the Nuclear Pore Complex Studied through Molecular Dynamics. Structure 2009, 17, (3), 449-459.

    • Mirsaidov, U.; Timp, W.; Zou, X.; Dimitrov, V.; Schulten, K.; Feinberg, A. P.; Timp, G., Nanoelectromechanics of Methylated DNA in a Synthetic Nanopore. Biophysical Journal 2009, 96, (4), L32-L34.

    • Sener, M.; Hsin, J.; Trabuco, L. G.; Villa, E.; Qian, P.; Hunter, C. N.; Schulten, K., Structural model and excitonic properties of the dimeric RC-LH1-Pufx complex from Rhodobacter sphaeroides. Chemical Physics 2009, 357, (1-3), 188-197.

    • Archambault, F.; Chipot, C.; Soteras, I.; Luque, F. J.; Schulten, K.; Dehez, F., Polarizable Intermolecular Potentials for Water and Benzene Interacting with Halide and Metal Ions. Journal of Chemical Theory and Computation 2009, 5, (11), 3022-3031.

    • Arkhipov, A.; Roos, W. H.; Wuite, G. J. L.; Schulten, K., Elucidating the Mechanism behind Irreversible Deformation of Viral Capsids. Biophysical Journal 2009, 97, (7), 2061-2069.

    • Arkhipov, A.; Yin, Y.; Schulten, K., Membrane-Bending Mechanism of Amphiphysin N-BAR Domains. Biophysical Journal 2009, 97, (10), 2727-2735.

    • Becker, T.; Bhushan, S.; Jarasch, A.; Armache, J. P.; Funes, S.; Jossinet, F.; Gumbart, J.; Mielke, T.; Berninghausen, O.; Schulten, K.; Westhof, E.; Gilmore, R.; Mandon, E. C.; Beckmann, R., Structure of Monomeric Yeast and Mammalian Sec61 Complexes Interacting with the Translating Ribosome. Science 2009, 326, (5958), 1369-1373.

    • Chandler, D. E.; Gumbart, J.; Stack, J. D.; Chipot, C.; Schulten, K., Membrane Curvature Induced by Aggregates of LH2s and Monomeric LH1s. Biophysical Journal 2009, 97, (11), 2978-2984.

    • Cruz-Chu, E. R.; Ritz, T.; Siwy, Z. S.; Schulten, K., Molecular control of ionic conduction in polymer nanopores. Faraday Discussions 2009, 143, 47-62.

    • Dunning, T. H.; Schulten, K.; Tromp, J.; Ostriker, J. P.; Droegemeier, K.; Xue, M.; Fussell, P., Science and Engineering in the Petascale Era. Computing in Science & Engineering 2009, 11, (5), 28-36.

    • Freddolino, P. L.; Schulten, K., Common Structural Transitions in Explicit-Solvent Simulations of Villin Headpiece Folding. Biophysical Journal 2009, 97, (8), 2338-2347.

    • Gumbart, J.; Trabuco, L. G.; Schreiner, E.; Villa, E.; Schulten, K., Regulation of the Protein-Conducting Channel by a Bound Ribosome. Structure 2009, 17, (11), 1453-1464.

    • Trabuco, L. G.; Villa, E.; Schreiner, E.; Harrison, C. B.; Schulten, K., Molecular dynamics flexible fitting: A practical guide to combine cryo-electron microscopy and X-ray crystallography. Methods 2009, 49, (2), 174-180.

    • Yin, Y.; Arkhipov, A.; Schulten, K., Simulations of Membrane Tubulation by Lattices of Amphiphysin N-BAR Domains. Structure 2009, 17, (6), 882-892.

    • Shih, A. Y.; Sligar, S. G.; Schulten, K., Maturation of high-density lipoproteins. Journal of the Royal Society Interface 2009, 6, (39), 863-871.

    • Aksimentiev, A.; Brunner, R.; Cruz-Chu, E. R.; Comer, J.; Schulten, K., Modeling Transport Through Synthetic Nanopores. IEEE Nanotechnology Magazine 2009, 3, 21-28.

