Leveraging uncertainty estimates and derivative information in Gaussian process regression for efficient collection and use of molecular simulation data

Autor: Jacob I. Monroe, William P. Krekelberg, Austin McDannald, Vincent K. Shen

Publikováno v: The Journal of Chemical Physics. 158

We introduce Gaussian Process Regression (GPR) as an enhanced method of thermodynamic extrapolation and interpolation. The heteroscedastic GPR models that we introduce automatically weight provided information by its estimated uncertainty, allowing f

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::c8a891ca2af8553a71f90b22b44d8717
https://doi.org/10.1063/5.0148488

Systematic control of collective variables learned from variational autoencoders

Autor: Jacob I. Monroe, Vincent K. Shen

Publikováno v: The Journal of chemical physics. 157(9)

Variational autoencoders (VAEs) are rapidly gaining popularity within molecular simulation for discovering low-dimensional, or latent, representations, which are critical for both analyzing and accelerating simulations. However, it remains unclear ho

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::eae0a9786c22ae153c269bf8c9a491e9
https://pubmed.ncbi.nlm.nih.gov/36075702

Performing solvation free energy calculations in LAMMPS using the decoupling approach

Autor: Vikram Khanna, Jacob I. Monroe, Michael F. Doherty, Baron Peters

Publikováno v: Journal of Computer-Aided Molecular Design. 34:641-646

The decoupling approach to solvation free energy calculations requires scaling the interactions between the solute and the solution with all intramolecular interactions preserved. This paper reports a new procedure that makes it possible to these cal

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8d269a85daac5e57c4b367004433b7d4
https://doi.org/10.1007/s10822-020-00303-3

Affinity of small-molecule solutes to hydrophobic, hydrophilic, and chemically patterned interfaces in aqueous solution

Autor: Sally Jiao, R. Justin Davis, Dennis Robinson Brown, Jacob I. Monroe, M. Scott Shell, Lynn E. Katz

Publikováno v: Proc Natl Acad Sci U S A
Proceedings of the National Academy of Sciences of the United States of America, vol 118, iss 1

Performance of membranes for water purification is highly influenced by the interactions of solvated species with membrane surfaces, including surface adsorption of solutes upon fouling. Current efforts toward fouling-resistant membranes often pursue

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7ada9a4dd34fd915f5e6ba7ff67a110e
https://pubmed.ncbi.nlm.nih.gov/33384327

Decoding signatures of structure, bulk thermodynamics, and solvation in three-body angle distributions of rigid water models

Autor: M. Scott Shell, Jacob I. Monroe

Publikováno v: The Journal of chemical physics. 151(9)

A tetrahedral structure resulting from hydrogen bonding is a hallmark of liquid water and plays a significant role in determining its unique thermophysical properties. This water feature has helped understand anomalous properties and physically inter

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d70ed14fefdb2a5965258a574583d5b2
https://pubmed.ncbi.nlm.nih.gov/31492058