Research at
a Glance

Molecules
to Organisms

Methodological
Focus

Collaborations

Research
in Progress

Outreach

References

Gallery

Research at a Glance:
References

[1]

H. Ritter, T. Martinetz, and K. Schulten, Textbook: Neural Computation and Self-Organizing Maps: An Introduction, Addison-Wesley, New York, revised English edition, 1992.

[2]

K. Obermayer, G. Blasdel, and K. Schulten, Statistical-mechanical analysis of self-organization and pattern formation during the development of visual maps, Phys. Rev. A, 45(10):7568-7589, May 1992.

[3]

K. Schulten and M. Tesch, Coupling of protein motion to electron transfer: Molecular dynamics and stochastic quantum mechanics study of photosynthetic reaction centers, Chem. Phys., 158:421-446, 1991.

[4]

K. Schulten, W. Humphrey, I. Logunov, M. Sheves, and D. Xu, Molecular dynamics studies of bacteriorhodopsin's photocycles , Israel J. Chem., 35:447-464, 1995.

[5]

I. Hofacker and K. Schulten, Oxygen and proton pathways in cytochrome c oxidase, Proteins: Structure, Function, and Genetics, 30(1):100-107, 1998.

[6]

X. Hu, A. Damjanovi\'c, T. Ritz, and K. Schulten, Architecture and function of the light harvesting apparatus of purple bacteria, Proc. Natl. Acad. Sci. USA, 95:5935-5941, 1998.

[7]

A. Damjanovi\'c, T. Ritz, and K. Schulten, Energy transfer between carotenoids and bacteriochlorophylls in a light harvesting protein, Phys. Rev. E, 59:3293-3311, 1999.

[8]

S. Izrailev, A. R. Crofts, E. A. Berry, and K. Schulten, Steered molecular dynamics simulation of the Rieske subunit motion in the cytochrome bc₁ complex, Biophys. J., 77:1753-1768, 1999.

[9]

D. Kosztin, T. C. Bishop, and K. Schulten, Binding of the estrogen receptor to DNA: The role of waters , Biophys. J., 73:557-570, 1997.

[10]

A. Balaeff, M. E. A. Churchill, and K. Schulten, Structure prediction of a complex between the chromosomal protein HMG-D and DNA, Proteins: Structure, Function, and Genetics, 30(1):113-135, 1998.

[11]

A. Balaeff, L. Mahadevan, and K. Schulten, Elastic rod model of a DNA loop in the lac operon, Phys. Rev. Lett., 83(23):4900-4903, 1999.

[12]

J. C. Phillips, W. Wriggers, Z. Li, A. Jonas, and K. Schulten, Predicting the structure of apolipoprotein A-I in reconstituted high density lipoprotein disks, Biophys. J., 73:2337-2346, 1997.

[13]

H. Lu, B. Isralewitz, A. Krammer, V. Vogel, and K. Schulten, Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation, Biophys. J., 75:662-671, 1998.

[14]

A. Szabo, K. Schulten, and Z. Schulten, First passage time approach to diffusion controlled reactions , J. Chem. Phys., 72:4350-4357, 1980.

[15]

W. Nadler and K. Schulten, Generalized moment expansion for Brownian relaxation processes , J. Chem. Phys., 82:151-160, 1985.

[16]

K. Schulen and I. R. Epstein, Recombination of radical pairs in high magnetic fields: A path integral-Monte Carlo treatment, J. Chem. Phys., 71:309-316, 1979.

[17]

G. Lamm and K. Schulten, Extended Brownian dynamics: II. Reactive, nonlinear diffusion , J. Chem. Phys., 78:2713-2734, 1983.

[18]

T. Martinetz and K. Schulten, Topology representing networks, Neural Networks, 7(3):507-522, 1994.

[19]

D. Xu and K. Schulten, Velocity reassignment echoes in proteins, J. Chem. Phys., 103:3124-3139, 1995.

[20]

B. Pütz, D. Barsky, and K. Schulten, Edge enhancement by diffusion in microscopic magnetic resonance imaging, J. Magn. Resn., 97:27-53, 1992.

[21]

D. Xu and K. Schulten, Coupling of protein motion to electron transfer in a photosynthetic reaction center: Investigating the low temperature behaviour in the framework of the spin-boson model, Chem. Phys., 182:91-117, 1994.

[22]

K. Schulten, Curve crossing in a protein: Coupling of the elementary quantum process to motions of the protein, In D. Bicout and M. J. Field, editors, Proceedings of the Ecole de Physique des Houches, pages 85-118, Paris, 1995. Les Editions de Physique, Springer.

[23]

K. Schulten and M. Karplus, On the origin of a low-lying forbidden transition in polyenes and related molecules, Chem. Phys. Lett., 14(3):305-309, 1972.

