TCB Publications - Search
301. Efficient light harvesting through carotenoids. Thorsten Ritz, Ana Damjanovic, Klaus Schulten, Jian-Ping Zhang, and Yasushi Koyama. Photosynthesis Research, 66:125-144, 2000.
300. The key event in force-induced unfolding of titin's immunoglobulin domains. Hui Lu and Klaus Schulten. Biophysical Journal, 79:51-65, 2000. (PMC: 1300915)
299. To students contemplating research in biomolecular modelling. Klaus Schulten. Journal of Molecular Graphics and Modeling, 18:218-220, 2000.
298. Calculations suggest a pathway for the transverse diffusion of a hydrophobic peptide across a lipid bilayer. Amit Kessel, Klaus Schulten, and Nir Ben-Tal. Biophysical Journal, 79:2322-2330, 2000. (PMC: 1301120)
297. Electron transfer: Exploiting thermal motion. Klaus Schulten. Science, 290:61-62, 2000.
296. Excitation transfer in the peridinin-chlorophyll-protein of Amphidinium carterae. Ana Damjanovic, Thorsten Ritz, and Klaus Schulten. Biophysical Journal, 79:1695-1705, 2000. (PMC: 1301064)
295. Simulated unbinding and binding of fatty acid substrates in the cyclooxygenase site of prostaglandin H2 synthase-1. Ferenc Molnar, Lawrence S. Norris, and Klaus Schulten. Progress in Reaction Kinetics and Mechanism, 25:263-298, 2000.
294. Speech/gesture interface to a visual-computing environment. Rajeev Sharma, Michael Zeller, Vladimir I. Pavlovic, Thomas S. Huang, Zion Lo, Stephen Chu, Yunxin Zhao, James C. Phillips, and Klaus Schulten. IEEE Computer Graphics and Applications, 20:29-37, 2000.
293. Characterization of a conical intersection between the ground and first excited state for a retinal analog. Ferenc Molnar, Michal Ben-Nun, Todd J. Martínez, and Klaus Schulten. Journal of Molecular Structure (THEOCHEM), WATOC special issue, 506:169-178, 2000.
292. The fast multipole algorithm. John Board and Klaus Schulten. IEEE Computational Science & Engineering, 2:56-59, 2000.
291. Group report: How does complexity lead to an apparently simple function? K. Moffat, J.-P. Changeux, D. M. Crothers, H. Grubmueller, G. U. Nienhaus, M. U. Palma, F. G. Parak, K. Schulten, and A. Warshel. In H. Frauenfelder, J. Deisenhofer, and P. G. Wolynes, editors, Simplicity and Complexity in Proteins and Nucleic Acids, pp. 255-280, Berlin, 1999. Dahlem University Press.
290. Elastic rod model of a DNA loop in the lac operon. Alexander Balaeff, L. Mahadevan, and Klaus Schulten. Physical Review Letters, 83:4900-4903, 1999.
289. Evolution of metabolisms: A new method for the comparison of metabolic pathways using genomics information. Christian Forst and Klaus Schulten. Journal of Computational Biology, 6:343-360, 1999.
288. Excitation energy trapping by the reaction center of Rhodobacter sphaeroides. Ana Damjanovic, Thorsten Ritz, and Klaus Schulten. Int. J. Quantum Chem., 77:139-151, 2000.
287. A model for photoreceptor-based magnetoreception in birds. Thorsten Ritz, Salih Adem, and Klaus Schulten. Biophysical Journal, 78:707-718, 2000. (PMC: 1300674)
286. Mechanical unfolding intermediates in titin modules. Piotr E. Marszalek, Hui Lu, Hongbin Li, Mariano Carrion-Vazquez, Andres F. Oberhauser, Klaus Schulten, and Julio M. Fernandez. Nature, 402:100-103, 1999.
285. Molecular dynamics study of the nature and origin of retinal's twisted structure in bacteriorhodopsin. Emad Tajkhorshid, Jerome Baudry, Klaus Schulten, and Sandor Suhai. Biophysical Journal, 78:683-693, 2000. (PMC: 1300671)
284. Computer modeling of force-induced titin domain unfolding. Hui Lu, André Krammer, Barry Isralewitz, Viola Vogel, and Klaus Schulten. In Jerry Pollack and Henk Granzier, editors, Elastic Filaments of the Cell, chapter 1, pp. 143-162. Kluwer Academic/Plenum Publishers, New York, NY, 2000.
283. Steered molecular dynamics simulation of the Rieske subunit motion in the cytochrome bc1 complex. Sergei Izrailev, Antony R. Crofts, Edward A. Berry, and Klaus Schulten. Biophysical Journal, 77:1753-1768, 1999.
