sjplimp's library 58 articles Export

	Control, exploitation and tolerance of intracellular noise [My Copy] Nature, Vol. 420, No. 6912. (14 November 2002), pp. 231-237. by Christopher V. Rao, Denise M. Wolf, Adam P. Arkin posted to cell by sjplimp on 2005-08-29 17:49:22 as along with 10 people and 1 group citemyface jjray rklancer bayesian shivakumar3_14 cudmore mhucka timflutre kfm9876 tvdbulck APprecision
	A dynamic model for determining the middle of Escherichia coli [My Copy] Biophysical Journal, Vol. 82, No. 2. (February 2002) by K. Kruse posted to cell by sjplimp on 2005-08-29 17:18:25 as
	Suppressing roughness of virtual times in parallel discrete-event simulations. [My Copy] Science, Vol. 299, No. 5607. (Jan 2003) by G. Korniss, M. A. Novotny, H. Guclu, Z. Toroczkai, P. A. Rikvold posted to kmc by sjplimp on 2005-08-29 17:18:25 as
	The structure of the protein universe and genome evolution. [My Copy] Nature, Vol. 420, No. 6912. (JanuaryApril 2002) by E. V. Koonin, Y. I. Wolf, G. P. Karev posted to cell by sjplimp on 2005-08-29 17:18:25 as
	Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models [My Copy] ACCOUNTS OF CHEMICAL RESEARCH, Vol. 33, No. 12. (DEC 2000) by P. A. Kollman, I. Massova, C. Reyes, et al.B. Kuhn, S. H. Huo, L. Chong, M. Lee, T. Lee, Y. Duan, W. Wang, O. Donini, P. Cieplak, J. Srinivasan, D. A. Case, T. E. Cheatham posted to biomd by sjplimp on 2005-08-29 17:18:25 as
	Computational systems biology. [My Copy] Nature, Vol. 420, No. 6912. (JanuaryApril 2002) by H. Kitano posted to cell by sjplimp on 2005-08-29 17:18:25 as
	Rough times ahead [My Copy] SCIENCE, Vol. 299, No. 5607. (JAN 2003) by S. Kirkpatrick posted to optimization parallel by sjplimp on 2005-08-29 17:18:25 as
	Hybrid simulation of cellular behavior. [My Copy] Bioinformatics (Oxford), Vol. 20, No. 3. (February 2004) by T. R. Kiehl, R. M. Mattheyses, M. K. Simmons posted to cell by sjplimp on 2005-08-29 17:18:25 as
	Structure and phase transitions in Langmuir monolayers. [My Copy] Reviews of Modern Physics, Vol. 71, No. 3. (APR 1999) by V. M. Kaganer, H. Mohwald, P. Dutta posted to biomd by sjplimp on 2005-08-29 17:18:25 as
	Mechanism of ABC transporters: A molecular dynamics simulation of a well characterized nucleotide-binding subunit [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 99, No. 20. (October 2002) by P. M. Jones, A. M. George posted to biomd by sjplimp on 2005-08-29 17:18:25 as
	Gaussian split Ewald: A fast Ewald mesh method for molecular simulation [My Copy] The Journal of Chemical Physics, Vol. 122, No. 5. (2005) by Yibing Shan, John L. Klepeis, Michael P. Eastwood, Ron O. Dror, David E. Shaw posted to dipole by sjplimp on 2005-08-23 17:56:37 as along with 4 people charris5 stephenbond r2s2 ruvido
	A Rapid Approximation to the Solvent Accessible Surface Areas of Atoms [My Copy] Tetrahedron Computer Methodology, Vol. 1, No. 2. (1988), pp. 103-116. by W. Hasel, T. F. Hendrickson, W. C. Still posted to solvent by sjplimp on 2005-08-22 15:34:13 as along with 1 person mijam
	A domain decomposition molecular dynamics program for the simulation of flexible molecules with an arbitrary topology of Lennard-Jones and/or Gay-Berne sites. [My Copy] Computer Physics Communications, Vol. 134, No. 1. (Feb 2001) by J. Ilnytskyi, M. R. Wilson posted to md by sjplimp on 2005-08-22 15:23:33 as
	Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth [My Copy] Nature (London), Vol. 420, No. 6912. (JanuaryApril 2002) by R. U. Ibarra, J. S. Edwards, B. O. Palsson posted to cell by sjplimp on 2005-08-22 15:23:33 as
	Molecular dynamics and free energy analyses of cathepsin D-inhibitor interactions: Insight into structure-based ligand design [My Copy] Journal of Medicinal Chemistry, Vol. 45, No. 7. (March 2002) by S. H. Huo, J. M. Wang, P. Cieplak, P. A. Kollman, I. D. Kuntz posted to docking by sjplimp on 2005-08-22 15:23:33 as
	From transition paths to transition states and rate coefficients. [My Copy] Journal of Chemical Physics, Vol. 120, No. 2. (Jan 2004) by G. Hummer posted to rubisco by sjplimp on 2005-08-22 15:23:33 as
	Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 100, No. 1. (January 2003) by N. Huang, N. K. Banavali, A. D. Mackerell posted to biomd by sjplimp on 2005-08-22 15:23:33 as
