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6 results in Keywords: Collective variables

Physical Chemistry

AMUSET-TICA: A Tensor-Based Approach for Identifying Slow Collective Variables in Biomolecular Dynamics

Siqin Cao, Feliks Nüske, Bojun Liu, Micheline Soley, Xuhui Huang

Version 1 posted 17 January 2025

262

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Theoretical and Computational Chemistry

Enhancing the Inhomogeneonus Photodynamics of Canonical Bacteriophytochrome

Jakub Rydzewski, Katarzyna Walczewska-Szewc, Sylwia Czach, Wiesław Nowak, Krzysztof Kuczera

Version 2 posted 17 December 2021

315

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Theoretical and Computational Chemistry

A GPU-Accelerated Machine Learning Framework for Molecular Simulation: HOOMD-blue with TensorFlow

Rainier Barrett, Maghesree Chakraborty, Dilnoza Amirkulova, Heta Gandhi, Andrew White

Version 3 posted 16 October 2019

2,480

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2

Citations

Biological and Medicinal Chemistry

Thermodynamic Insights of Base Flipping in TNA Duplex: Force Fields, Salt Concentrations, and Free Energy Simulation Methods

Zhaoxi Sun, John Z. H. Zhang

Version 1 posted 02 January 2020

688

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1

Citations

Theoretical and Computational Chemistry

A Mode Evolution Metric to Extract Converged Reaction Coordinates for Biomolecular Conformational Transitions

Mitradip Das, Ravindra Venkatramani

Version 1 posted 27 February 2024

316

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Physical Chemistry

Machine Learning Nucleation Collective Variables with Graph Neural Networks

Florian Dietrich, Xavier Rosas Advincula, Gianpaolo Gobbo, Michael Bellucci, Matteo Salvalaglio

Version 3 posted 06 October 2023

1,123

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