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” …
TRANSITION PATH SAMPLING: Throwing Ropes Over Rough Mountain Passes, in the Dark
▪ Abstract This article reviews the concepts and methods of transition path sampling. These
methods allow computational studies of rare events without requiring prior knowledge of …
methods allow computational studies of rare events without requiring prior knowledge of …
Energy landscapes
DJ Wales - Atomic clusters and nanoparticles. Agregats atomiques …, 2002 - Springer
This overview of energy landscapes will focus on some rigorous properties of potential
energy surfaces (PES's), especially the symmetry properties of steepest-descent paths, and …
energy surfaces (PES's), especially the symmetry properties of steepest-descent paths, and …
Molecular simulations of zeolites: adsorption, diffusion, and shape selectivity
B Smit, TLM Maesen - Chemical reviews, 2008 - ACS Publications
Zeolites are intriguing materials. The basic building blocks are corner sharing TO4 units,
where the T-atoms usually refer to Si, Al, or in some cases also P. These tetrahedrals can …
where the T-atoms usually refer to Si, Al, or in some cases also P. These tetrahedrals can …
[图书][B] Free energy computations: A mathematical perspective
This monograph provides a general introduction to advanced computational methods for
free energy calculations, from the systematic and rigorous point of view of applied …
free energy calculations, from the systematic and rigorous point of view of applied …
Forward flux sampling for rare event simulations
RJ Allen, C Valeriani… - Journal of physics …, 2009 - iopscience.iop.org
Rare events are ubiquitous in many different fields, yet they are notoriously difficult to
simulate because few, if any, events are observed in a conventional simulation run. Over the …
simulate because few, if any, events are observed in a conventional simulation run. Over the …
Transition path sampling
C Dellago, PG Bolhuis… - Advances in chemical …, 2002 - Wiley Online Library
In this chapter we present the foundations and methodology of transition path sampling
comprehensively, including details important for its implementation. We first discuss the …
comprehensively, including details important for its implementation. We first discuss the …
Quantum mechanical methods for enzyme kinetics
J Gao, DG Truhlar - Annual Review of Physical Chemistry, 2002 - annualreviews.org
▪ Abstract This review discusses methods for the incorporation of quantum mechanical
effects into enzyme kinetics simulations in which the enzyme is an explicit part of the model …
effects into enzyme kinetics simulations in which the enzyme is an explicit part of the model …
A novel path sampling method for the calculation of rate constants
TS Van Erp, D Moroni, PG Bolhuis - The Journal of chemical physics, 2003 - pubs.aip.org
We derive a novel efficient scheme to measure the rate constant of transitions between
stable states separated by high free energy barriers in a complex environment within the …
stable states separated by high free energy barriers in a complex environment within the …
Ab initio molecular dynamics: basic concepts, current trends and novel applications
ME Tuckerman - Journal of Physics: Condensed Matter, 2002 - iopscience.iop.org
The field of ab initio molecular dynamics (AIMD), in which finite temperature molecular
dynamics (MD) trajectories are generated with forces obtained from accurate'on the …
dynamics (MD) trajectories are generated with forces obtained from accurate'on the …