An automated method to find transition states using chemical dynamics simulations

Efficient Basin-Hopping Sampling of Reaction Intermediates through Molecular Fragmentation and Graph Theory

(2014) Yeonjoon Kim et al.   Journal of Chemical Theory and Computation

Recent applications of boxed molecular dynamics: a simple multiscale technique for atomistic simulations

(2014) J. Booth et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Metrics for measuring distances in configuration spaces

(2013) Ali Sadeghi et al.   JOURNAL OF CHEMICAL PHYSICS

Localized saddle-point search and application to temperature-accelerated dynamics

(2013) Yunsic Shim et al.   JOURNAL OF CHEMICAL PHYSICS

PathOpt-A global transition state search approach: Outline of algorithm

(2013) Christoph Grebner et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Peptide kinetics from picoseconds to microseconds using boxed molecular dynamics: Power law rate coefficients in cyclisation reactions

(2012) Dmitrii V. Shalashilin et al.   JOURNAL OF CHEMICAL PHYSICS

Optimizing transition states via kernel-based machine learning

(2012) Zachary D. Pozun et al.   JOURNAL OF CHEMICAL PHYSICS

Improving Upon String Methods for Transition State Discovery

(2012) Hugh Chaffey-Millar et al.   Journal of Chemical Theory and Computation

Automated Exploration of Photolytic Channels of HCOOH: Conformational Memory via Excited-State Roaming

(2012) Satoshi Maeda et al.   Journal of Physical Chemistry Letters

Comment on “Fast and Accurate Modeling of Molecular Atomization Energies with Machine Learning”

(2012) Jonathan E. Moussa   PHYSICAL REVIEW LETTERS

Roaming Radicals

(2011) Joel M. Bowman et al.   Annual Review of Physical Chemistry

Determination of reaction coordinates via locally scaled diffusion map

(2011) Mary A. Rohrdanz et al.   JOURNAL OF CHEMICAL PHYSICS

Incorporating Linear Synchronous Transit Interpolation into the Growing String Method: Algorithm and Applications

(2011) Andrew Behn et al.   Journal of Chemical Theory and Computation

Boxed Molecular Dynamics: Decorrelation Time Scales and the Kinetic Master Equation

(2011) David R. Glowacki et al.   Journal of Chemical Theory and Computation

Ab Initio and RRKM Study of the HCN/HNC Elimination Channels from Vinyl Cyanide

(2011) Zahra Homayoon et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Roaming Radical Reactions

(2011) Nuradhika Herath et al.   Journal of Physical Chemistry Letters

Roaming-mediated isomerization in the photodissociation of nitrobenzene

(2011) Michael L. Hause et al.   Nature Chemistry

Umbrella sampling

(2011) Johannes Kästner   Wiley Interdisciplinary Reviews-Computational Molecular Science

Instantaneous Normal Modes as an Unforced Reaction Coordinate for Protein Conformational Transitions

(2010) Cheng Peng et al.   BIOPHYSICAL JOURNAL

Communication: κ-dynamics—An exact method for accelerating rare event classical molecular dynamics

(2010) Chun-Yaung Lu et al.   JOURNAL OF CHEMICAL PHYSICS

Dominant reaction pathways in protein folding: A direct validation against molecular dynamics simulations

(2010) Pietro Faccioli et al.   JOURNAL OF CHEMICAL PHYSICS

Roaming Radical Pathways for the Decomposition of Alkanes

(2010) Lawrence B. Harding et al.   Journal of Physical Chemistry Letters

Markovian milestoning with Voronoi tessellations

(2009) Eric Vanden-Eijnden et al.   JOURNAL OF CHEMICAL PHYSICS

Free Energy and Kinetics of Conformational Transitions from Voronoi Tessellated Milestoning with Restraining Potentials

(2009) Luca Maragliano et al.   Journal of Chemical Theory and Computation

Kinetics of Helix Unfolding: Molecular Dynamics Simulations with Milestoning†

(2009) Krzysztof Kuczera et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Theoretical and Computational Studies of Non-RRKM Unimolecular Dynamics†

(2009) Upakarasamy Lourderaj et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Boxed Molecular Dynamics: A Simple and General Technique for Accelerating Rare Event Kinetics and Mapping Free Energy in Large Molecular Systems

(2009) David R. Glowacki et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Transition-Path Theory and Path-Finding Algorithms for the Study of Rare Events

(2008) Weinan E et al.   Annual Review of Physical Chemistry

A new global reaction route map on the potential energy surface of H2CO with unrestricted level

(2008) Satoshi Maeda et al.   CHEMICAL PHYSICS LETTERS

Covalent radii revisited

(2008) Beatriz Cordero et al.   DALTON TRANSACTIONS

On the assumptions underlying milestoning

(2008) Eric Vanden-Eijnden et al.   JOURNAL OF CHEMICAL PHYSICS

Superlinearly converging dimer method for transition state search

(2008) Johannes Kästner et al.   JOURNAL OF CHEMICAL PHYSICS

Crystal structure prediction from first principles

(2008) Scott M. Woodley et al.   NATURE MATERIALS

Automated exploration of reaction channels

(2008) K Ohno et al.   PHYSICA SCRIPTA