148 citations · 745 across the 26 of their papers we have counts for
27 papers
Simulation and Network Assembly Pipelines for Dynamically Bonded Soft Materials
Tanner A. Wilcoxson, Tianhao Li, Tyla R. Holoman +3
Soft materials linked by reversible covalent or supramolecular bonds form a diverse class of assemblies with promising applications from nanoscience to medicine. Experiments typica…
Sampling Free Energy Landscapes of Ionic Colloidal Crystal Systems using Machine-Learned Proxy Collective Variables
Michael S. Chen, Stefano Sacanna, Glen M. Hocky
Charged colloids coated with a polymer brush can be designed to preferentially self-assemble into different crystal structures by varying easy-to-tune experimental conditions. For…
PACSim: A Flexible Simulation Framework for Polymer-Attenuated Coulombic Self-Assembly
Philipp Höllmer, Nicole Smina, John P. Marquardt +4
Polymer-Attenuated Coulombic Self-Assembly (PACS) is a flexible experimental approach for generating crystals from simple colloidal building blocks. The central components are char…
Stepping up enhanced rate calculations with EATR-flooding
Nicodemo Mazzaferro, Willmor J Pena Ccoa, Pilar Cossio +1
Several recent methods have shown that it is possible to compute rate constants of very slow biomolecular processes using simulations where a time-dependent bias is added along one…
Simulating dynamic bonding in soft materials
Tyla R. Holoman, B. P. Prajwal, Glen M. Hocky +1
Dynamic bonding is an essential feature of many soft materials. Molecular simulations have proven to be a powerful tool for modeling bonding kinetics and thermodynamics in these ma…
PLUMED Tutorials: a collaborative, community-driven learning ecosystem
Gareth A. Tribello, Massimiliano Bonomi, Giovanni Bussi +60
In computational physics, chemistry, and biology, the implementation of new techniques in a shared and open source software lowers barriers to entry and promotes rapid scientific p…
Large-Scale Multi-omic Biosequence Transformers for Modeling Protein-Nucleic Acid Interactions
Sully F. Chen, Robert J. Steele, Glen M. Hocky +3
The transformer architecture has revolutionized bioinformatics and driven progress in the understanding and prediction of the properties of biomolecules. To date, most biosequence…
Good rates from bad coordinates: the exponential average time-dependent rate approach
Nicodemo Mazzaferro, Subarna Sasmal, Pilar Cossio +1
Our ability to calculate rates of biochemical processes using molecular dynamics simulations is severely limited by the fact that the time scales for reactions, or changes in confo…
Molecular simulation approaches to probing the effects of mechanical forces in the actin cytoskeleton
Fatemah Mukadum, Willmor J. Pena Ccoa, Glen M. Hocky
In this article we give our perspective on the successes and promise of various molecular and coarse-grained simulation approaches to probing the effect of mechanical forces in the…
Improved prediction of molecular response to pulling by combining force tempering with replica exchange methods
Yuvraj Singh, Glen M. Hocky
Small mechanical forces play important functional roles in many crucial cellular processes, including in the dynamical behavior of the cytoskeleton and in the regulation of osmotic…
Computing equilibrium free energies through a nonequilibrium quench
Kangxin Liu, Grant M. Rotskoff, Eric Vanden-Eijnden +1
Many methods to accelerate sampling of molecular configurations are based on the idea that temperature can be used to accelerate rare transitions. These methods typically compute e…
Reaction Coordinates for Conformational Transitions using Linear Discriminant Analysis on Positions
Subarna Sasmal, Martin McCullagh, Glen M. Hocky
In this work, we demonstrate that Linear Discriminant Analysis (LDA) applied to atomic positions in two different states of a biomolecule produces a good reaction coordinate betwee…
A Coarse-Grained Simulation Model for Self-Assembly of Liquid Droplets Featuring Explicit Mobile Binders
Gaurav Mitra, Chuan Chang, Angus McMullen +3
Colloidal particles with mobile binding molecules constitute a powerful platform for probing the physics of self-assembly. Binding molecules are free to diffuse and rearrange on th…
Assessing models of force-dependent unbinding rates via infrequent metadynamics
Willmor J. Peña Ccoa, Glen M. Hocky
Protein-ligand interactions are crucial for a wide range of physiological processes. Many cellular functions result in these non-covalent `bonds' being mechanically strained, and t…
Size-and-Shape Space Gaussian Mixture Models for Structural Clustering of Molecular Dynamics Trajectories
Heidi Klem, Glen M. Hocky, Martin McCullagh
Determining the optimal number and identity of structural clusters from an ensemble of molecular configurations continues to be a challenge. Recent structural clustering methods ha…
Natural Language Processing Models That Automate Programming Will Transform Chemistry Research and Teaching
Glen M. Hocky, Andrew D. White
Natural language processing models have emerged that can generate usable software and automate a number of programming tasks with high fidelity. These tools have yet to have an imp…
A strong non-equilibrium bound for sorting of crosslinkers on growing biopolymers
Yuqing Qiu, Michael Nguyen, Glen M. Hocky +2
Understanding the role of non-equilibrium driving in self-organization is crucial for developing a predictive description of biological systems, yet it is impeded by their complexi…
A Minimal Experimental Bias on the Hydrogen Bond Greatly Improves Ab Initio Molecular Dynamics Simulations of Water
Paul B. Calio, Glen M. Hocky, Gregory A. Voth
Experiment Directed Simulations (EDS) is a method within a class of techniques seeking to improve molecular simulations by minimally biasing the system Hamiltonian to reproduce cer…
Infinite Switch Simulated Tempering in Force (FISST)
Michael J. Hartmann, Yuvraj Singh, Eric Vanden-Eijnden +1
Many proteins in cells are capable of sensing and responding to piconewton scale forces, a regime in which conformational changes are small but significant for biological processes…
Design principles for selective self-assembly of active networks
Simon L. Freedman, Glen M. Hocky, Shiladitya Banerjee +1
Living cells dynamically modulate the local morphologies of their actin cytoskeletons to perform biological functions, including force transduction, intracellular transport, and ce…
A versatile framework for simulating the dynamic mechanical structure of cytoskeletal networks
Simon L. Freedman, Shiladitya Banerjee, Glen M. Hocky +1
Computer simulations can aid in understanding how collective materials properties emerge from interactions between simple constituents. Here, we introduce a coarse-grained model th…
Improved Ab Initio Molecular Dynamics by Minimal Biasing with Experimental Data
Andrew D. White, Chris Knight, Glen M. Hocky +1
Accounting for electrons and nuclei simultaneously is a powerful capability of ab initio molecular dynamics (AIMD). However, AIMD is often unable to accurately reproduce properties…
Equilibrium ultrastable glasses produced by random pinning
Glen M Hocky, Ludovic Berthier, David R. Reichman
Ultrastable glasses have risen to prominence due to their potentially useful material properties and the tantalizing possibility of a general method of preparation via vapor deposi…
Correlation of Local Order with Particle Mobility in Supercooled Liquids is Highly System Dependent
Glen M. Hocky, Daniele Coslovich, Atsushi Ikeda +1
We investigate the connection between local structure and dynamical heterogeneity in supercooled liquids. Through the study of four different models we show that the correlation be…