27 citations · 27 across the 1 of their papers we have counts for
6 papers
Reconstruction of the interatomic forces from dynamic Scanning Transmission Electron Microscopy data
M. Chakraborty, M. Ziatdinov, O. Dyck +3
We explore the possibility for the reconstruction of the generative physical models describing interactions between atomic units in solids from observational electron microscopy da…
Investigating Active Learning and Meta-Learning for Iterative Peptide Design
Rainier Barrett, Andrew D. White
Often the development of novel functional peptides is not amenable to high throughput or purely computational screening methods. Peptides must be synthesized one at a time in a pro…
Recent Advances in Maximum Entropy Biasing Techniques for Molecular Dynamics
Dilnoza B. Amirkulova, Andrew D. White
This review describes recent advances by the authors and others on the topic of incorporating experimental data into molecular simulations through maximum entropy methods. Methods…
Classifying Antimicrobial and Multifunctional Peptides with Bayesian Network Models
Rainier Barrett, Shaoyi Jiang, Andrew D White
Bayesian network models are finding success in characterizing enzyme-catalyzed reactions, slow conformational changes, predicting enzyme inhibition, and genomics. In this work, we…
Combining Enhanced Sampling with Experiment Directed Simulation of the GYG peptide
Dilnoza B Amirkulova, Andrew D White
Experiment directed simulation is a technique to minimally bias molecular dynamics simulations to match experimentally observed results. The method improves accuracy but does not a…
Encoding and Selecting Coarse-Grain Mapping Operators with Hierarchical Graphs
Maghesree Chakraborty, Chenliang Xu, Andrew D. White
Coarse grain (CG) molecular dynamics (MD) can simulate systems inaccessible to fine grain (FG) MD simulations. A CG simulation decreases the degrees of freedom by mapping atoms fro…