    • Arkhipov, A.; Schulten, K., Limits for reduction of effective focal volume in multiple-beam light microscopy. Optics Express 2009, 17, (4), 2861-2870.

  • 2008
    • Arkhipov, A.; Yin, Y.; Schulten, K., Four-scale description of membrane sculpting by BAR domains. Biophysical Journal 2008, 95, (6), 2806-2821.

    • Chandler, D. E.; Hsin, J.; Harrison, C. B.; Gumbart, J.; Schulten, K., Intrinsic curvature properties of photosynthetic proteins in chromatophores. Biophysical Journal 2008, 95, (6), 2822-2836.

    • Chen, Z. Z.; Lou, J. H.; Zhu, C.; Schulten, K., Flow-induced structural transition in the beta-switch region of glycoprotein Ib. Biophysical Journal 2008, 95, (3), 1303-1313.

    • Cohen, J.; Olsen, K. W.; Schulten, K., Finding gas migration pathways in proteins using implicit ligand sampling. In Globins and Other Nitric Oxide-Reactive Proteins, Part B, Elsevier Academic Press Inc: San Diego, 2008; Vol. 437, pp 439-457.

    • Sotomayor, M.; Schulten, K., The allosteric role of the Ca2+ switch in adhesion and elasticity of C-cadherin. Biophysical Journal 2008, 94, (12), 4621-4633.

    • Aksimentiev, A.; Brunner, R.; Cohen, J.; Comer, J.; Cruz-Chu, E.; Hardy, D.; Rajan, A.; Shih, A.; Sigalov, G.; Yin, Y.; Schulten, K., Computer Modeling in Biotechnology, a Partner in Development. In Protocols in Nanostructure Design, Methods in Molecular Biology, Humana Press: 2008; pp 181-234.

    • Kosztin, I.; Schulten, K., Molecular dynamics methods for bioelectronic systems in photo-synthesis. In Biophysical Techniques in Photosynthesis II, volume 26 of Advances in Photosynthesis and Respiration, Aartsma, T.; Matysik, J., Eds. Springer, Dordrecht: 2008; pp 445-464.

    • Shih, A. Y.; Sligar, S. G.; Schulten, K., Molecular models need to be tested: The case of a solar flares discoidal HDL model. Biophysical Journal 2008, 94, (12), L87-L89.

    • Trabuco, L. G.; Villa, E.; Mitra, K.; Frank, J.; Schulten, K., Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. Structure 2008, 16, (5), 673-683.

    • Vasquez, V.; Sotomayor, M.; Cortes, D. M.; Roux, B.; Schulten, K.; Perozo, E., Three-dimensional architecture of membrane-embedded MscS in the closed conformation. Journal of Molecular Biology 2008, 378, (1), 55-70.

    • Chipot, C.; Schulten, K., Understanding structure and function of membrane proteins using free energy calculations. In Biophysical Analysis of Membrane Proteins: Investigating Structure and Function, Peyroula, E. P., Ed. Wiley, Weinheim: 2008; pp 187-211.

    • Freddolino, P. L.; Liu, F.; Gruebele, M.; Schulten, K., Ten-microsecond molecular dynamics simulation of a fast-folding WW domain. Biophysical Journal 2008, 94, (10), L75-L77.

    • Henin, J.; Tajkhorshid, E.; Schulten, K.; Chipot, C., Diffusion of glycerol through Escherichia coli aquaglyceroporin GlpF. Biophysical Journal 2008, 94, (3), 832-839.

    • Lim, B. B. C.; Lee, E. H.; Sotomayor, M.; Schulten, K., Molecular basis of fibrin clot elasticity. Structure 2008, 16, (3), 449-459.

    • Rajan, A.; Strano, M. S.; Heller, D. A.; Hertel, T.; Schulten, K., Length-dependent optical effects in single walled carbon nanotubes. Journal of Physical Chemistry B 2008, 112, (19), 6211-6213.

