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 …
Collective Variable-Based Enhanced Sampling: From Human Learning to Machine Learning
H Fu, H Bian, X Shao, W Cai - The Journal of Physical Chemistry …, 2024 - ACS Publications
Enhanced-sampling algorithms relying on collective variables (CVs) are extensively
employed to study complex (bio) chemical processes that are not amenable to brute-force …
employed to study complex (bio) chemical processes that are not amenable to brute-force …
[HTML][HTML] Explaining reaction coordinates of alanine dipeptide isomerization obtained from deep neural networks using Explainable Artificial Intelligence (XAI)
A method for obtaining appropriate reaction coordinates is required to identify transition
states distinguishing the product and reactant in complex molecular systems. Recently …
states distinguishing the product and reactant in complex molecular systems. Recently …
Multiscale topological indices for the quantitative prediction of SARS CoV-2 binding affinity change upon mutations
The Coronavirus disease 2019 (COVID-19) has affected people's lives and the development
of the global economy. Biologically, protein–protein interactions between SARS-CoV-2 …
of the global economy. Biologically, protein–protein interactions between SARS-CoV-2 …
Exact reaction coordinates for flap opening in HIV-1 protease
The primary goal of protein science is to understand how proteins function, which requires
understanding the functional dynamics responsible for transitions between different …
understanding the functional dynamics responsible for transitions between different …
[HTML][HTML] Exact probability landscapes of stochastic phenotype switching in feed-forward loops: phase diagrams of multimodality
Feed-forward loops (FFLs) are among the most ubiquitously found motifs of reaction
networks in nature. However, little is known about their stochastic behavior and the variety of …
networks in nature. However, little is known about their stochastic behavior and the variety of …
Reactive Vortexes in a Naturally Activated Process: Non-Diffusive Rotational Fluxes at Transition State Uncovered by Persistent Homology
The dynamics of reaction coordinates during barrier-crossing are key to understanding
activated processes in complex systems such as proteins. The default assumption from …
activated processes in complex systems such as proteins. The default assumption from …
Unveiling interatomic distances influencing the reaction coordinates in alanine dipeptide isomerization: An explainable deep learning approach
The present work shows that the free energy landscape associated with alanine dipeptide
isomerization can be effectively represented by specific interatomic distances without explicit …
isomerization can be effectively represented by specific interatomic distances without explicit …
Interpretation of autoencoder-learned collective variables using Morse–Smale complex and sublevelset persistent homology: An application on molecular trajectories
SC Lee - The Journal of Chemical Physics, 2024 - pubs.aip.org
Dimensionality reduction often serves as the first step toward a minimalist understanding of
physical systems as well as the accelerated simulations of them. In particular, neural …
physical systems as well as the accelerated simulations of them. In particular, neural …
Identifying Transient Cells During Reprogramming via Persistent Homology
A Petenkaya, F Manuchehrfar… - 2022 44th Annual …, 2022 - ieeexplore.ieee.org
Single-cell RNA sequencing is a powerful method that helps delineate the regulatory
mechanisms shaping the diverse cellular populations. Heterogeneous cell populations …
mechanisms shaping the diverse cellular populations. Heterogeneous cell populations …