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 …

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 …

From A to B in free energy space

D Branduardi, FL Gervasio, M Parrinello - The Journal of chemical …, 2007 - pubs.aip.org
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 …

[图书][B] Nano mechanics and materials: theory, multiscale methods and applications

WK Liu, EG Karpov, HS Park - 2006 - books.google.com
Nanotechnology is a progressive research and development topic with large amounts of
venture capital and government funding being invested worldwide. Nano mechanics, in …

[图书][B] Advanced computer simulation approaches for soft matter sciences III

C Holm, K Kremer - 2008 - Springer
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 …

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 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 …

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 …

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 …

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 …