    • Rodrigues, C. I.; Hardy, D. J.; Stone, J. E.; Schulten, K.; Hwu, W. W. GPU acceleration of cutoff pair potentials for molecular modeling applications, In CF’08: Proceedings of the 2008 Conference on Computing Frontiers, ACM: New York, NY, 2008; pp 273-282.

    • Schulten, K.; Phillips, J. C.; Kale, L. V.; Bhatele, A. Biomolecular modeling in the era of petascale computing, In Petascale Computing: Algorithms and Applications, Bader, D., Ed. Chapman and Hall/CRC Press, Taylor and Francis Group: New York, 2008; pp 165-181.

    • Shih, A. Y.; Freddolino, P. L.; Arkhipov, A.; Sligar, S. G.; Schulten, K., Molecular modeling of the structural properties and formation of high-density lipoprotein particles. In Computational Modeling of Membrane Bilayers, Elsevier Academic Press Inc: San Diego, 2008; Vol. 60, pp 313-342.

    • Vasquez, V.; Sotomayor, M.; Cordero-Morales, J.; Schulten, K.; Perozo, E., A structural mechanism for MscS gating in lipid bilayers. Science 2008, 321, (5893), 1210-1214.

    • Isin, B.; Schulten, K.; Tajkhorshid, E.; Bahar, I., Mechanism of signal propagation upon retinal isomerization: Insights from molecular dynamics simulations of rhodopsin restrained by normal modes. Biophysical Journal 2008, 95, (2), 789-803.

    • Gumbart, J.; Schulten, K., The Roles of Pore Ring and Plug in the SecY Protein-conducting Channel. Journal of General Physiology 2008, 132, (6), 709-719.

    • Yao, Y.; Harrison, C. B.; Freddolino, P. L.; Schulten, K.; Mayer, M. L., Molecular mechanism of ligand recognition by NR3 subtype glutamate receptors. EMBO Journal 2008, 27, (15), 2158-2170.

  • 2007
    • Sener, M. K.; Olsen, J. D.; Hunter, C. N.; Schulten, K., Atomic-level structural and functional model of a bacterial photosynthetic membrane vesicle. Proceedings of the National Academy of Sciences of the United States of America 2007, 104, (40), 15723-15728.

    • Shih, A. Y.; Arkhipov, A.; Freddolino, P. L.; Sligar, S. G.; Schulten, K., Assembly of lipids and proteins into lipoprotein particles. Journal of Physical Chemistry B 2007, 111, (38), 11095-11104.

    • Shih, A. Y.; Freddolino, P. L.; Sligar, S. G.; Schulten, K., Disassembly of nanodiscs with cholate. Nano Letters 2007, 7, (6), 1692-1696.

    • Hohng, S.; Zhou, R. B.; Nahas, M. K.; Yu, J.; Schulten, K.; Lilley, D. M. J.; Ha, T. J., Fluorescence-force spectroscopy maps two-dimensional reaction landscape of the Holliday junction. Science 2007, 318, (5848), 279-283.

    • Isgro, T. A.; Schulten, K., Cse1p-binding dynamics reveal a binding pattern for FG-repeat nucleoporins on transport receptors. Structure 2007, 15, (8), 977-991.

    • Jensen, M. O.; Yin, Y.; Tajkhorshid, E.; Schulten, K., Sugar transport across lactose permease probed by steered molecular dynamics. Biophysical Journal 2007, 93, (1), 92-102.

    • Johnson, B. J.; Cohen, J.; Welford, R. W.; Pearson, A. R.; Schulten, K.; Klinman, J. P.; Wilmot, C. M., Exploring molecular oxygen pathways in Hansenula polymorpha copper-containing amine oxidase. Journal of Biological Chemistry 2007, 282, (24), 17767-17776.

    • Gumbart, J.; Schulten, K., Structural determinants of lateral gate opening in the protein translocon. Biochemistry 2007, 46, (39), 11147-11157.

    • Isgro, T. A.; Schulten, K., Association of nuclear pore FG-repeat domains to NTF2 import and export complexes. Journal of Molecular Biology 2007, 366, (1), 330-345.