	Pressure tensor of partial-charge and point-dipole lattices with bulk and surface geometries. [My Copy] Physical Review B (Condensed Matter), Vol. 49, No. 2. (JAN 1994) by D. M. Heyes posted to dipole by sjplimp on 2005-08-22 15:23:33 as
	On the calculation of derivatives for Coulomb-type interaction energies and general anisotropic pair potentials. [My Copy] Chemical Physics Letters, Vol. 268, No. 5/6. (APR 1997) by C. Hattig posted to md by sjplimp on 2005-08-22 15:23:33 as
	Engineered gene circuits [My Copy] Nature (London), Vol. 420, No. 6912. (JanuaryApril 2002) by J. Hasty, D. Mcmillen, J. J. Collins posted to cell by sjplimp on 2005-08-22 15:23:33 as
	Parallel tempering algorithm for conformational studies of biological molecules. [My Copy] Chemical Physics Letters, Vol. 281, No. 1/3. (DEC 1997) by U. H. E. Hansmann posted to md by sjplimp on 2005-08-22 15:23:33 as
	Free energy calculations for theophylline binding to an RNA aptamer: Comparison of MM-PBSA and thermodynamic integration methods. [My Copy] Biopolymers, Vol. 68, No. 1. (January 2003) by Hiroaki Gouda, Irwin D. Kuntz, David A. Case, Peter A. Kollman posted to docking by sjplimp on 2005-08-19 15:49:38 as
	Peptide folding simulations. [My Copy] Current Opinion in Structural Biology, Vol. 13, No. 2. (April 2003) by S. Gnanakaran, H. Nymeyer, J. Portman, K. Y. Sanbonmatsu, A. E. Garcia posted to biomd by sjplimp on 2005-08-19 15:49:38 as
	Molecular and mesoscale simulation methods for polymer materials [My Copy] Annual Review of Materials Science, Vol. 32 (February00February 2002) by Sharon C. Glotzer, Wolfgang Paul posted to polymers by sjplimp on 2005-08-19 15:49:38 as
	Efficient exact stochastic simulation of chemical systems with many species and many channels [My Copy] JOURNAL OF PHYSICAL CHEMISTRY A, Vol. 104, No. 9. (MAR 2000) by M. A. Gibson, J. Bruck posted to cell by sjplimp on 2005-08-19 15:49:38 as
	Multi-basin dynamics of a protein in a crystal environment. [My Copy] Physica D In Landscape Paradigms in Physics and Biology. Concepts, Structures and Dynamics. Papers originating from the 16th Annual International Conference of the Center for Nonlinear Studies, 13-17 May 1996, Los Alamos, NM, USA, Vol. 107, No. 2/4. (SEP 1997) by A. E. Garcia, R. Blumenfeld, G. Hummer, J. A. Krumhansl posted to biomd by sjplimp on 2005-08-19 15:49:38 as
	Large-amplitude nonlinear motions in proteins. [My Copy] Physical Review Letters, Vol. 68, No. 17. (APR 1992) by A. E. Garcia posted to biomd by sjplimp on 2005-08-19 15:49:38 as
	Exploring the energy landscape of a beta hairpin in explicit solvent [My Copy] Proteins, Vol. 42, No. 3. (February 2001) by A. E. Garcia, K. Y. Sanbonmatsu posted to biomd by sjplimp on 2005-08-19 15:49:38 as
	Phospholipids undergo hop diffusion in compartmentalized cell membrane [My Copy] Journal of Cell Biology, Vol. 157, No. 6. (June 2002) by T. Fujiwara, K. Ritchie, H. Murakoshi, K. Jacobson, A. Kusumi posted to cell by sjplimp on 2005-08-19 15:25:27 as
	An efficient mean solvation force model for use in molecular dynamics simulations of proteins in aqueous solution [My Copy] Journal of Molecular Biology, Vol. 256, No. 5. (JanuarySeptemberSeptemberJune 1996) by F. Fraternali, W. F. Vangunsteren posted to solvent by sjplimp on 2005-08-19 15:25:27 as
	Evaluation of a fast implicit solvent model for molecular dynamics simulations [My Copy] Proteins, Vol. 46, No. 1. (January 2002) by P. Ferrara, J. Apostolakis, A. Caflisch posted to solvent by sjplimp on 2005-08-19 15:25:27 as
	Soft protein-protein docking in internal coordinates [My Copy] Protein Science, Vol. 11, No. 2. (2002) by J. Fernandez-Recio, M. Totrov, R. Abagyan posted to docking by sjplimp on 2005-08-19 15:25:27 as
	Force field influence on the observation of pi -helical protein structures in molecular dynamics simulations. [My Copy] Journal of Physical Chemistry B, Vol. 107, No. 12. (Mar 2003) by M. Feig, Jr, Iii C. L. Brooks posted to biomd by sjplimp on 2005-08-19 15:25:27 as
	A hybrid particle level set method for improved interface capturing. [My Copy] Journal of Computational Physics, Vol. 183, No. 1. (NOV 2002) by D. Enright, R. Fedkiw, J. Ferziger, I. Mitchell posted to levelset by sjplimp on 2005-08-19 15:25:27 as
