Memory unlocks the future of biomolecular dynamics: Transformative tools to uncover physical insights accurately and efficiently
Conformational changes underpin function and encode complex biomolecular mechanisms.
Gaining atomic-level detail of how such changes occur has the potential to reveal these …
Gaining atomic-level detail of how such changes occur has the potential to reveal these …
[HTML][HTML] Transition rate theory, spectral analysis, and reactive paths
B Roux - The Journal of Chemical Physics, 2022 - pubs.aip.org
The kinetics of a dynamical system dominated by two metastable states is examined from
the perspective of the activated-dynamics reactive flux formalism, Markov state eigenvalue …
the perspective of the activated-dynamics reactive flux formalism, Markov state eigenvalue …
String method with swarms-of-trajectories, mean drifts, lag time, and committor
B Roux - The Journal of Physical Chemistry A, 2021 - ACS Publications
The kinetics of a dynamical system comprising two metastable states is formulated in terms
of a finite-time propagator in phase space (position and velocity) adapted to the …
of a finite-time propagator in phase space (position and velocity) adapted to the …
Tyrosine kinases: complex molecular systems challenging computational methodologies
Classical molecular dynamics (MD) simulations based on atomic models play an
increasingly important role in a wide range of applications in physics, biology, and …
increasingly important role in a wide range of applications in physics, biology, and …
Dynamics of activation in the voltage-sensing domain of Ciona intestinalis phosphatase Ci-VSP
The Ciona intestinalis voltage-sensing phosphatase (Ci-VSP) is a membrane protein
containing a voltage-sensing domain (VSD) that is homologous to VSDs from voltage-gated …
containing a voltage-sensing domain (VSD) that is homologous to VSDs from voltage-gated …
Integrative generalized master equation: A method to study long-timescale biomolecular dynamics via the integrals of memory kernels
The generalized master equation (GME) provides a powerful approach to study
biomolecular dynamics via non-Markovian dynamic models built from molecular dynamics …
biomolecular dynamics via non-Markovian dynamic models built from molecular dynamics …
Long-time-scale predictions from short-trajectory data: A benchmark analysis of the trp-cage miniprotein
Elucidating physical mechanisms with statistical confidence from molecular dynamics
simulations can be challenging owing to the many degrees of freedom that contribute to …
simulations can be challenging owing to the many degrees of freedom that contribute to …
[HTML][HTML] Learning forecasts of rare stratospheric transitions from short simulations
Rare events arising in nonlinear atmospheric dynamics remain hard to predict and attribute.
We address the problem of forecasting rare events in a prototypical example, sudden …
We address the problem of forecasting rare events in a prototypical example, sudden …
EnGens: a computational framework for generation and analysis of representative protein conformational ensembles
Proteins are dynamic macromolecules that perform vital functions in cells. A protein structure
determines its function, but this structure is not static, as proteins change their conformation …
determines its function, but this structure is not static, as proteins change their conformation …
Tutorial on how to build non-Markovian dynamic models from molecular dynamics simulations for studying protein conformational changes
Protein conformational changes play crucial roles in their biological functions. In recent
years, the Markov State Model (MSM) constructed from extensive Molecular Dynamics (MD) …
years, the Markov State Model (MSM) constructed from extensive Molecular Dynamics (MD) …