    • Isin, B.; Tajkhorshid, E.; Schulten, K.; Bahar, I., Conformational changes of rhodopsin explored by using normal modes in steered molecular dynamics simulations. Biophysical Journal 2007, 20A-20A.

    • Cohen, J.; Schulten, K., O-2 migration pathways are not conserved across proteins of a similar fold. Biophysical Journal 2007, 93, (10), 3591-3600.

    • Cruz, E.; Aksimentiev, A.; Schulten, K., Computational studies of ionic conduction through silica nanopores. Biophysical Journal 2007, 651A-651A.

    • Cui, S. X.; Yu, J.; Kuhner, F.; Schulten, K.; Gaub, H. E., Double-stranded DNA dissociates into single strands when dragged into a poor solvent. Journal of the American Chemical Society 2007, 129, (47), 14710-14716.

    • Dehez, F.; Angyan, J. G.; Gutierrez, I. S.; Luque, F. J.; Schulten, K.; Chipot, C., Modeling induction phenomena in intermolecular interactions with an Ab initio force field. Journal of Chemical Theory and Computation 2007, 3, (6), 1914-1926.

    • Freddolino, P. L.; Arkhipov, A.; Schulten, K., Coarse-grained molecular dynamics simulations of rotation-induced structural transitions in the bacterial flagellum. Biophysical Journal 2007, 142A-142A.

    • Yin, Y.; Jensen, M.; Tajkhorshid, E.; Schulten, K., Sugar transport across lactose permease probed by molecular dynamics simulations. Biophysical Journal 2007, 64A-64A.

    • Yu, J.; Ha, T.; Schulten, K., How directional translocation is regulated in a DNA helicase motor. Biophysical Journal 2007, 93, (11), 3783-3797.

    • Sotomayor, M.; Vasquez, V.; Perozo, E.; Schulten, K., Ion conduction through MscS as determined by electrophysiology and simulation. Biophysical Journal 2007, 92, (3), 886-902.

    • Lee, E. H.; Hsin, J.; Mayans, O.; Schulten, K., Secondary and tertiary structure elasticity of titin Z1Z2 and a titin chain model. Biophysical Journal 2007, 93, (5), 1719-1735.

    • Arkhipov, A.; Huve, J.; Kahms, M.; Peters, R.; Schulten, K., Continuous fluorescence microphotolysis and correlation spectroscopy using 4Pi microscopy. Biophysical Journal 2007, 93, (11), 4006-4017.

    • Stone, J. E.; Phillips, J. C.; Freddolino, P. L.; Hardy, D. J.; Trabuco, L. G.; Schulten, K., Accelerating molecular modeling applications with graphics processors. Journal of Computational Chemistry 2007, 28, (16), 2618-2640.

    • Arkhipov, A. S.; Freddolino, P. L.; Schulten, K., Stability and dynamics of virus capsids described by coarse-grained modeling. Biophysical Journal 2007, 540A-540A.

    • Chen, H. N.; Ilan, B.; Wu, Y. J.; Zhu, F. Q.; Schulten, K.; Voth, G. A., Charge delocalization in proton channels, I: The aquaporin channels and proton blockage. Biophysical Journal 2007, 92, (1), 46-60.

    • Chen, Z.; Freddolino, P.; Arkhipov, A.; Schulten, K., Simulation of protein translocation in a growing flagellum. Biophysical Journal 2007, 643A-643A.

    • Dittrich, M.; Yu, J.; Schulten, K., PcrA helicase, a molecular motor studied from the electronic to the functional level. Atomistic Approaches in Modern Biology: from Quantum Chemistry to Molecular Simulations 2007, 268, 319-347.

    • Aird, A.; Wrachtrup, J.; Schulten, K.; Tietz, C., Possible pathway for ubiquinone shuttling in Rhodospirillum rubrum revealed by molecular dynamics simulation. Biophysical Journal 2007, 92, (1), 23-33.

    • Gumbart, J. C.; Schulten, K., Opening of the lateral gate of the translocon SecY. Biophysical Journal 2007, 597A-597A.

