Parallel algorithms for hyperdynamics and local hyperdynamics

gen.parRep: A first implementation of the Generalized Parallel Replica dynamics for the long time simulation of metastable biochemical systems

(2019) Florent Hédin et al.   COMPUTER PHYSICS COMMUNICATIONS

Multiply accelerated ReaxFF molecular dynamics: coupling parallel replica dynamics with collective variable hyper dynamics

(2019) Karthik Ganeshan et al.   MOLECULAR SIMULATION

Markov State Models: From an Art to a Science

(2018) Brooke E. Husic et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Accelerated molecular dynamics simulations for characterizing plastic deformation in crystalline materials with cracks

(2016) Subhendu Chakraborty et al.   COMPUTATIONAL MATERIALS SCIENCE

Multiscale diffusion method for simulations of long-time defect evolution with application to dislocation climb

(2016) K.L. Baker et al.   JOURNAL OF THE MECHANICS AND PHYSICS OF SOLIDS

The parallel replica dynamics method – Coming of age

(2015) Danny Perez et al.   COMPUTATIONAL MATERIALS SCIENCE

Hyperdynamics boost factor achievable with an ideal bias potential

(2015) Chen Huang et al.   JOURNAL OF CHEMICAL PHYSICS

Long-Time Dynamics through Parallel Trajectory Splicing

(2015) Danny Perez et al.   Journal of Chemical Theory and Computation

Markov state models of biomolecular conformational dynamics

(2014) John D Chodera et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Extending atomistic simulation timescale in solid/liquid systems: Crystal growth from solution by a parallel-replica dynamics and continuum hybrid method

(2014) Chun-Yaung Lu et al.   JOURNAL OF CHEMICAL PHYSICS

Adaptive Accelerated ReaxFF Reactive Dynamics with Validation from Simulating Hydrogen Combustion

(2014) Tao Cheng et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Local hyperdynamics

(2013) Soo Young Kim et al.   JOURNAL OF CHEMICAL PHYSICS

Accelerated molecular dynamics simulation of low-velocity frictional sliding

(2010) W K Kim et al.   MODELLING AND SIMULATION IN MATERIALS SCIENCE AND ENGINEERING

Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics

(2010) C. F. Abrams et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Visualization and analysis of atomistic simulation data with OVITO–the Open Visualization Tool

(2009) Alexander Stukowski   MODELLING AND SIMULATION IN MATERIALS SCIENCE AND ENGINEERING

Accelerated Molecular Dynamics of Temperature-Programed Desorption

(2009) Kelly E. Becker et al.   PHYSICAL REVIEW LETTERS