[24]

P. Tavan and K. Schulten, Electronic excitations in finite and infinite polyenes, Phys. Rev. B, 36(8):4337-4358, 1987.

[25]

K. Schulten and P. Tavan, A mechanism for the light-driven proton pump of Halobacterium halobium, Nature, 272:85-86, 1978.

[26]

P. Tavan, K. Schulten, and D. Oesterhelt, The effect of protonation and electrical interactions on the stereochemistry of retinal Schiff bases, Biophys. J., 47:415-430, 1985.

[27]

I. Logunov and K. Schulten, Quantum chemistry - molecular dynamics study of the dark adaptation process in bacteriorhodopsin, J. Am. Chem. Soc., 118:9727-9735, 1996.

[28]

M. Ben-Nun, F. Molnar, H. Lu, J. C. Phillips, T. J. Martínez, and K. Schulten, Quantum dynamics of retinal's femtosecond photoisomerization in bacteriorhodopsin, In Faraday Discussions, No. 110, pages 447-462. Faraday Publications, December 1998.

[29]

F. Molnar, M. Ben-Nun, T. J. Martínez, and K. Schulten, Characterization of a conical intersection between the ground and first excited state for a retinal analog, Journal of Molecular Structure (THEOCHEM), a special WATOC issue, 1999, In press.

[30]

H. Grubmüller, H. Heller, A. Windemuth, and K. Schulten, Generalized Verlet algorithm for efficient molecular dynamics simulations with long-range interactions, Molecular Simulation, 6:121-142, 1991.

[31]

J. A. Board, Jr., J. W. Causey, J. F. Leathrum, Jr., A. Windemuth, and K. Schulten, Accelerated molecular dynamics simulation with the parallel fast multipole algorithm, Chem. Phys. Lett., 198:89-94, 1992.

[32]

K. Sarkar and K. Schulten, Topology representing network in robotics , In J. L. van Hemmen, E. Domany, and K. Schulten, editors, Models of Neural Networks, volume 3 of Physics of Neural Networks, pages 281-302. Springer-Verlag, New York, 1996.

[33]

M. Zeller, R. Sharma, and K. Schulten, Motion planning of a pneumatic robot using a neural network , IEEE Control Systems Magazine, 17:89-98, 1997.

[34]

H. Heller, H. Grubmüller, and K. Schulten, Molecular dynamics simulation on a parallel computer , Molecular Simulation, 5:133-165, 1990.

[35]

M. Nelson, W. Humphrey, A. Gursoy, A. Dalke, L. Kalé, R. Skeel, K. Schulten, and R. Kufrin, MDScope - A visual computing environment for structural biology , Comput. Phys. Commun., 91(1, 2 and 3):111-134, 1995.

[36]

L. Kalé, R. Skeel, M. Bhandarkar, R. Brunner, A. Gursoy, N. Krawetz, J. Phillips, A. Shinozaki, K. Varadarajan, and K. Schulten, NAMD2: Greater scalability for parallel molecular dynamics , J. Comp. Phys., 151:283-312, 1999.

[37]

W. F. Humphrey, A. Dalke, and K. Schulten, VMD - Visual Molecular Dynamics , J. Mol. Graphics, 14:33-38, 1996.

[38]

M. Bhandarkar, G. Budescu, W. F. Humphrey, J. A. Izaguirre, S. Izrailev, L. V. Kalé, D. Kosztin, F. Molnar, J. C. Phillips, and K. Schulten, BioCoRE: A collaboratory for structural biology , In A. G. Bruzzone, A. Uchrmacher, and E. H. Page, editors, Proceedings of the SCS International Conference on Web-Based Modeling and Simulation, pages 242-251, San Francisco, California, 1999.

[39]

R. Peters, A. Brünger, and K. Schulten, Continuous fluorescence microphotolysis: A sensitive method for study of diffusion processes in single cells, Proc. Natl. Acad. Sci. USA, 78:962-966, 1981.

[40]

K. Schulten, H. Staerk, A. Weller, H.-J. Werner, and B. Nickel, Magnetic field dependence of the geminate recombination of radical ion pairs in polar solvents, Z. Phys. Chem., NF101:371-390, 1976.

[41]

D. Barsky, B. Pütz, K. Schulten, and R. L. Magin, Theory of paramagnetic contrast agents in liposome systems , Magn. Reson. Med., 24:1-13, 1992.

[42]

J. Koepke, X. Hu, C. Münke, K. Schulten, and H. Michel, The crystal structure of the light harvesting complex II (B800-850) from Rhodospirillum molischianum, Structure, 4:581-597, 1996.

