TCB Publications - Search
379. Conformational model of the Holliday junction transition deduced from molecular dynamics simulations. Jin Yu, Taekjip Ha, and Klaus Schulten. Nucleic Acids Research, 32:6683-6695, 2004. (PMC: 545448)
378. Collective diffusion model for water permeation through microscopic channels. Fangqiang Zhu, Emad Tajkhorshid, and Klaus Schulten. Physical Review Letters, 93:224501, 2004. (4 pages).
377. Finite-size effect and wall polarization in a carbon nanotube channel. Deyu Lu, Yan Li, Slava V. Rotkin, Umberto Ravaioli, and Klaus Schulten. Nano Letters, 4:2383-2387, 2004.
376. Fluctuation-driven molecular transport through an asymmetric membrane channel. Ioan Kosztin and Klaus Schulten. Physical Review Letters, 93:238102, 2004. (4 pages).
375. Role of water in transient cytochrome c2 docking. Felix Autenrieth, Emad Tajkhorshid, Klaus Schulten, and Zaida Luthey-Schulten. Journal of Physical Chemistry B, 108:20376-20387, 2004.
374. Structural insights into how the MIDAS ion stabilizes integrin binding to an RGD peptide under force. David Craig, Mu Gao, Klaus Schulten, and Viola Vogel. Structure, 12:2049-2058, 2004.
373. Molecular dynamics study of gating in the mechanosensitive channel of small conductance MscS. Marcos Sotomayor and Klaus Schulten. Biophysical Journal, 87:3050-3065, 2004. (PMC: 1304777)
372. ATP hydrolysis in the βTP and βDP catalytic sites of F1-ATPase. Markus Dittrich, Shigehiko Hayashi, and Klaus Schulten. Biophysical Journal, 87:2954-2967, 2004. (PMC: 1304769)
371. Microscopic kinetics of DNA translocation through synthetic nanopores. Aleksij Aksimentiev, Jiunn Benjamin Heng, Gregory Timp, and Klaus Schulten. Biophysical Journal, 87:2086-2097, 2004. (PMC: 1304610)
370. Sizing DNA using a nanometer-diameter pore. J. B. Heng, C. Ho, T. Kim, R. Timp, A. Aksimentiev, Y. V. Grinkova, S. Sligar, K. Schulten, and G. Timp. Biophysical Journal, 87:2905-2911, 2004. (PMC: 1304707)
369. Role of hydrogen-bond network in energy storage of bacteriorhodopsin's light-driven proton pump revealed by ab initio normal mode analysis. Shigehiko Hayashi, Emad Tajkhorshid, Hideki Kandori, and Klaus Schulten. Journal of the American Chemical Society, 126:10516-10517, 2004.
368. Computational studies of membrane channels. Benoit Roux and Klaus Schulten. Structure, 12:1343-1351, 2004.
367. A similarity measure for partially folded proteins: application to unfolded and native-like conformational fluctuations. Edgar Larios, Wei Y. Yang, Klaus Schulten, and Martin Gruebele. Chemical Physics, 307:217-225, 2004.
366. Electronic structure and dielectric behavior of finite-length single-walled carbon nanotubes. Yan Li, Deyu Lu, Slava V. Rotkin, Klaus Schulten, and Umberto Ravaioli. In Proceedings of the Fourth IEEE Conference on Nanotechnology, pp. 273-275, Munich, Germany, 2004.
365. Complementarities and convergence of results in bacteriorhodopsin trimer simulations. Jerome Baudry, Emad Tajkhorshid, and Klaus Schulten. Biophysical Journal, 87:1394-1395, 2004. (PMC: 1304478)
364. Forced dissociation of the strand dimer interface between C-cadherin ectodomains. M. V. Bayas, K. Schulten, and D. Leckband. Mechanics and Chemistry of Biosystems, 1:101-111, 2004.
363. Integrin activation in vivo and in silico. Mu Gao and Klaus Schulten. Structure, 12:2096-2098, 2004.
362. Multi-scale method for simulating protein-DNA complexes. Elizabeth Villa, Alexander Balaeff, L. Mahadevan, and Klaus Schulten. Multiscale Modeling and Simulation, 2:527-553, 2004.
361. Molecular dynamics simulations of micelle formation around dimeric glycophorin A transmembrane helices. Rosemary Braun, Donald M. Engelman, and Klaus Schulten. Biophysical Journal, 87:754-763, 2004. (PMC: 1304485)
360. Multiple probes reveal a native-like intermediate during the low-temperature refolding of ubiquitin. E. Larios, J. S. Li, K. Schulten, H. Kihara, and M. Gruebele. Journal of Molecular Biology, 340:115-125, 2004.
