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Enhanced Sampling for Molecular Systems
This special topic highlights recent developments in enhanced sampling methods for molecular-level simulations of chemical and biological systems. These methods are designed to enable more efficient exploration of phase space and extend the time scales that can be explored by simulations. We hope this collection of articles will provide readers with an up-to-date snapshot of some of the most important methods used to address sampling in a broad spectrum of molecular systems.
Guest Editors: Alessandro Laio, Athanassios Z. Panagiotopoulos, and Daniel M. Zuckerman
Theoretical Methods and Algorithms
Bayesian calibration of force-fields from experimental data: TIP4P water
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Ritabrata Dutta; Zacharias Faidon Brotzakis; Antonietta Mira
Theoretical Methods and Algorithms
Conformational change of a biomolecule studied by the weighted ensemble method: Use of the diffusion map method to extract reaction coordinates
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Hiroshi Fujisaki; Kei Moritsugu; Ayori Mitsutake; Hiromichi Suetani
Theoretical Methods and Algorithms
Building maps in collective variable space
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Ilaria Gimondi; Gareth A. Tribello; Matteo Salvalaglio
Theoretical Methods and Algorithms
Gianmarc Grazioli; Ioan Andricioaei
Theoretical Methods and Algorithms
Advances in milestoning. II. Calculating time-correlation functions from milestoning using stochastic path integrals
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Gianmarc Grazioli; Ioan Andricioaei
Articles
Vinícius Wilian D. Cruzeiro; Marcos S. Amaral; Adrian E. Roitberg
Articles
An efficient Bayesian kinetic lumping algorithm to identify metastable conformational states via Gibbs sampling
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Wei Wang; Tong Liang; Fu Kit Sheong; Xiaodan Fan; Xuhui Huang
Preface
Alessandro Laio; Athanassios Z. Panagiotopoulos; Daniel M. Zuckerman
Articles
Transition path theory from biased simulations
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G. Bartolucci; S. Orioli; P. Faccioli
Articles
Girsanov reweighting for metadynamics simulations
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Luca Donati; Bettina G. Keller
Articles
Isomerization kinetics of flexible molecules in the gas phase: Atomistic versus coarse-grained sampling
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Cyril Falvo; Antonio Gamboa-Suárez; Samuel Cazayus-Claverie; Pascal Parneix; Florent Calvo
Articles
Glassy dynamics in mutant huntingtin proteins
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Hongsuk Kang; Binquan Luan; Ruhong Zhou
Articles
Shingo Ito; Ying Wang; Yuko Okamoto; Stephan Irle
Articles
Robert F. DeJaco; Bahman Elyassi; Matheus Dorneles de Mello; Nitish Mittal; Michael Tsapatsis; J. Ilja Siepmann
Articles
Surl-Hee Ahn; Jay W. Grate; Eric F. Darve
Articles
Exploring potential crossing seams in periodic systems: Intersystem crossing pathways in the benzene crystal
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Kenichiro Saita; Makito Takagi; Yu Harabuchi; Haruki Okada; Satoshi Maeda
Articles
Coupled-perturbed DFTB-QM/MM metadynamics: Application to proton-coupled electron transfer
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Natacha Gillet; Marcus Elstner; Tomáš Kubař
Articles
Heterogeneous seeded molecular dynamics as a tool to probe the ice nucleating ability of crystalline surfaces
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Philipp Pedevilla; Martin Fitzner; Gabriele C. Sosso; Angelos Michaelides
Articles
Nicholas E. Jackson; Michael A. Webb; Juan J. de Pablo
Articles
A mixed alchemical and equilibrium dynamics to simulate heterogeneous dense fluids: Illustrations for Lennard-Jones mixtures and phospholipid membranes
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Arman Fathizadeh; Ron Elber