	[SMMP] a modern package for simulation of proteins. [My Copy] Computer Physics Communications, Vol. 138, No. 2. (Aug 2001) by F. Eisenmenger, U. H. E. Hansmann, S. Hayryan, C. K. Hu posted to solvent by sjplimp on 2005-08-19 15:25:27 as
	Simulating intracellular stochastic reaction-diffusion systems [My Copy] (2004) by Andreas Doncic posted to cell by sjplimp on 2005-08-18 23:26:45 as
	How to support inheritance and run-time polymorphism in Fortran 90. [My Copy] Computer Physics Communications, Vol. 115, No. 1. (Dec 1998) by V. K. Decyk, C. D. Norton, B. K. Szymanski posted to language by sjplimp on 2005-08-18 23:23:47 as
	The transition between the open and closed states of rubisco is triggered by the inter-phosphate distance of the bound bisphosphate [My Copy] Journal of Molecular Biology, Vol. 298, No. 5. (JanuarySeptember 2000) by A. P. Duff, T. J. Andrews, P. M. G. Curmi posted to rubisco by sjplimp on 2005-08-18 23:09:07 as
	Mesoscopic reaction-diffusion in intracellular signaling. [My Copy] Proceedings of the SPIE - The International Society for Optical Engineering In Fluctuations and Noise in Biological, Biophysical, and Biomedical Systems; Jun 2-4 2003; Santa Fe, NM, United States, Vol. 5110 (February00March 2003) by J. Elf, A. Doncic, M. Ehrenberg posted to cell by sjplimp on 2005-08-18 23:09:07 as
	Surface-stress-induced phase transformation in metal nanowires. [My Copy] Nature Materials, Vol. 2, No. 10. (OCT 2003) by J. K. Diao, K. Gall, M. L. Dunn posted to md by sjplimp on 2005-08-18 23:09:07 as
	A configurational bias Monte Carlo method for linear and cyclic peptides. [My Copy] Molecular Physics, Vol. 87, No. 6. (APR 1996) by M. W. Deem, J. S. Bader posted to mc by sjplimp on 2005-08-18 23:09:07 as
	How to express C++ concepts in Fortran90. [My Copy] Scientific Programming, Vol. 6, No. 4. (1997) by V. K. Decyk, C. D. Norton, B. K. Szymanski posted to language by sjplimp on 2005-08-18 23:09:07 as
	Peptide folding simulations: no solvent required?. [My Copy] Computer Physics Communications, Vol. 123, No. 1/3. (JanuarySeptemberSeptemberSeptember 1999) by X. Daura, A. E. Mark, W. F. van Gunsteren posted to biomd by sjplimp on 2005-08-18 23:09:07 as
	The structure of the tetratricopeptide repeats of protein phosphatase 5: Implications for TPR-mediated protein-protein interactions [My Copy] EMBO (European Molecular Biology Organization) Journal, Vol. 17, No. 5. (March 1998) by A. K. Das, P. T. W. Cohen, D. Barford posted to docking by sjplimp on 2005-08-18 23:09:07 as
	MBO(N)D: a multibody method for long-time molecular dynamics simulations. [My Copy] Journal of Computational Chemistry, Vol. 21, No. 3. (FEB 2000) by H. M. Chun, C. E. Padilla, D. N. Chin, et al.M. Watanabe, V. I. Karlov, H. E. Alper, K. Soosaar, K. B. Blair, O. M. Becker, L. S. D. Caves, R. Nagle, D. N. Haney, B. L. Farmer posted to smmd by sjplimp on 2005-08-18 23:09:07 as
	Dynamical properties of the soft sticky dipole model of water: Molecular dynamics simulations. [My Copy] Journal of Chemical Physics, Vol. 111, No. 6. (AUG 1999) by A. Chandra, T. Ichiye posted to md by sjplimp on 2005-08-18 23:09:07 as
	Comparison of C++ and Fortran 90 for object-oriented scientific programming. [My Copy] Computer Physics Communications, Vol. 105, No. 1. (SEP 1997) by J. R. Cary, S. G. Shasharina, J. C. Cummings, J. V. W. Reynders, P. J. Hinker posted to language by sjplimp on 2005-08-18 23:09:07 as
	An alternative derivation of the equations of motion in torsion space for a branched linear chain [My Copy] Protein Engineering, Vol. 14, No. 11. (November 2001) by C. Bystroff posted to smmd by sjplimp on 2005-08-18 22:50:15 as
	Method for including protein flexibility in protein-ligand docking: improving tools for database mining and virtual screening [My Copy] Journal of Molecular Graphics and Modelling, Vol. 18, No. 3. (Jun 2000) by H. B. Broughton posted to docking by sjplimp on 2005-08-18 22:50:15 as
	Absolute binding free energies: A quantitative approach for their calculation [My Copy] Journal of Physical Chemistry B, Vol. 107, No. 35. (Sep 2003) by S. Boresch, F. Tettinger, M. Leitgeb, M. Karplus posted to biomd by sjplimp on 2005-08-18 22:50:15 as

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