    • Wang, Y.; Cohen, J.; Boron, W.; Schulten, K.; Tajkhorshid, E., Aquaporin-mediated gas conduction across biological membranes. Biophysical Journal 2007, 264A-264A.

    • Wang, Y.; Cohen, J.; Boron, W. F.; Schulten, K.; Tajkhorshid, E., Exploring gas permeability of cellular membranes and membrane channels with molecular dynamics. Journal of Structural Biology 2007, 157, (3), 534-544.

    • Villa, E.; Schulten, K., Multiscale simulations of the DNA loop topologies induced by the lac repressor. Biophysical Journal 2007, 185A-185A.

    • Vasquez, V.; Sotomayor, M.; Cortes, D. M.; Roux, B.; Schulten, K.; Perozo, E., Three dimensional architecture of MscS N-terminus and transmembrane segments in the closed state. Biophysical Journal 2007, 114A-114A.

    • Trabuco, L. G.; Falck, E.; Villa, E.; Schulten, K., Modeling and simulations of a bacterial ribosome. Biophysical Journal 2007, 571A-571A.

    • Solov'yov, I. A.; Chandler, D. E.; Schulten, K., Magnetic field effects in Arabidopsis thaliana cryptochrome-1. Biophysical Journal 2007, 92, (8), 2711-2726.

    • Sotomayor, M.; Schulten, K., Single-molecule experiments in vitro and in silico. Science 2007, 316, (5828), 1144-1148.

    • Sotomayor, M.; Schulten, K., Tertiary and secondary structure elasticity of repeat proteins. Biophysical Journal 2007, 524A-524A.

    • Khalili-Araghi, F.; Tajkhorshid, E.; Schulten, K., Dynamics of K+ ion conduction through Kv1.2. Biophysical Journal 2007, 616A-616A.

    • Lee, E. H.; Hsin, J.; Mulhe-Goll, C.; Mayans, O.; Schulten, K., Tertiary and secondary elasticity of titin Z1Z2 tandem repeats. Biophysical Journal 2007, 521A-522A.

    • Sotomayor, M.; Vasquez, V.; Perozo, E.; Schulten, K., Ion conduction through MscS as determined by electrophysiology and simulation. Biophysical Journal 2007, 114A-114A.

    • Shih, A. Y.; Freddolino, P. L.; Arkhipov, A.; Schulten, K., Assembly of lipoprotein particles revealed by coarse-grained molecular dynamics simulations. Journal of Structural Biology 2007, 157, (3), 579-592.

    • Shih, A. Y.; Freddolino, P. L.; Arkhipov, A.; Schulten, K., Assembly of lipoproteins revealed by coarse-grained molecular dynamics simulations. Biophysical Journal 2007, 250A-250A.

    • Shih, A. Y.; Freddolino, P. L.; Sligar, S. G.; Schulten, K., Disassembly of nanodiscs: using coarse-grained MD simulations to interpret SAXS patterns. Biophysical Journal 2007, 330A-330A.

  • 2006
    • Puklin-Faucher, E.; Gao, M.; Schulten, K.; Vogel, V., How the headpiece hinge angle is opened: new insights into the dynamics of integrin activation. Journal of Cell Biology 2006, 175, (2), 349-360.

    • Meyer, G. R.; Gullingsrud, J.; Schulten, K.; Martinac, B., Molecular dynamics study of MscL interactions with a curved lipid bilayer. Biophysical Journal 2006, 91, (5), 1630-1637.

    • Yu, J.; Yool, A. J.; Schulten, K.; Tajkhorshid, E., Mechanism of gating and ion conductivity of a possible tetrameric pore in aquaporin-1. Structure 2006, 14, (9), 1411-1423.

    • Yu, J.; Ha, T.; Schulten, K., Structure-based model of the stepping motor of PcrA helicase. Biophysical Journal 2006, 91, (6), 2097-2114.

    • Yin, Y.; Jensen, M. O.; Tajkhorshid, E.; Schulten, K., Sugar binding and protein conformational changes in lactose permease. Biophysical Journal 2006, 91, (11), 3972-3985.