282. Probing the role of structural water in a duplex oligodeoxyribonucleotide containing a water-mimicking base analogue. Dorina Kosztin, Richard Gumport, and Klaus Schulten. Nucleic Acids Research, 27:3550-3556, 1999. (PMC: 148600)
281. Steered molecular dynamics simulation of conformational changes of immunoglobulin domain I27 interpret atomic force microscopy observations. Hui Lu and Klaus Schulten. Chemical Physics, 247:141-153, 1999.
280. Evolution of metabolisms: A new method for the comparison of metabolic pathways. Christian V. Forst and Klaus Schulten. In Sorin Istrail, Pavel Pevzner, and Michael Waterman, editors, Proceedings of the Third Annual International Conference on Computational Molecular Biology, pp. 174-180, Lyon, France, 1999. ACM Press, New York.
279. Steered molecular dynamics simulations of force-induced protein domain unfolding. Hui Lu and Klaus Schulten. PROTEINS: Structure, Function, and Genetics, 35:453-463, 1999.
278. Algorithmic challenges in computational molecular biophysics. Tamar Schlick, Robert Skeel, Axel Brünger, Laxmikant Kalé, John A. Board Jr., Jan Hermans, and Klaus Schulten. Journal of Computational Physics, 151:9-48, 1999.
277. Forced unfolding of the fibronectin type III module reveals a tensile molecular recognition switch. André Krammer, Hui Lu, Barry Isralewitz, Klaus Schulten, and Viola Vogel. Proceedings of the National Academy of Sciences, USA, 96:1351-1356, 1999. (PMC: 15466)
276. NAMD2: Greater scalability for parallel molecular dynamics. Laxmikant Kalé, Robert Skeel, Milind Bhandarkar, Robert Brunner, Attila Gursoy, Neal Krawetz, James Phillips, Aritomo Shinozaki, Krishnan Varadarajan, and Klaus Schulten. Journal of Computational Physics, 151:283-312, 1999.
275. Reconstructing potentials of mean force through time series analysis of steered molecular dynamics simulations. Justin Gullingsrud, Rosemary Braun, and Klaus Schulten. Journal of Computational Physics, 151:190-211, 1999.
274. Investigating a back door mechanism of actin phosphate release by steered molecular dynamics. Willy Wriggers and Klaus Schulten. PROTEINS: Structure, Function, and Genetics, 35:262-273, 1999.
273. Self-organizing neural networks bridge the biomolecular resolution gap. Willy Wriggers, Ronald A. Milligan, Klaus Schulten, and J. Andrew McCammon. Journal of Molecular Biology, 284:1247-1254, 1998.
272. BioCoRE: A collaboratory for structural biology. Milind Bhandarkar, Gila Budescu, William Humphrey, Jesus A. Izaguirre, Sergei Izrailev, Laxmikant V. Kalé, Dorina Kosztin, Ferenc Molnar, James C. Phillips, and Klaus Schulten. In Agostino G. Bruzzone, Adelinde Uchrmacher, and Ernest H. Page, editors, Proceedings of the SCS International Conference on Web-Based Modeling and Simulation, pp. 242-251, San Francisco, California, 1999.
271. Light-harvesting and photoprotection by carotenoids: Structure-based calculations for photosynthetic antenna systems. Thorsten Ritz, Ana Damjanovic, and Klaus Schulten. In G. Garab, editor, Photosynthesis: Mechanisms and Effects (Proceedings of the XIth International Congress on Photosynthesis), volume 1, pp. 487-490, Dordrecht, 1998. Kluwer Academic Publications.
270. Unbinding of retinoic acid from its receptor studied by steered molecular dynamics. Dorina Kosztin, Sergei Izrailev, and Klaus Schulten. Biophysical Journal, 76:188-197, 1999.
269. Electronic excitations in aggregates of bacteriochlorophylls. Marshall G. Cory, Michael C. Zerner, Xiche Hu, and Klaus Schulten. Journal of Physical Chemistry B, 102:7640-7650, 1998.
268. From simplicity to complexity and back: Function, architecture and mechanism of light harvesting systems in photosynthetic bacteria. Klaus Schulten. In H. Frauenfelder, J. Deisenhofer, and P. G. Wolynes, editors, Simplicity and Complexity in Proteins and Nucleic Acids, pp. 227-253, Berlin, 1999. Dahlem University Press. (pdf available from author upon request).