359. Excitation migration in trimeric cyanobacterial photosystem I. Melih K. Sener, Sanghyun Park, Deyu Lu, Ana Damjanovic, Thorsten Ritz, Petra Fromme, and Klaus Schulten. Journal of Chemical Physics, 120:11183-11195, 2004.
358. Extending the molecular modeling methodology to study insertion of membrane nanopores. Aleksij Aksimentiev and Klaus Schulten. Proceedings of the National Academy of Sciences, USA, 101:4337-4338, 2004. (PMC: 384746)
357. Lipid bilayer pressure profiles and mechanosensitive channel gating. Justin Gullingsrud and Klaus Schulten. Biophysical Journal, 86:3496-3509, 2004. (PMC: 1304254)
356. Calculating potentials of mean force from steered molecular dynamics simulations. Sanghyun Park and Klaus Schulten. Journal of Chemical Physics, 120:5946-5961, 2004.
355. The mechanism of proton exclusion in aquaporin channels. Boaz Ilan, Emad Tajkhorshid, Klaus Schulten, and Gregory A. Voth. PROTEINS: Structure, Function, and Bioinformatics, 55:223-228, 2004.
354. Mechanism of anionic conduction across CLC. Jordi Cohen and Klaus Schulten. Biophysical Journal, 86:836-845, 2004. (PMC: 1303931)
353. Modeling DNA loops using continuum and statistical mechanics. Alexander Balaeff, Christophe R. Koudella, L. Mahadevan, and Klaus Schulten. Philosophical Transactions of the Royal Society of London A. (Mathematical, Physical and Engineering Sciences), 362:1355-1371, 2004.
352. Insights into the molecular mechanism of rotation in the Fo sector of ATP synthase. Aleksij Aksimentiev, Ilya A. Balabin, Robert H. Fillingame, and Klaus Schulten. Biophysical Journal, 86:1332-1344, 2004. (PMC: 1303972)
351. Tuning the mechanical stability of fibronectin type III modules through sequence variation. David Craig, Mu Gao, Klaus Schulten, and Viola Vogel. Structure, 12:21-30, 2004.
350. Theory and simulation of water permeation in aquaporin-1. Fangqiang Zhu, Emad Tajkhorshid, and Klaus Schulten. Biophysical Journal, 86:50-57, 2004. (PMC: 1303818)
349. Structural basis for cooperative DNA binding by CAP and Lac repressor. Alexander Balaeff, L. Mahadevan, and Klaus Schulten. Structure, 12:123-132, 2004.
348. Molecular biomimetics: nanotechnology through biology. Mehmet Sarikaya, Candan Tamerler, Alex K. -Y. Jen, Klaus Schulten, and François Baneyx. Nature Materials, 2:577-585, 2003.
347. Structure and functional significance of mechanically unfolded fibronectin type III1 intermediates. Mu Gao, David Craig, Olivier Lequin, Iain D. Campbell, Viola Vogel, and Klaus Schulten. Proceedings of the National Academy of Sciences, USA, 100:14784-14789, 2003. (PMC: 299803)
346. On the mechanism of ATP hydrolysis in F1-ATPase. Markus Dittrich, Shigehiko Hayashi, and Klaus Schulten. Biophysical Journal, 85:2253-2266, 2003. (PMC: 1303451)
345. Glycerol conductance and physical asymmetry of the Escherichia coli glycerol facilitator GlpF. Deyu Lu, Paul Grayson, and Klaus Schulten. Biophysical Journal, 85:2977-2987, 2003. (PMC: 1303576)
344. Electrostatic tuning of permeation and selectivity in aquaporin water channels. Morten Ø. Jensen, Emad Tajkhorshid, and Klaus Schulten. Biophysical Journal, 85:2884-2899, 2003. (PMC: 1303569)
343. Gating of MscL studied by steered molecular dynamics. Justin Gullingsrud and Klaus Schulten. Biophysical Journal, 85:2087-2099, 2003. (PMC: 1303438)
342. Free energy calculation from steered molecular dynamics simulations using Jarzynski's equality. Sanghyun Park, Fatemeh Khalili-Araghi, Emad Tajkhorshid, and Klaus Schulten. Journal of Chemical Physics, 119:3559-3566, 2003.
341. Molecular dynamics simulation of bacteriorhodopsin's photoisomerization using ab initio forces for the excited chromophore. Shigehiko Hayashi, Emad Tajkhorshid, and Klaus Schulten. Biophysical Journal, 85:1440-1449, 2003. (PMC: 1303320)
340. Large scale simulation of protein mechanics and function. Emad Tajkhorshid, Aleksij Aksimentiev, Ilya Balabin, Mu Gao, Barry Isralewitz, James C. Phillips, Fangqiang Zhu, and Klaus Schulten. In Frederic M. Richards, David S. Eisenberg, and John Kuriyan, editors, Advances in Protein Chemistry, volume 66, pp. 195-247. Elsevier Academic Press, New York, 2003.