    • Sotomayor, M.; van der Straaten, T. A.; Ravaioli, U.; Schulten, K., Electrostatic properties of the mechanosensitive channel of small conductance MscS. Biophysical Journal 2006, 90, (10), 3496-3510.

    • Henin, J.; Schulten, K.; Chipot, C., Conformational equilibrium in alanine-rich peptides probed by reversible stretching simulations. Journal of Physical Chemistry B 2006, 110, (33), 16718-16723.

    • Hoffmann, M.; Wanko, M.; Strodel, P.; Konig, P. H.; Frauenheim, T.; Schulten, K.; Thiel, W.; Tajkhorshid, E.; Elstner, M., Color tuning in rhodopsins: The mechanism for the spectral shift between bacteriorhodopsin and sensory rhodopsin II. Journal of the American Chemical Society 2006, 128, (33), 10808-10818.

    • Arkhipov, A.; Freddolino, P. L.; Imada, K.; Namba, K.; Schulten, K., Coarse-grained molecular dynamics simulations of a rotating bacterial flagellum. Biophysical Journal 2006, 91, (12), 4589-4597.

    • Arkhipov, A.; Freddolino, P. L.; Schulten, K., Stability and dynamics of virus capsids described by coarse-grained modeling. Structure 2006, 14, (12), 1767-1777.

    • Freddolino, P. L.; Arkhipov, A. S.; Larson, S. B.; McPherson, A.; Schulten, K., Molecular dynamics simulations of the complete satellite tobacco mosaic virus. Structure 2006, 14, (3), 437-449.

    • Freddolino, P. L.; Dittrich, M.; Schulten, K., Dynamic switching mechanisms in LOV1 and LOV2 domains of plant phototropins. Biophysical Journal 2006, 91, (10), 3630-3639.

    • Gao, M.; Schulten, K., Onset of anthrax toxin pore formation. Biophysical Journal 2006, 90, (9), 3267-3279.

    • Gao, M.; Sotomayor, M.; Villa, E.; Lee, E. H.; Schulten, K., Molecular mechanisms of cellular mechanics. Physical Chemistry Chemical Physics 2006, 8, (32), 3692-3706.

    • Cohen, J.; Arkhipov, A.; Braun, R.; Schulten, K., Imaging the migration pathways for O-2, CO, NO, and Xe inside myoglobin. Biophysical Journal 2006, 91, (5), 1844-1857.

    • Cruz-Chu, E. R.; Aksimentiev, A.; Schulten, K., Water-silica force field for simulating nanodevices. Journal of Physical Chemistry B 2006, 110, (43), 21497-21508.

    • Dittrich, M.; Schulten, K., PcrA helicase, a prototype ATP-driven molecular motor. Structure 2006, 14, (9), 1345-1353.

    • Khalili-Araghi, F.; Tajkhorshid, E.; Schulten, K., Dynamics of K+ ion conduction through Kv1.2. Biophysical Journal 2006, 91, (6), L72-L74.

  • 2004
    • Park, S., and Schulten, K. (2004), "Calculating potentials of mean force from steered molecular dynamics simulations," Journal of Chemical Physics, In press.

    • Aksimentiev, A., Balabin, I.A., Fillingame, R.H., and Schulten, K. (2004), "Insights into the molecular mechanism of rotation in the Fo sector of ATP synthase," Biophysical Journal, In press.

    • Zhu, F., Tajkhoshid, E., and Schulten, K. (2004), "Theory and simulation of water permeation in aquaporin-1," Biophysical Journal, 86, pp. 50-57.

    • Balaeff, A., Mahadevan, L., and Schulten, K. (2004), "Structural basis for cooperative DNA binding by CAP and Lac repressor," Structure, 12, pp. 123-132.

  • 2003
    • Gao, M., Craig, D., Lequin, O., Campbell, I.D., Vogel, V., and Schulten, K. (2003), "Structure and functional significance of mechanically unfolded fibronectin type III1 intermediates," Proceedings of the National Academy of Sciences, USA , 100, pp. 14784-14789.

Press

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