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Biophysical Journal, ISSN 0006-3495, 2007, Volume 93, Issue 9, pp. 3046 - 3057
We investigate A β 17-42 protofibril structures in solution using molecular dynamics simulations. Recently, NMR and computations modeled the A β protofibril as... 
Biophysical Theory and Modeling
Journal Article
Biophysical Journal, ISSN 0006-3495, 2004, Volume 87, Issue 6, pp. 3657 - 3664
The 16–22 amino-acid fragment of the β -amyloid peptide associated with the Alzheimer's disease, A β , is capable of forming amyloid fibrils. Here we study the... 
Biophysical Theory and Modeling
Journal Article
Biophysical Journal, ISSN 0006-3495, 2007, Volume 92, Issue 11, pp. 3817 - 3829
We present here the parmbsc0 force field, a refinement of the AMBER parm99 force field, where emphasis has been made on the correct representation of the /... 
Models, Molecular | DNA - chemistry | Nucleic Acid Conformation | RNA - chemistry | Computer Simulation | Biophysical Theory and Modeling
Journal Article
Biophysical Journal, ISSN 0006-3495, 2006, Volume 91, Issue 9, pp. 3217 - 3229
Several neurodegenerative diseases such as Alzheimer's, Parkinson's, and Huntington's diseases are associated with amyloid fibrils formed by different... 
Biophysical Theory and Modeling
Journal Article
Biophysical Journal, ISSN 0006-3495, 2007, Volume 93, Issue 8, pp. 2622 - 2634
We explore the conformational dynamics of a homology model of the human 7 nicotinic acetylcholine receptor using molecular dynamics simulation and analyses of... 
Biophysical Theory and Modeling
Journal Article
Biophysical Journal, ISSN 0006-3495, 2004, Volume 86, Issue 1, pp. 75 - 84
We develop a mathematical model of the phage lysis/lysogeny switch, taking into account recent experimental evidence demonstrating enhanced cooperativity... 
Biophysical Theory and Modeling
Journal Article
Biophysical Journal, ISSN 0006-3495, 2005, Volume 89, Issue 6, pp. 3680 - 3685
We derive the analytical form of a rate-equilibrium free-energy relationship (with slope Φ) for a bounded, linear chain of coupled reactions having arbitrary... 
Biophysical Theory and Modeling
Journal Article
Biophysical Journal, ISSN 0006-3495, 03/2008, Volume 94, Issue 6, pp. 2007 - 2016
Using a coarse-grained model of the A β peptide, we analyze the Arctic (E22G), Dutch (E22Q), and Flemish (A21G) familial Alzheimer's disease (FAD) mutants for... 
Biophysical Theory and Modeling
Journal Article
Biophysical Journal, ISSN 0006-3495, 2007, Volume 92, Issue 12, pp. 4289 - 4303
A systematic new approach to derive multiscale coarse-grained (MS-CG) models has been recently developed. The approach employs information from atomistically... 
BIOPHYSICS | POTENTIALS | MOLECULAR-DYNAMICS SIMULATION | FORCE-MATCHING METHOD | FIELD | Models, Molecular | Protein Conformation | Algorithms | Models, Chemical | Peptides - chemistry | Computer Simulation | Peptides | Analysis | Models | Molecules | Biophysical Theory and Modeling
Journal Article
Biophysical Journal, ISSN 0006-3495, 12/2008, Volume 95, Issue 12, pp. 5606 - 5617
Journal Article
Biophysical Journal, ISSN 0006-3495, 2004, Volume 87, Issue 4, pp. 2203 - 2214
Major histocompatibility complex class I proteins play a key role in the recognition and presentation of peptide antigens to the host immune system. The... 
Biophysical Theory and Modeling
Journal Article
Biophysical Journal, ISSN 0006-3495, 2004, Volume 87, Issue 5, pp. 2954 - 2967
The enzyme F 1 -adenosine triphosphatase (ATPase) is a molecular motor that converts the chemical energy stored in the molecule adenosine triphosphate (ATP)... 
Biophysical Theory and Modeling
Journal Article
Biophysical Journal, ISSN 0006-3495, 07/2008, Volume 95, Issue 1, pp. 155 - 165
Journal Article
Biophysical Journal, ISSN 0006-3495, 2007, Volume 93, Issue 10, pp. 3382 - 3391
A properly identified transition state ensemble (TSE) in a molecular dynamics (MD) simulation can reveal a tremendous amount about how a protein folds and... 
Biophysical Theory and Modeling
Journal Article