339. Reaction paths based on mean first-passage times. Sanghyun Park, Melih K. Sener, Deyu Lu, and Klaus Schulten. Journal of Chemical Physics, 119:1313-1319, 2003.
338. Water and proton conduction through carbon nanotubes as models for biological channels. Fangqiang Zhu and Klaus Schulten. Biophysical Journal, 85:236-244, 2003. (PMC: 1303080)
337. Mechanisms of selectivity in channels and enzymes studied with interactive molecular dynamics. Paul Grayson, Emad Tajkhorshid, and Klaus Schulten. Biophysical Journal, 85:36-48, 2003. (PMC: 1303063)
336. Forced detachment of the CD2-CD58 complex. M. V. Bayas, Klaus Schulten, and D. Leckband. Biophysical Journal, 84:2223-2233, 2003. (PMC: 1302789)
335. Identifying unfolding intermediates of FN-III10 by steered molecular dynamics. Mu Gao, David Craig, Viola Vogel, and Klaus Schulten. Journal of Molecular Biology, 323:939-950, 2002.
334. Unfolding of titin domains studied by molecular dynamics simulations. Mu Gao, Hui Lu, and Klaus Schulten. Journal of Muscle Research and Cell Motility, 23:513-521, 2002.
333. Molecular dynamics investigation of primary photoinduced events in the activation of rhodopsin. Jan Saam, Emad Tajkhorshid, Shigehiko Hayashi, and Klaus Schulten. Biophysical Journal, 83:3097-3112, 2002. (PMC: 1302389)
332. Steered molecular dynamics studies of titin I1 domain unfolding. Mu Gao, Matthias Wilmanns, and Klaus Schulten. Biophysical Journal, 83:3435-3445, 2002. (PMC: 1302418)
331. Robustness and optimality of light harvesting in cyanobacterial photosystem I. Melih K. Sener, Deyu Lu, Thorsten Ritz, Sanghyun Park, Petra Fromme, and Klaus Schulten. Journal of Physical Chemistry B, 106:7948-7960, 2002.
330. Genetically engineered gold-binding polypeptides: Structure prediction and molecular dynamics. Rosemary Braun, Mehmet Sarikaya, and Klaus Schulten. Journal of Biomaterials Science, 13:747-758, 2002.
329. Control of the selectivity of the aquaporin water channel family by global orientational tuning. Emad Tajkhorshid, Peter Nollert, Morten O. Jensen, Larry J. W. Miercke, Joseph O'Connell, Robert M. Stroud, and Klaus Schulten. Science, 296:525-530, 2002.
328. Energetics of glycerol conduction through aquaglyceroporin GlpF. Morten O. Jensen, Sanghyun Park, Emad Tajkhorshid, and Klaus Schulten. Proceedings of the National Academy of Sciences, USA, 99:6731-6736, 2002. (PMC: 124471)
327. Pressure-induced water transport in membrane channels studied by molecular dynamics. Fangqiang Zhu, Emad Tajkhorshid, and Klaus Schulten. Biophysical Journal, 83:154-160, 2002. (PMC: 1302135)
326. What causes hyperfluorescence: folding intermediates or conformationally flexible native states? John Ervin, Edgar Larios, Szabolcs Osvath, Klaus Schulten, and Martin Gruebele. Biophysical Journal, 83:473-483, 2002.
325. Structural changes during the formation of early intermediates in the bacteriorhodopsin photocycle. Shigehiko Hayashi, Emad Tajkhorshid, and Klaus Schulten. Biophysical Journal, 83:1281-1297, 2002. (PMC: 1302228)
324. High pressure gel mobility shift analysis and molecular dynamics: Investigating specific protein-nucleic acid recognition. Thomas W. Lynch, Mark A. McLean, Dorina Kosztin, Klaus Schulten, and Stephen G. Sligar. In R. Hayashi, editor, Trends in High Pressure Bioscience and Biotechnology, pp. 87-94. Elsevier, 2002.
323. Mechanical force generation by G-proteins. Ioan Kosztin, Robijn Bruinsma, Paul O'Lague, and Klaus Schulten. Proceedings of the National Academy of Sciences, USA, 99:3575-3580, 2002. (PMC: 122565)
322. Quasicontinuum representations of atomic-scale mechanics: From proteins to dislocations. Rob Phillips, Markus Dittrich, and Klaus Schulten. Annual Review of Materials Research, 32:219-233, 2002.