267. Expansion method for stationary states of quantum billiards. David Kaufman, Ioan Kosztin, and Klaus Schulten. American Journal of Physics, 67:133-141, 1999.
266. Three electronic state model of the primary phototransformation of bacteriorhodopsin. W. Humphrey, H. Lu, I. Logunov, H. J. Werner, and K. Schulten. Biophysical Journal, 75:1689-1699, 1998.
265. Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation. Hui Lu, Barry Isralewitz, André Krammer, Viola Vogel, and Klaus Schulten. Biophysical Journal, 75:662-671, 1998.
264. Energy transfer between carotenoids and bacteriochlorophylls in a light harvesting protein. Ana Damjanovic, Thorsten Ritz, and Klaus Schulten. Physical Review E, 59:3293-3311, 1999.
263. A model for the light-harvesting complex I (B875) of Rhodobacter sphaeroides. Xiche Hu and Klaus Schulten. Biophysical Journal, 75:683-694, 1998.
262. Quantum dynamics of retinal's femtosecond photoisomerization in bacteriorhodopsin. Michal Ben-Nun, Ferenc Molnar, Hui Lu, James C. Phillips, Todd J. Martínez, and Klaus Schulten. In Faraday Discussions, No. 110, pp. 447-462. Faraday Publications, 1998.
261. Structure and dynamics of calmodulin in solution. Willy Wriggers, Ernest Mehler, Felicia Pitici, Harel Weinstein, and Klaus Schulten. Biophysical Journal, 74:1622-1639, 1998.
260. The use of solid physical models for the study of macromolecular assembly. Michael Bailey, Klaus Schulten, and John E. Johnson. Current Opinion in Structural Biology, 8:202-208, 1998.
259. Architecture and function of the light harvesting apparatus of purple bacteria. Xiche Hu, Ana Damjanovic, Thorsten Ritz, and Klaus Schulten. Proceedings of the National Academy of Sciences, USA, 95:5935-5941, 1998. (PMC: 34498)
258. Nucleotide-dependent movements of the kinesin motor domain predicted by simulated annealing. Willy Wriggers and Klaus Schulten. Biophysical Journal, 75:646-661, 1998.
257. A three-dimensional model of the morphogenesis of the rhesus lateral geniculate nucleus. Svilen Tzonev, Joseph Malpeli, and Klaus Schulten. Beckman Institute Technical Report, University of Illinois, 1998.
256. Avoiding algorithmic obfuscation in a message-driven parallel MD code. James C. Phillips, Robert Brunner, Aritomo Shinozaki, Milind Bhandarkar, Neal Krawetz, Laxmikant Kalé, Robert D. Skeel, and Klaus Schulten. In P. Deuflhard, J. Hermans, B. Leimkuhler, A. Mark, S. Reich, and R. D. Skeel, editors, Computational Molecular Dynamics: Challenges, Methods, Ideas, volume 4 of Lecture Notes in Computational Science and Engineering, pp. 472-482. Springer-Verlag, 1998.
255. Steered molecular dynamics. Sergei Izrailev, Sergey Stepaniants, Barry Isralewitz, Dorina Kosztin, Hui Lu, Ferenc Molnar, Willy Wriggers, and Klaus Schulten. In P. Deuflhard, J. Hermans, B. Leimkuhler, A. E. Mark, S. Reich, and R. D. Skeel, editors, Computational Molecular Dynamics: Challenges, Methods, Ideas, volume 4 of Lecture Notes in Computational Science and Engineering, pp. 39-65. Springer-Verlag, Berlin, 1998.
254. Excitons and excitation transfer in the photosynthetic unit of purple bacteria. Thorsten Ritz, Xiche Hu, Ana Damjanovic, and Klaus Schulten. Journal of Luminescence, 76-77:310-321, 1998.
253. Structure prediction of a complex between the chromosomal protein HMG-D and DNA. Alexander Balaeff, Mair E. A. Churchill, and Klaus Schulten. PROTEINS: Structure, Function, and Genetics, 30:113-135, 1998.
252. Oxygen and proton pathways in cytochrome c oxidase. Ivo Hofacker and Klaus Schulten. PROTEINS: Structure, Function, and Genetics, 30:100-107, 1998.
251. Extraction of lipids from phospholipid membranes by steered molecular dynamics. Sergey Stepaniants, Sergei Izrailev, and Klaus Schulten. Journal of Molecular Modeling, 3:473-475, 1997.
