87 citations · 410 across the 29 of their papers we have counts for
16 papers · 1 filter
Bosonic Condensed Phase Real-time Dynamics from Ring Polymer Molecular Dynamics
Yotam M. Y. Feldman, Sourav Karmakar, Sutirtha Paul +3
We present a method for approximating real-time correlation functions and quantum transport coefficients of bosonic condensed phases. The direct evaluation of quantum real-time cor…
Stochastic Resetting: A Non-Equilibrium Framework for Prediction, Inference and Design
Tommer D. Keidar, Sagi Meir, Nir Sherf +4
Stochastic resetting has evolved from a simple model of diffusive search acceleration into a general framework for predicting, inferring, and controlling stochastic dynamics far fr…
Generalized Suzuki-Chin Factorization in Bosonic Path Integral Molecular Dynamics
Jacob Higer, Barak Hirshberg
Modern implementations of path integral molecular dynamics (PIMD) simulations of distinguishable particles frequently make use of high order factorization schemes for the Boltzmann…
fix pimd/langevin: An Efficient Implementation of Path Integral Molecular Dynamics in LAMMPS
Yifan Li, Axel Gomez, Kehan Cai +10
Path integral molecular dynamics (PIMD), which maps a quantum particle onto a fictitious classical system of ring polymers and propagates the "beads" of this extended classical sys…
Have you tried turning it off and on again? Stochastic resetting for enhanced sampling
Ofir Blumer, Barak Hirshberg
Molecular dynamics simulations are widely used across chemistry, physics, and biology, providing quantitative insight into complex processes with atomic detail. However, their limi…
Periodic Boundary Conditions for Bosonic Path Integral Molecular Dynamics
Jacob Higer, Yotam M. Y. Feldman, Barak Hirshberg
We develop an algorithm for bosonic path integral molecular dynamics (PIMD) simulations with periodic boundary conditions (PBC) that scales quadratically with the number of particl…
Inference of non-exponential kinetics through stochastic resetting
Ofir Blumer, Shlomi Reuveni, Barak Hirshberg
We present an inference scheme of long timescale, non-exponential kinetics from Molecular Dynamics simulations accelerated by stochastic resetting. Standard simulations provide val…
Accelerating Molecular Dynamics through Informed Resetting
Jonathan R. Church, Ofir Blumer, Tommer D. Keidar +3
We present a procedure for enhanced sampling of molecular dynamics simulations through informed stochastic resetting. Many phenomena, such as protein folding and crystal nucleation…
i-PI 3.0: a flexible and efficient framework for advanced atomistic simulations
Yair Litman, Venkat Kapil, Yotam M. Y. Feldman +13
Atomic-scale simulations have progressed tremendously over the past decade, largely due to the availability of machine-learning interatomic potentials. These potentials combine the…
Unveiling a crystal's entropy of disorder via electron diffraction. A statistical mechanics approach
Dongxin Liu, Oren Elishav, Jiarui Fu +5
Upon melting, the molecules in the crystal explore numerous configurations, reflecting an increase in disorder. The molar entropy of disorder can be defined by Bolzmann's formula d…
The effect of ligands on the size distribution of copper nanoclusters: insights from molecular dynamics simulations
Oren Elishav, Ofir Blumer, T. Kyle Vanderlick +1
Controlling the size distribution in the nucleation of copper particles is crucial for achieving nanocrystals with desired physical and chemical properties. However, their synthesi…
Short-Time Infrequent Metadynamics for Improved Kinetics Inference
Ofir Blumer, Shlomi Reuveni, Barak Hirshberg
Infrequent Metadynamics is a popular method to obtain the rates of long timescale processes from accelerated simulations. The inference procedure is based on rescaling the first-pa…
Resetting Metadynamics
Ofir Blumer, Shlomi Reuveni, Barak Hirshberg
Metadynamics is a powerful method to accelerate molecular dynamics simulations, but its efficiency critically depends on the identification of collective variables that capture the…
Collective Variables for Conformational Polymorphism in Molecular Crystals
Oren Elishav, Roy Podgaetsky, Olga Meikler +1
Controlling polymorphism in molecular crystals is crucial in the pharmaceutical, dye, and pesticide industries. However, its theoretical description is extremely challenging, due t…
Stochastic Resetting for Enhanced Sampling
Ofir Blumer, Shlomi Reuveni, Barak Hirshberg
We present a method for enhanced sampling of molecular dynamics simulations using stochastic resetting. Various phenomena, ranging from crystal nucleation to protein folding, occur…
Path Integral Molecular Dynamics for Fermions: Alleviating the Sign Problem with the Bogoliubov Inequality
Barak Hirshberg, Michele Invernizzi, Michele Parrinello
We present a method for performing path integral molecular dynamics (PIMD) simulations for fermions and address its sign problem. PIMD simulations are widely used for studying many…