321. The role of intersection topography in bond selectivity of cis-trans photoisomerization. Michal Ben-Nun, Ferenc Molnar, Klaus Schulten, and Todd J. Martinez. Proceedings of the National Academy of Sciences, USA, 99:1769-1773, 2002. (PMC: 122268)
320. Excitons in a photosynthetic light-harvesting system: A combined molecular dynamics, quantum chemistry and polaron model study. Ana Damjanovic, Ioan Kosztin, Ulrich Kleinekathoefer, and Klaus Schulten. Physical Review E, 65:031919, 2002. (24 pages).
319. A structural model for force regulated integrin binding to fibronectin's RGD-synergy site. André Krammer, David Craig, Wendy E. Thomas, Klaus Schulten, and Viola Vogel. Matrix Biology, 21:139-147, 2002.
318. The mechanism of glycerol conduction in aquaglyceroporins. Morten Ø. Jensen, Emad Tajkhorshid, and Klaus Schulten. Structure, 9:1083-1093, 2001.
317. Photosynthetic apparatus of purple bacteria. Xiche Hu, Thorsten Ritz, Ana Damjanovic, Felix Autenrieth, and Klaus Schulten. Quarterly Reviews of Biophysics, 35:1-62, 2002.
316. The quantum physics of photosynthesis. Thorsten Ritz, Ana Damjanovic, and Klaus Schulten. ChemPhysChem, 3:243-248, 2002.
315. A general random matrix approach to account for the effect of static disorder on the spectral properties of light harvesting systems. Melih Sener and Klaus Schulten. Physical Review E, 65:031916, 2002. (12 pages).
314. Dissecting the molecular origins of protein-nucleic acid recognition: Hydrostatic pressure and molecular dynamics. Thomas W. Lynch, Dorina Kosztin, Mark A. McLean, Klaus Schulten, and Stephen G. Sligar. Biophysical Journal, 82:93-98, 2002. (PMC: 1302451)
313. Molecular dynamics study of aquaporin-1 water channel in a lipid bilayer. Fangqiang Zhu, Emad Tajkhorshid, and Klaus Schulten. FEBS Letters, 504:212-218, 2001.
312. Structural determinants of spectral tuning in retinal proteins - bacteriorhodopsin vs sensory rhodopsin II. Shigehiko Hayashi, Emad Tajkhorshid, Eva Pebay-Peyroula, Antoine Royant, Ehud M. Landau, Javier Navarro, and Klaus Schulten. Journal of Physical Chemistry B, 105:10124-10131, 2001.
311. Kinetics of excitation migration and trapping in the photosynthetic unit of purple bacteria. Thorsten Ritz, Sanghyun Park, and Klaus Schulten. Journal of Physical Chemistry B, 105:8259-8267, 2001.
310. Simulated refolding of stretched titin immunoglobulin domains. Mu Gao, Hui Lu, and Klaus Schulten. Biophysical Journal, 81:2268-2277, 2001. (PMC: 1301698)
309. Comparison of the early stages of forced unfolding of fibronectin type III modules. David Craig, André Krammer, Klaus Schulten, and Viola Vogel. Proceedings of the National Academy of Sciences, USA, 98:5590-5595, 2001. (PMC: 33257)
308. Structural determinants of MscL gating studied by molecular dynamics simulations. Justin Gullingsrud, Dorina Kosztin, and Klaus Schulten. Biophysical Journal, 80:2074-2081, 2001. (PMC: 1301400)
307. Steered molecular dynamics and mechanical functions of proteins. Barry Isralewitz, Mu Gao, and Klaus Schulten. Current Opinion in Structural Biology, 11:224-230, 2001.
306. Physik der Photosynthese. Thorsten Ritz and Klaus Schulten. Physikalische Blaetter, 57:49-53, 2001.
305. Phylogenetic analysis of metabolic pathways. Christian Forst and Klaus Schulten. Journal of Molecular Evolution, 52:471-489, 2001.
304. A system for interactive molecular dynamics simulation. John E. Stone, Justin Gullingsrud, Paul Grayson, and Klaus Schulten. In John F. Hughes and Carlo H. Séquin, editors, 2001 ACM Symposium on Interactive 3D Graphics, pp. 191-194, New York, 2001. ACM SIGGRAPH.
303. Steered molecular dynamics investigations of protein function. Barry Isralewitz, Jerome Baudry, Justin Gullingsrud, Dorina Kosztin, and Klaus Schulten. Journal of Molecular Graphics and Modeling, 19:13-25, 2001. Also in Protein Flexibility and Folding, L. A. Kuhn and M. F. Thorpe, editors, Biological Modeling Series (Elsevier).
302. Molecular dynamics study of bacteriorhodopsin and the purple membrane. Jerome Baudry, Emad Tajkhorshid, Ferenc Molnar, James Phillips, and Klaus Schulten. Journal of Physical Chemistry B, 105:905-918, 2001.