QM/MM methods for biomolecular systems
HM Senn, W Thiel - Angewandte Chemie International Edition, 2009 - Wiley Online Library
Two are better than one: Quantum mechanics/molecular mechanics (QM/MM) methods are
the state‐of‐the‐art computational technique for treating reactive and other “electronic” …
the state‐of‐the‐art computational technique for treating reactive and other “electronic” …
Nonequilibrium fluctuations, fluctuation theorems, and counting statistics in quantum systems
Fluctuation theorems (FTs), which describe some universal properties of nonequilibrium
fluctuations, are examined from a quantum perspective and derived by introducing a two …
fluctuations, are examined from a quantum perspective and derived by introducing a two …
[图书][B] Statistical mechanics of nonequilbrium liquids
DJ Evans, GP Morriss - 2007 - library.oapen.org
During the 1980's there were many developments regarding the nonequilibrium statistical
mechanics of dense classical atomic fluids. These developments have had a major impact …
mechanics of dense classical atomic fluids. These developments have had a major impact …
Optimal finite-time processes in stochastic thermodynamics
T Schmiedl, U Seifert - Physical review letters, 2007 - APS
For a small system like a colloidal particle or a single biomolecule embedded in a heat bath,
the optimal protocol of an external control parameter minimizes the mean work required to …
the optimal protocol of an external control parameter minimizes the mean work required to …
QM/MM methods for biological systems
HM Senn, W Thiel - Atomistic approaches in modern biology: from …, 2007 - Springer
Thirty years after the seminal contribution by Warshel and Levitt, we review the state of the
art of combined quantum-mechanics/molecular-mechanics (QM/MM) methods, with a focus …
art of combined quantum-mechanics/molecular-mechanics (QM/MM) methods, with a focus …
Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation
Metropolis Monte Carlo simulation is a powerful tool for studying the equilibrium properties
of matter. In complex condensed-phase systems, however, it is difficult to design Monte …
of matter. In complex condensed-phase systems, however, it is difficult to design Monte …
Optimal protocols for minimal work processes in underdamped stochastic thermodynamics
A Gomez-Marin, T Schmiedl, U Seifert - The Journal of chemical …, 2008 - pubs.aip.org
For systems in an externally controllable time-dependent potential, the optimal protocol
minimizes the mean work spent in a finite-time transition between two given equilibrium …
minimizes the mean work spent in a finite-time transition between two given equilibrium …
Recent developments in methodologies for calculating the entropy and free energy of biological systems by computer simulation
H Meirovitch - Current opinion in structural biology, 2007 - Elsevier
The Helmholtz free energy, F, plays an important role in proteins because of their rugged
potential energy surface, which is 'decorated'with a tremendous number of local wells …
potential energy surface, which is 'decorated'with a tremendous number of local wells …
Computing equilibrium free energies using non-equilibrium molecular dynamics
As shown by Jarzynski, free energy differences between equilibrium states can be
expressed in terms of the statistics of work carried out on a system during non-equilibrium …
expressed in terms of the statistics of work carried out on a system during non-equilibrium …
Escorted free energy simulations: Improving convergence by reducing dissipation
S Vaikuntanathan, C Jarzynski - Physical Review Letters, 2008 - APS
Nonequilibrium,“fast switching” estimates of equilibrium free energy differences Δ F are often
plagued by poor convergence due to dissipation. We propose a method to improve these …
plagued by poor convergence due to dissipation. We propose a method to improve these …