Kinetics from metadynamics: Principles, applications, and outlook
Metadynamics is a popular enhanced sampling algorithm for computing the free energy
landscape of rare events by using molecular dynamics simulation. Ten years ago, Tiwary …
landscape of rare events by using molecular dynamics simulation. Ten years ago, Tiwary …
Collective variables from local fluctuations
We introduce a method to obtain one-dimensional collective variables for studying rarely
occurring transitions between two metastable states separated by a high free energy barrier …
occurring transitions between two metastable states separated by a high free energy barrier …
Rare event kinetics from adaptive bias enhanced sampling
We introduce a novel enhanced sampling approach named on-the-fly probability enhanced
sampling (OPES) flooding for calculating the kinetics of rare events from atomistic molecular …
sampling (OPES) flooding for calculating the kinetics of rare events from atomistic molecular …
Metadynamics with discriminants: A tool for understanding chemistry
We introduce an extension of a recently published method [Mendels et al. J. Phys. Chem.
Lett. 2018, 9, 2776− 2781] to obtain low-dimensional collective variables for studying …
Lett. 2018, 9, 2776− 2781] to obtain low-dimensional collective variables for studying …
Short-Time Infrequent Metadynamics for Improved Kinetics Inference
Infrequent Metadynamics is a popular method to obtain the rates of long time-scale
processes from accelerated simulations. The inference procedure is based on rescaling the …
processes from accelerated simulations. The inference procedure is based on rescaling the …
Microscopic description of acid–base equilibrium
Acid–base reactions are ubiquitous in nature. Understanding their mechanisms is crucial in
many fields, from biochemistry to industrial catalysis. Unfortunately, experiments give only …
many fields, from biochemistry to industrial catalysis. Unfortunately, experiments give only …
Efficient exploration of complex free energy landscapes by stepwise multi-subphase space metadynamics
YG Fang, X Li, Y Gao, YH Cui, JS Francisco… - The Journal of …, 2022 - pubs.aip.org
We present an efficient method based on an extension of metadynamics for exploring
complex free energy landscapes (FELs). The method employs two-step metadynamics …
complex free energy landscapes (FELs). The method employs two-step metadynamics …
Metadynamics of paths
We present a method to sample reactive pathways via biased molecular dynamics
simulations in trajectory space. We show that the use of enhanced sampling techniques …
simulations in trajectory space. We show that the use of enhanced sampling techniques …
Combining metadynamics and integrated tempering sampling
The simulation of rare events is one of the key problems in atomistic simulations. Toward its
solution, a plethora of methods have been proposed. Here we combine two such methods …
solution, a plethora of methods have been proposed. Here we combine two such methods …
Mechanistic insight into the competition between interfacial and bulk reactions in microdroplets through N2O5 ammonolysis and hydrolysis
YG Fang, B Tang, C Yuan, Z Wan, L Zhao… - Nature …, 2024 - nature.com
Reactive uptake of dinitrogen pentaoxide (N2O5) into aqueous aerosols is a major loss
channel for NOx in the troposphere; however, a quantitative understanding of the uptake …
channel for NOx in the troposphere; however, a quantitative understanding of the uptake …