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Publications

Search Publications by

Vincent K. Shen (Fed)

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Displaying 1 - 25 of 69

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

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

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 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

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 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