Transition path sampling and other advanced simulation techniques for rare events
C Dellago, PG Bolhuis - … computer simulation approaches for soft matter …, 2009 - Springer
Computer simulations of molecular processes such as nucleation in first-order phase
transitions or the folding of a protein are often complicated by widely disparate time scales …
transitions or the folding of a protein are often complicated by widely disparate time scales …
Long-timescale simulation methods
R Elber - Current opinion in structural biology, 2005 - Elsevier
The outstanding challenges in computer simulations of biological macromolecules are
related to their complexity. Part of the complexity of biological systems concerns their …
related to their complexity. Part of the complexity of biological systems concerns their …
From A to B in free energy space
The authors present a new method for searching low free energy paths in complex
molecular systems at finite temperature. They introduce two variables that are able to …
molecular systems at finite temperature. They introduce two variables that are able to …
[图书][B] Nano mechanics and materials: theory, multiscale methods and applications
Nanotechnology is a progressive research and development topic with large amounts of
venture capital and government funding being invested worldwide. Nano mechanics, in …
venture capital and government funding being invested worldwide. Nano mechanics, in …
[图书][B] Advanced computer simulation approaches for soft matter sciences III
The series Advances in Polymer Science presents critical reviews of the present and future
trends in polymer and biopolymer science including chemistry, physical chemistry, physics …
trends in polymer and biopolymer science including chemistry, physical chemistry, physics …
Automated prediction of catalytic mechanism and rate law using graph-based reaction path sampling
S Habershon - Journal of Chemical Theory and Computation, 2016 - ACS Publications
In a recent article [J. Chem. Phys. 2015, 143, 094106], we introduced a novel graph-based
sampling scheme which can be used to generate chemical reaction paths in many-atom …
sampling scheme which can be used to generate chemical reaction paths in many-atom …
Sampling reactive pathways with random walks in chemical space: Applications to molecular dissociation and catalysis
S Habershon - The Journal of chemical physics, 2015 - pubs.aip.org
Automatically generating chemical reaction pathways is a significant computational
challenge, particularly in the case where a given chemical system can exhibit multiple …
challenge, particularly in the case where a given chemical system can exhibit multiple …
Coherent Mixing of Singlet and Triplet States in Acrolein and Ketene: A Computational Strategy for Simulating the Electron–Nuclear Dynamics of Intersystem Crossing
D Danilov, AJ Jenkins, MJ Bearpark… - The Journal of …, 2023 - ACS Publications
We present a theoretical study of intersystem crossing (ISC) in acrolein and ketene with the
Ehrenfest method that can describe a superposition of singlet and triplet states. Our …
Ehrenfest method that can describe a superposition of singlet and triplet states. Our …
Rare Events Sampling Methods for Quantum and Classical Ab Initio Molecular Dynamics
SS Iyengar, HB Schlegel, I Sumner… - The Journal of Physical …, 2024 - ACS Publications
We provide an approach to sample rare events during classical ab initio molecular dynamics
and quantum wavepacket dynamics. For classical AIMD, a set of fictitious degrees of …
and quantum wavepacket dynamics. For classical AIMD, a set of fictitious degrees of …
Development of interatomic reaxff potentials for Au–S–C–H systems
TT Järvi, ACT Van Duin, K Nordlund… - The Journal of …, 2011 - ACS Publications
We present fully reactive interatomic potentials for systems containing gold, sulfur, carbon,
and hydrogen, employing the ReaxFF formalism. The potential is designed especially for …
and hydrogen, employing the ReaxFF formalism. The potential is designed especially for …