Enhanced sampling methods for molecular dynamics simulations
Enhanced sampling algorithms have emerged as powerful methods to extend the utility of
molecular dynamics simulations and allow the sampling of larger portions of the …
molecular dynamics simulations and allow the sampling of larger portions of the …
Thermodynamically driven assemblies and liquid–liquid phase separations in biology
The sustenance of life depends on the high degree of organization that prevails through
different levels of living organisms, from subcellular structures such as biomolecular …
different levels of living organisms, from subcellular structures such as biomolecular …
Modeling and simulations of polymers: a roadmap
Molecular modeling and simulations are invaluable tools for the polymer science and
engineering community. These computational approaches enable predictions and provide …
engineering community. These computational approaches enable predictions and provide …
Signatures of a liquid–liquid transition in an ab initio deep neural network model for water
The possible existence of a metastable liquid–liquid transition (LLT) and a corresponding
liquid–liquid critical point (LLCP) in supercooled liquid water remains a topic of much …
liquid–liquid critical point (LLCP) in supercooled liquid water remains a topic of much …
Adaptive biasing force method for scalar and vector free energy calculations
E Darve, D Rodríguez-Gómez… - The Journal of chemical …, 2008 - pubs.aip.org
In free energy calculations based on thermodynamic integration, it is necessary to compute
the derivatives of the free energy as a function of one (scalar case) or several (vector case) …
the derivatives of the free energy as a function of one (scalar case) or several (vector case) …
On the inner workings of Monte Carlo codes
We review state-of-the-art Monte Carlo (MC) techniques for computing fluid coexistence
properties (Gibbs simulations) and adsorption simulations in nanoporous materials such as …
properties (Gibbs simulations) and adsorption simulations in nanoporous materials such as …
A new approach to Monte Carlo simulations in statistical physics: Wang-Landau sampling
DP Landau, SH Tsai, M Exler - American Journal of Physics, 2004 - pubs.aip.org
We describe a Monte Carlo algorithm for doing simulations in classical statistical physics in
a different way. Instead of sampling the probability distribution at a fixed temperature, a …
a different way. Instead of sampling the probability distribution at a fixed temperature, a …
Direct calculation of liquid–vapor phase equilibria from transition matrix Monte Carlo simulation
JR Errington - The Journal of chemical physics, 2003 - pubs.aip.org
An approach for directly determining the liquid–vapor phase equilibrium of a model system
at any temperature along the coexistence line is described. The method relies on transition …
at any temperature along the coexistence line is described. The method relies on transition …
[HTML][HTML] Phase diagrams—Why they matter and how to predict them
Understanding the thermodynamic stability and metastability of materials can help us to, for
example, gauge whether crystalline polymorphs in pharmaceutical formulations are likely to …
example, gauge whether crystalline polymorphs in pharmaceutical formulations are likely to …
Fast algorithm to calculate density of states
RE Belardinelli, VD Pereyra - Physical Review E—Statistical, Nonlinear, and …, 2007 - APS
An algorithm to calculate the density of states, based on the well-known Wang-Landau
method, is introduced. Independent random walks are performed in different restricted …
method, is introduced. Independent random walks are performed in different restricted …