250. Binding pathway of retinal to bacterio-opsin: A prediction by molecular dynamics simulations. Barry Isralewitz, Sergei Izrailev, and Klaus Schulten. Biophysical Journal, 73:2972-2979, 1997. (PMC: 1181203)
249. Predicting the structure of apolipoprotein A-I in reconstituted high density lipoprotein disks. James C. Phillips, Willy Wriggers, Zhigang Li, Ana Jonas, and Klaus Schulten. Biophysical Journal, 73:2337-2346, 1997. (PMC: 1181137)
248. How nature harvests sunlight. Xiche Hu and Klaus Schulten. Physics Today, 50:28-34, 1997.
247. A visual computing environment for very large scale biomolecular modeling. Michael Zeller, James C. Phillips, Andrew Dalke, William Humphrey, Klaus Schulten, Rajeev Sharma, T. S. Huang, V. I. Pavlovic, Y. Zhao, Z. Lo, and S. Chu. In Proceedings of the 1997 IEEE International Conference on Application-specific Systems, Architectures and Processors (ASAP), pp. 3-12. IEEE Computer Society Press, 1997.
246. Learning the perceptual control manifold for sensor-based robot path planning. Michael Zeller, Rajeev Sharma, and Klaus Schulten. In Proceedings of the 1997 IEEE International Symposium on Computational Intelligence in Robotics and Automation (CIRA'97), pp. 48-53. IEEE Computer Society Press, 1997.
245. Stability and dynamics of G-actin: Back door water diffusion and behavior of a subdomain 3/4 loop. Willy Wriggers and Klaus Schulten. Biophysical Journal, 73:624-639, 1997. (PMC: 1180962)
244. Reconstructing potential energy functions from simulated force-induced unbinding processes. Manel Balsera, Sergey Stepaniants, Sergei Izrailev, Yoshitsugu Oono, and Klaus Schulten. Biophysical Journal, 73:1281-1287, 1997.
243. Binding of the estrogen receptor to DNA: The role of waters. Dorina Kosztin, Thomas C. Bishop, and Klaus Schulten. Biophysical Journal, 73:557-570, 1997. (PMC: 1180957)
242. Difficulties with multiple time stepping and the fast multipole algorithm in molecular dynamics. Thomas C. Bishop, Robert D. Skeel, and Klaus Schulten. Journal of Computational Chemistry, 18:1785-1791, 1997.
241. Protein domain movements: Detection of rigid domains and visualization of hinges in comparisons of atomic coordinates. Willy Wriggers and Klaus Schulten. PROTEINS: Structure, Function, and Genetics, 29:1-14, 1997.
240. Pigment organization and transfer of electronic excitation in the purple bacteria. Xiche Hu, Thorsten Ritz, Ana Damjanovic, and Klaus Schulten. Journal of Physical Chemistry B, 101:3854-3871, 1997.
239. Boundary integral method for stationary states of two-dimensional quantum systems. Ioan Kosztin and Klaus Schulten. Int. J. of Modern Phys. C, 8:293-325, 1997.
238. Vision-based robot motion planning using a topology representing neural network. Michael Zeller, Rajeev Sharma, and Klaus Schulten. In Jens Kalkkuhl, Ken Hunt, Rafal Zbikowski, and Andrzej Dzielinski, editors, Applications of Neural Adaptive Control Technology, volume 17 of World Scientific Series in Robotics and Intelligent Systems, pp. 181-204. World Scientific Publishing, 1997.
237. How hormone receptor-DNA binding affects nucleosomal DNA: The role of symmetry. Tom Connor Bishop, Dorina Kosztin, and Klaus Schulten. Biophysical Journal, 72:2056-2067, 1997. (PMC: 1184400)
236. Molecular dynamics study of unbinding of the avidin-biotin complex. Sergei Izrailev, Sergey Stepaniants, Manel Balsera, Yoshi Oono, and Klaus Schulten. Biophysical Journal, 72:1568-1581, 1997. (PMC: 1184352)
235. Motion planning of a pneumatic robot using a neural network. Michael Zeller, Rajeev Sharma, and Klaus Schulten. IEEE Control Systems Magazine, 17:89-98, 1997.
234. Photoproducts of bacteriorhodopsin mutants: A molecular dynamics study. William Humphrey, Ernst Bamberg, and Klaus Schulten. Biophysical Journal, 72:1347-1356, 1997. (PMC: 1184517)
233. Theory of heterogeneous relaxation in compartmentalized tissues. Daniel Barsky, Benno Pütz, and Klaus Schulten. Magnetic Resonance in Medicine, 37:666-675, 1997.
232. Using TCL for molecular visualization and analysis. Andrew Dalke and Klaus Schulten. In Proceedings of the Pacific Symposium on Biocomputing '97, volume 2, pp. 85-96, 1997.