[43]

D. Barsky, B. Pütz, K. Schulten, J. Schoeniger, E. W. Hsu, and S. Blackband, Diffusional edge enhancement observed by NMR in thin glass capillaries, Chem. Phys. Lett., 200:88-96, 1992.

[44]

S. Tzonev, J. Malpeli, and K. Schulten, Morphogenesis of the lateral geniculate nucleus: How singularities affect global structure, In G. Tesauro, D. Touretzky, and T. Leen, editors, Advances in Neural Information Processing Systems 7, pages 133-140, Cambridge, Mass and London, England, 1995. MIT Press.

[45]

Q. Sheng, K. Schulten, and C. Pidgeon, A molecular dynamics simulation of immobilized artificial membranes , J. Phys. Chem., 99(27):11018-11027, 1995.

[46]

D. Kosztin, R. Gumport, and K. Schulten, Probing the role of structural water in a duplex oligodeoxyribonucleotide containing a water-mimicking base analogue, Nucleic Acids Research, 27(17):3550-3556, 1999.

[47]

P. E. Marszalek, H. Lu, H. Li, M. Carrion-Vazquez, A. F. Oberhauser, K. Schulten, and J. M. Fernandez, Mechanical unfolding intermediates in titin modules , Nature, 402:100-103, 1999.

[48]

K. Schulten, From simplicity to complexity and back: Function, architecture and mechanism of light harvesting systems in photosynthetic bacteria, In H. Frauenfelder, J. Deisenhofer, and P. G. Wolynes, editors, Simplicity and Complexity in Proteins and Nucleic Acids, Berlin, 1998. Dahlem University Press, In press.

[49]

H. Heller, M. Schaefer, and K. Schulten, Molecular dynamics simulation of a bilayer of 200 lipids in the gel and in the liquid crystal-phases, J. Phys. Chem., 97:8343-8360, 1993.

[50]

F. Zhou and K. Schulten, Molecular dynamics study of a membrane-water interface, J. Phys. Chem., 99:2194-2208, 1995.

[51]

X. Hu and K. Schulten, A model for the light-harvesting complex I (B875) of Rhodobacter sphaeroides, Biophys. J., 75:683-694, 1998.

[52]

M. Bailey, K. Schulten, and J. E. Johnson, The use of solid physical models for the study of macromolecular assembly, Current Opinion in Structural Biology, 8:202-208, 1998.

[53]

W. Wriggers, R. A. Milligan, K. Schulten, and J. A. McCammon, Self-organizing neural networks bridge the biomolecular resolution gap, J. Mol. Biol., 284:1247-1254, 1998.

[54]

J. Gullingsrud, R. Braun, and K. Schulten, Reconstructing potentials of mean force through time series analysis of steered molecular dynamics simulations, J. Comp. Phys., 151:190-211, 1999.

[55]

S. Izrailev, S. Stepaniants, M. Balsera, Y. Oono, and K. Schulten, Molecular dynamics study of unbinding of the avidin-biotin complex , Biophys. J., 72:1568-1581, 1997.

[56]

B. Isralewitz, S. Izrailev, and K. Schulten, Binding pathway of retinal to bacterio-opsin: A prediction by molecular dynamics simulations, Biophys. J., 73:2972-2979, 1997.

[57]

W. Wriggers and K. Schulten, Investigating a back door mechanism of actin phosphate release by steered molecular dynamics, Proteins: Structure, Function, and Genetics, 35:262-273, 1999.

[58]

D. Kosztin, S. Izrailev, and K. Schulten, Unbinding of retinoic acid from its receptor studied by steered molecular dynamics, Biophys. J., 76:188-197, 1999.

[59]

S. Stepaniants, S. Izrailev, and K. Schulten, Extraction of lipids from phospholipid membranes by steered molecular dynamics, Journal of Molecular Modeling, 3:473-475, 1997.

[60]

A. Krammer, H. Lu, B. Isralewitz, K. Schulten, and V. Vogel, Forced unfolding of the fibronectin type III module reveals a tensile molecular recognition switch, Proc. Natl. Acad. Sci. USA, 96:1351-1356, 1999.

[61]

H. Lu and K. Schulten, Steered molecular dynamics simulations of force-induced protein domain unfolding, Proteins: Structure, Function, and Genetics, 35:453-463, 1999.

[62]

H. Lu and K. Schulten, Steered molecular dynamics simulation of conformational changes of immunoglobulin domain I27 interpret atomic force microscopy observations, Chem. Phys., 247:141-153, 1999.

[63]

T. Schlick, R. Skeel, A. Brünger, L. Kalé, J. A. Board Jr., J. Hermans, and K. Schulten, Algorithmic challenges in computational molecular biophysics , J. Comp. Phys., 151:9-48, 1999.