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Search Publications by: Nathan A. Mahynski (Fed)

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Displaying 1 - 25 of 28

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

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

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

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

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

Void-based Assembly of Colloidal Crystals

June 1, 2017
Author(s)
Nathan Mahynski, Lorenzo Rovigatti, Christos Likos, Athanassios Panagiotopoulos
We have used computer simulations to reveal how colloidal crystals may be assembled by engineering the shape and charge of polymeric additives, which act as structure-directing agents (SDAs). Using these agents, only a single desired polymorph may be

Predicting low-temperature free energy landscapes with flat-histogram Monte Carlo methods

February 21, 2017
Author(s)
Nathan Mahynski, Marco A. Blanco Medina, Jeffrey R. Errington, Vincent K. Shen
We present a method of predicting the free energy landscape of fluids at low temperatures from flat-histogram grand canonical Monte Carlo simulations performed at higher ones. We illustrate our approach for both pure and multicomponent systems using two