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Journal of Physical Chemistry B, ISSN 1520-6106, 02/2019, Volume 123, Issue 5, pp. 1116 - 1128
We perform molecular dynamics simulations to study the effects of temperature and pressure on the water-mediated interaction (WMI) between two nanoscale... 
HYDROPHOBIC INTERACTIONS | TRANSITION | FORCE | STABILITY | CHEMISTRY, PHYSICAL | TRP-CAGE | MODEL | COLD DENATURATION | PHASE-DIAGRAM | HYDRATION | DEPENDENCE
Journal Article
Journal of Physical Chemistry B, ISSN 1520-6106, 05/2004, Volume 108, Issue 21, pp. 6571 - 6581
A rigorous formalism for the extraction of state-to-state transition functions from a Boltzmann-weighted ensemble of microcanonical molecular dynamics... 
TOPOLOGY | BETA-HAIRPIN | MARKOV-CHAINS | LANDSCAPE | LUMPABILITY | MASTER EQUATION | CHEMISTRY, PHYSICAL | BLUE GENE | TRP-CAGE | FREE-ENERGY | SURFACES
Journal Article
Journal of Physical Chemistry B, ISSN 1520-6106, 12/2018, Volume 122, Issue 50, pp. 11931 - 11952
The stability and folding of proteins is governed by the underlying single-molecule free energy surface (smFES) mapping the free energy of the molecule as a... 
ATTRACTORS | DESIGN | VARIATIONAL APPROACH | FREE-ENERGY LANDSCAPES | NONLINEAR DIMENSIONALITY REDUCTION | DYNAMICS | CHEMISTRY, PHYSICAL | TRP-CAGE | DIFFUSION MAPS | SIMULATIONS | FORCED SYSTEMS
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 04/2013, Volume 9, Issue 4, pp. 2020 - 2034
Journal Article
BIOPHYSICAL JOURNAL, ISSN 0006-3495, 08/2014, Volume 107, Issue 4, pp. 991 - 997
Cooperativity is a central feature in the formation of secondary structures in proteins. However, the driving forces behind this cooperativity are poorly... 
POLARIZABLE FORCE-FIELD | BETA-HAIRPIN | ALPHA-HELIX | BIOPHYSICS | COIL TRANSITION | ALANINE-BASED PEPTIDES | PROTEIN-FOLDING SIMULATIONS | TRP-CAGE | HUMAN LYSOZYME | MOLECULAR-DYNAMICS SIMULATIONS | CHARMM
Journal Article
Nature Physics, ISSN 1745-2473, 10/2010, Volume 6, Issue 10, pp. 751 - 758
Journal Article
Journal Article
JOURNAL OF PHYSICAL CHEMISTRY B, ISSN 1520-6106, 07/2010, Volume 114, Issue 26, pp. 8790 - 8798
Despite initial successes in folding of proteins by molecular simulation, it is becoming increasingly evident that current energy functions (force fields) tend... 
HAIRPIN FORMATION | EXPLICIT SOLVENT | FREE-ENERGY LANDSCAPE | TRP-CAGE MINIPROTEIN | DATA-BANK | FORCE-FIELD PARAMETERS | CHEMISTRY, PHYSICAL | UNFOLDED PROTEINS | MOLECULAR-DYNAMICS SIMULATIONS | REPLICA-EXCHANGE SIMULATIONS | IMPLICIT SOLVENT
Journal Article
The Journal of Chemical Physics, ISSN 0021-9606, 01/2019, Volume 150, Issue 2, pp. 024103 - 024103
Many rare event transitions involve multiple collective variables (CVs), and the most appropriate combination of CVs is generally unknown a priori. We thus... 
DEFINITION | PATHWAYS | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | DYNAMICS | CHEMISTRY, PHYSICAL | TRP-CAGE | NUCLEATION | MODEL | SIMULATION | Potential energy | Alanine | Shape | Sampling | Contours | Physics - Statistical Mechanics
Journal Article
The Journal of Chemical Physics, ISSN 0021-9606, 03/2017, Volume 146, Issue 11, pp. 115101 - 115101
Metadynamics is an important collective-coordinate-based enhanced sampling simulation method. Its performance depends significantly on the capability of... 
DYNAMICS | CHEMISTRY, PHYSICAL | TRP-CAGE | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | Computer simulation | Deviation | Sampling | Mathematical analysis | Complex systems | Floating structures
Journal Article
Journal Article
by Piana, S and Laio, A
JOURNAL OF PHYSICAL CHEMISTRY B, ISSN 1520-6106, 05/2007, Volume 111, Issue 17, pp. 4553 - 4559
Journal Article
The Journal of Chemical Physics, ISSN 0021-9606, 08/2018, Volume 149, Issue 7, pp. 072304 - 072304
Replica-exchange molecular dynamics (REMD) and their variants have been widely used in simulations of the biomolecular structure and dynamics. Replica exchange... 
HYBRID-PARALLEL | ACCELERATED MOLECULAR-DYNAMICS | ENHANCED SAMPLING ALGORITHMS | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | IMPLEMENTATION | CHEMISTRY, PHYSICAL | TRP-CAGE | BINDING | EFFICIENT | ENERGY LANDSCAPE | PEPTIDE | SOLVENT | Index Medicus
Journal Article
Physical Review Letters, ISSN 0031-9007, 09/2017, Volume 119, Issue 10, pp. 108102 - 108102
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 11/2012, Volume 8, Issue 11, pp. 4413 - 4424
PACE, a hybrid force field that couples united-atom protein models with coarse-grained (CG) solvent (J. Chem. Theory Comput. 2010, 6, 3373), has been further... 
BIOMOLECULAR SIMULATIONS | SOLVATION FREE-ENERGIES | BETA-HAIRPIN | FREE-ENERGY LANDSCAPE | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | HELIX-COIL TRANSITION | TRP-CAGE | MOLECULAR-DYNAMICS SIMULATIONS | 3-HELIX BUNDLE PROTEIN | STRUCTURE PREDICTION | IMPLICIT SOLVENT
Journal Article
Journal Article