Screening Fast-Mode Motion in Collective Variable Discovery for Biochemical Processes

Screening Fast-Mode Motion in Collective Variable Discovery for Biochemical Processes

Collective variables (CVs) describing slow degrees of freedom (DOFs) in biomolecular assemblies are crucial for analyzing molecular dynamics trajectories, creating Markov models and performing CV-based enhanced sampling simulations. While time-lagged independent component analysis (tICA) and its non...

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Bibliographic Details
Main Author: Donghui Shao (20347008) (author)
Other Authors: Zhiteng Zhang (2033161) (author), Xuyang Liu (310954) (author), Haohao Fu (1351521) (author), Xueguang Shao (1271313) (author), Wensheng Cai (1271310) (author)
Published: 2024
Subjects:
Biochemistry
Genetics
Biotechnology
Sociology
Cancer
Biological Sciences not elsewhere classified
Mathematical Sciences not elsewhere classified
Information Systems not elsewhere classified
providing reliable insights
negligible computational cost
dimensionality reduction techniques
creating markov models
collective variable discovery
protein simulation trajectories
describing slow degrees
screen fast motion
slow motion
fast motion
protein dynamics
screening fast
mode motion
wide range
sampling calculations
remarkable ability
often struggle
nonlinear successor
lagged autoencoder
frequency signals
finding algorithms
finding algorithm
conformational changes
biomolecular assemblies
alanine dipeptide
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