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Publications

Search Publications by Vincent K. Shen

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Displaying 1 - 25 of 60

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

Chemometric Outlier Classification of 2D-NMR Spectra to Enable Higher Order Structure Characterization of Protein Therapeutics

April 15, 2020
Author(s)
David A. Sheen, Vincent K. Shen, Robert G. Brinson, Luke W. Arbogast, John P. Marino, Frank Delaglio
Protein therapeutics are vitally important clinically and commercially, with monoclonal antibody (mAb) therapeutic sales alone accounting for $115 billion in revenue for 2018.[1] In order for these therapeutics to be safe and efficacious, their protein

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

Using Symmetry To Elucidate the Role Of Stoichiometry In Colloidal Crystal Assembly

May 2, 2019
Author(s)
Nathan Mahynski, Evan Pretti, Vincent K. Shen, Jeetain Mittal
We demonstrate a method based on symmetry to predict the structure of multi-component colloidal mixtures. In this work we focus on two-dimensional systems, for which the method allows us to exhaustively enumerate candidates from all wallpaper groups

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

March 19, 2019
Author(s)
Tiara A. Maula, Harold W. 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 W. 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

The Ninth Industrial Fluid Properties Simulation Challenge

May 1, 2018
Author(s)
Jonathan D. Moore, Raymond D. Mountain, Richard B. Ross, Vincent K. Shen, Daniel W. Siderius, Kenneth D. Smith
The Ninth Industrial Fluid Properties Simulation Challenge aimed to test the ability of molecular modeling approaches to predict water/oil interfacial tension (IFT) at conditions of high temperature and pressure. In particular, the challenge featured water

Molecular Simulation of Capillary Phase Transitions in Flexible Porous Materials

March 27, 2018
Author(s)
Vincent K. Shen, Daniel W. Siderius, Nathan Mahynski
We used at-histogram sampling Monte Carlo to study capillary phase transitions in deformable adsorbent materials. Specifically, we considered a pure adsorbate fluid below its bulk critical temperature within a slit pore of variable pore width. The

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

Multivariable Extrapolation of Grand Canonical Free Energy Landscapes

December 21, 2017
Author(s)
Nathan Mahynski, Jeffrey R. Errington, Vincent K. Shen
We derive an approach for extrapolating the free energy landscape of multicomponent systems in the grand canonical ensemble, obtained from flat- histogram Monte Carlo simulations, from one set of temperature and chemical potentials to another. This is

Quasi-Two-dimensional Phase Transition of Methane Adsorbed in Cylindrical Silica Mesopores

November 29, 2017
Author(s)
Daniel W. Siderius, William P. Krekelberg, Wei-Shan NMN Chiang, Vincent K. Shen, Yun Liu
Using Monte Carlo and molecular dynamics simulations, we examine the adsorption of methane in cylindrical silica mesopores in an effort to understand a possible phase transition of adsorbed methane in MCM-41 and SBA-15 silica that was previously identified

Temperature extrapolation of multicomponent grand canonical free energy landscapes

August 7, 2017
Author(s)
Nathan Mahynski, Jeffrey R. Errington, Vincent K. Shen
We derive a method for extrapolating the grand canonical free energy landscape of a multicomponent fluid system from one temperature to another. Previously, we introduced this statistical mechanical framework for the case where kinetic energy contributions

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

Connection between thermodynamics and dynamics of simple fluids in pores: impact of fluid-fluid interaction range and fluid-solid interaction strength

July 5, 2017
Author(s)
William P. Krekelberg, Daniel W. Siderius, Vincent K. Shen, Thomas M. Truskett, Jeffrey R. Errington
Using molecular simulations, we investigate how the range of fluid-fluid (adsorbate-adsorbate) interactions and the strength of fluid-solid (adsorbate-adsorbent) interactions impact the strong connection between distinct adsorptive regimes and distinct

Molecular Dynamics Simulation of Trimer Self-Assembly Under Shear

March 6, 2017
Author(s)
Raymond D. Mountain, Harold W. Hatch, Vincent K. Shen
The self-assembly of patchy trimer particles with one attractive bead and two repulsive beads is investigated with nonequilibrium molecular dynamics simulations in the presence of a velocity gradient, as would be produced by the application of a shear