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Search Publications by: Harold Wickes Hatch (Fed)

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Displaying 1 - 25 of 29

Anisotropic coarse-grain Monte Carlo simulations of lysozyme, lactoferrin, and NISTmAb by precomputing atomistic models

September 5, 2024
Author(s)
Harold Hatch, Christina Bergonzo, Marco Blanco, Guangcui Yuan, Sergei Grudinin, Mikael Lund, Joseph E. Curtis, Alexander Grishaev, Yun Liu, Vincent K. Shen
We develop a multiscale coarse-grain model of the NIST Monoclonal Antibody Reference Material 8671 (NISTmAb) to enable systematic computational investigations of high-concentration physical instabilities such as phase separation, clustering, and

Monte Carlo molecular simulations with FEASST version 0.25.1

September 5, 2024
Author(s)
Harold Hatch, Daniel Siderius, Vincent K. Shen
FEASST is an open-source Monte Carlo software for particle-based simulations. This software, which was released in 2017, has been used to study phase equilibrium, self-assembly, aggregation or gelation in biological materials, colloids, polymers, ionic

Flow Activation Energy of High-Concentration Monoclonal Antibody Solutions and Protein-Protein Interactions Influenced by NaCl and Sucrose

August 20, 2024
Author(s)
Guangcui Yuan, Paul Salipante, Steven D. Hudson, Richard Gillilan, Qingqiu Huang, Harold Hatch, Vincent Shen, Alexander Grishaev, Suzette Pabit, Rahul Upadhya, Sudeep Adhikari, Jainik Panchal, Marco Blanco, Yun Liu
The solution viscosity and protein−protein interactions (PPIs) as a function of temperature (4−40 °C) were measured at a series of protein concentrations for a monoclonal antibody (mAb) with different formulation conditions, which include NaCl and sucrose

pH response of sequence-controlled polyampholyte brushes

May 31, 2023
Author(s)
Xin Yuan, Harold Hatch, Jacinta Conrad, Amanda Marciel, Jeremy Palmer
We use molecular simulation to investigate the pH response of sequence-controlled polyampholyte brushes (PABs) with polymer chains consisting of alternating blocks of weakly acidic and basic monomers. Changes in the ionization state, height, lateral

Extrapolation And Interpolation Strategies For Efficiently Estimating Structural Observables As a Function Of Temperature And Density

October 8, 2020
Author(s)
Jacob I. Monroe, Harold Wickes Hatch, Nathan NMN Mahynski, M. Scott Shell, Vincent K. Shen
Thermodynamic extrapolation has previously been used to predict arbitrary structural observables in molecular simulations at temperatures (or relative chemical potentials in open- system mixtures) different from those at which the simulation was performed

Parallel Prefetching for Canonical Ensemble Monte Carlo Simulations

August 25, 2020
Author(s)
Harold Wickes Hatch
In order to enable large-scale molecular simulations, algorithms must efficiently utilize multi-core processors that continue to increase in total core count over time with relatively stagnant clock speeds. Although parallelized molecular dynamics (MD)

Flat-Histogram Extrapolation as a Useful Tool in the Age of Big Data

April 13, 2020
Author(s)
Nathan Mahynski, Harold Hatch, Matthew Witman, David Sheen, Jeffrey R. Errington, Vincent K. Shen
Here we review recent work by the authors to revisit the concept of extrapolating thermodynamic properties of classical systems using statistical mechanical principles. Specifically, we discuss how the combination of these principles with biased sampling

Dynamic Arrest of Adhesive Hard Rod Dispersions

February 7, 2020
Author(s)
Ryan P Murphy, Harold Wickes Hatch, Nathan NMN Mahynski, Vincent K. Shen, Norman J. Wagner
Dynamic arrest transitions of model, thermoreversible dispersions of adhesive hard rods are measured as a function of absolute temperature Τ = 15 -40 °C, aspect ration L/D{approximately equal}3-7, and volume fraction φ0.1-0.5. The critical gel temperature

Designing Molecular Building Blocks for the Self-assembly of Complex Porous Networks

March 19, 2019
Author(s)
Tiara A. Maula, Harold Hatch, Vincent K. Shen, Rangarajan Srinivas, Jeetain Mittal
Molecular building blocks which self-assemble into large ordered porous networks have been long sought-after, and have led to the development of metal organic frameworks and covalent organic frameworks. However, despite the great potential possessed by

Monte Carlo Simulation of Cylinders with Short-Range Attractions

September 12, 2018
Author(s)
Harold W. Hatch, Nathan Mahynski, R. P. Murphy, Marco Blanco, Vincent K. Shen
Cylindrical or rod-like particles are promising materials for the applications of fillers in nanocomposite ma- terials and additives to control rheological properties of colloidal suspensions. Recent advances in particle synthesis allows for cylinders to

Programmable assembly of three-dimensional binary superlattices from multi-flavored DNA- functionalized particles

July 10, 2018
Author(s)
Evan Pretti, Hasan Zerze, Minseok Song, Yajun Ding, Nathan Mahynski, Harold Hatch, Vincent K. Shen, Jeetain Mittal
Programmable self-assembly of nano- or micron-sized colloidal particles can be achieved by grafting single- stranded DNA sequences onto the surfaces of colloids. However, this assembly is traditionally premised on the pairwise interaction between a single

Predicting structural properties of fluids by thermodynamic extrapolation

May 16, 2018
Author(s)
Nathan Mahynski, Sally Jiao, Harold W. Hatch, Marco A. Blanco Medina, Vincent K. Shen
We describe a methodology for extrapolating the structural properties of multicomponent fluids from one thermodynamic state to another. These properties generally include features of a system that may be computed from an individual configuration such as

FEASST: Free Energy and Advanced Sampling Simulation Toolkit

March 1, 2018
Author(s)
Harold W. Hatch, Nathan Mahynski, Vincent K. Shen
The Free Energy and Advanced Sampling Simulation Toolkit (FEASST) is a free, open-source, modular program to conduct molecular and particle-based simulations with Metropolis, Wang-Landau and Transition-Matrix Monte Carlo methods. FEASST is implemented in C

Assembly of Multi-flavored Two-Dimensional Colloidal Crystals

July 12, 2017
Author(s)
Nathan Mahynski, Hasan Zerze, Harold W. Hatch, Vincent K. Shen, Jeetain Mittal
We systematically investigate the assembly of binary multi-flavored colloidal mixtures in two dimensions. In these mixtures all pairwise interactions between species may be tuned independently. This introduces an additional degree of freedom over more