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Search Publications by: Vincent K. Shen (Fed)

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Displaying 1 - 25 of 87

Computational and Theoretical Study of Colloidal Monolayers with Short-Range Attractions and Dipolar Repulsions

March 21, 2025
Author(s)
Chieh-Chih Yeh, Harold Hatch, Adithya Sreenivasan, Bhuvnesh Bharti, Vincent Shen, Zachary Sherman, Thomas Truskett
This study explores the structure and phase behavior of monolayers of model colloids with short-range attractions and long-range repulsions, The model is motivated by recent experiments of hard-sphere-like microspheres that effectively interact via

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

Programming Interfacial Porosity and Symmetry with Escherized Colloids

February 22, 2024
Author(s)
Nathan Mahynski, Vincent K. Shen
We simultaneously design the porosity and plane symmetry of self-assembling colloidal films by using isohedral tiles to determine the location and shape of enthalpically interacting surface patches on motifs being functionalized. The symmetries of both the

Role of Domain-Domain Interactions on the Self-Association and Physical Stability of Monoclonal Antibodies: Effect of pH and Salt

September 26, 2023
Author(s)
Amy Xu, Marco Blanco, Maria Castellanos, Curtis Meuse, Kevin Mattison, Ioannis Karageorgos, Harold Hatch, Vincent Shen, Joseph E. Curtis
Monoclonal antibodies (mAbs) make up a major class of biotherapeutics with a wide range of clinical applications. Their physical stability can be affected by various environmental factors. For instance, an acidic pH can be encountered during different

Classification and Authentication of Materials using Prompt Gamma Ray Activation Analysis

July 12, 2023
Author(s)
Nathan Mahynski, Jacob Monroe, David Sheen, Rick L. Paul, Heather H. Chen-Mayer, Vincent K. Shen
Prompt gamma ray activation analysis (PGAA) is a non-destructive nuclear measurement technique that quantifies isotopes present in a sample. Here, we use PGAA spectra to train different types of models to elucidate how discriminating these spectra are for

Derivable genetic programming for two-dimensional colloidal materials

September 21, 2022
Author(s)
Nathan Mahynski, Bliss Han, Daniel Markiewitz, Vincent K. Shen
We describe a method for deriving surface functionalization patterns for colloidal systems that can induce self-assembly into any chosen periodic symmetry at a planar interface. The result is a sequence of letters, s ∈ A,T,C,G}, or a gene, that describes

Seabird Tissue Archival and Monitoring Project (STAMP) Data from 1999-2010

December 17, 2021
Author(s)
Nathan Mahynski, Jared Ragland, Stacy Schuur, Rebecca Pugh, Vincent K. Shen
The multi-entity, long-term Seabird Tissue Archival and Monitoring Project (STAMP) has collected eggs from various avian species throughout the North Pacific Ocean for over 20 years to create a geospatial and temporal record of environmental conditions

On the virial expansion of model adsorptive systems

November 9, 2021
Author(s)
William P. Krekelberg, Vincent K. Shen
We investigate super critical adsorptive properties of various model systems of variable fluid- solid attractive strengths using the confined-density virial expansion, with coefficients calculated using the Mayer-sampling Monte Carlo method up to fifth

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

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

Symmetry-based crystal structure enumeration in two dimensions

March 16, 2020
Author(s)
Evan Pretti, Vincent K. Shen, Jeetain Mittal, Nathan Mahynski
The accurate prediction of stable crystalline phases is a long-standing problem encountered in the study of conventional atomic and molecular solids as well as soft materials. One possible solution involves enumerating a reasonable set of candidate

Grand Canonical Inverse Design of Multicomponent Colloidal Crystals

February 19, 2020
Author(s)
Nathan Mahynski, Evan Pretti, Runfang Mao, Vincent K. Shen, Jeetain Mittal
Inverse design methods are powerful computational approaches for creating colloidal systems which self-assemble into a target morphology by reverse engineering the Hamiltonian of the system. Despite this, these optimization procedures tend to yield