Machine learning approaches for analyzing and enhancing molecular dynamics simulations
Highlights•Machine learning and artificial intelligence approaches have been leveraged for
MD.•One machine learning contribution is in removing noise to make MD data human …
MD.•One machine learning contribution is in removing noise to make MD data human …
Dynamical reweighting for biased rare event simulations
Dynamical reweighting techniques aim to recover the correct molecular dynamics from a
simulation at a modified potential energy surface. They are important for unbiasing …
simulation at a modified potential energy surface. They are important for unbiasing …
Reweighted autoencoded variational Bayes for enhanced sampling (RAVE)
Here we propose the reweighted autoencoded variational Bayes for enhanced sampling
(RAVE) method, a new iterative scheme that uses the deep learning framework of variational …
(RAVE) method, a new iterative scheme that uses the deep learning framework of variational …
Spectral gap optimization of order parameters for sampling complex molecular systems
In modern-day simulations of many-body systems, much of the computational complexity is
shifted to the identification of slowly changing molecular order parameters called collective …
shifted to the identification of slowly changing molecular order parameters called collective …
Collective variable-based enhanced sampling and machine learning
M Chen - The European Physical Journal B, 2021 - Springer
Collective variable-based enhanced sampling methods have been widely used to study
thermodynamic properties of complex systems. Efficiency and accuracy of these enhanced …
thermodynamic properties of complex systems. Efficiency and accuracy of these enhanced …
Advances in automated and reactive flow cytometry for synthetic biotechnology
F Delvigne, JA Martinez - Current Opinion in Biotechnology, 2023 - Elsevier
Highlights•The accessibility to automated flow cytometry equipment has recently been
increased through the open science initiative.•Automated and reactive flow cytometry can be …
increased through the open science initiative.•Automated and reactive flow cytometry can be …
The maximum caliber variational principle for nonequilibria
Ever since Clausius in 1865 and Boltzmann in 1877, the concepts of entropy and of its
maximization have been the foundations for predicting how material equilibria derive from …
maximization have been the foundations for predicting how material equilibria derive from …
[HTML][HTML] Bridging microscopic and macroscopic mechanisms of p53-MDM2 binding with kinetic network models
Under normal cellular conditions, the tumor suppressor protein p53 is kept at low levels in
part due to ubiquitination by MDM2, a process initiated by binding of MDM2 to the …
part due to ubiquitination by MDM2, a process initiated by binding of MDM2 to the …
Manifold learning in atomistic simulations: a conceptual review
Analyzing large volumes of high-dimensional data requires dimensionality reduction: finding
meaningful low-dimensional structures hidden in their high-dimensional observations. Such …
meaningful low-dimensional structures hidden in their high-dimensional observations. Such …
Choice of adaptive sampling strategy impacts state discovery, transition probabilities, and the apparent mechanism of conformational changes
Interest in atomically detailed simulations has grown significantly with recent advances in
computational hardware and Markov state modeling (MSM) methods, yet outstanding …
computational hardware and Markov state modeling (MSM) methods, yet outstanding …