Eric Jankowski
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View article: Achieving Reproducibility and Replicability of Molecular Dynamics and Monte Carlo Simulations Using the Molecular Simulation Design Framework (MoSDeF)
Achieving Reproducibility and Replicability of Molecular Dynamics and Monte Carlo Simulations Using the Molecular Simulation Design Framework (MoSDeF) Open
Molecular simulations are increasingly used to predict thermophysical properties and explore molecular-level phenomena beyond modern imaging techniques. To make these tools accessible to nonexperts, several open-source molecular dynamics (…
View article: Validating Structural Predictions of Conjugated Macromolecules in Espaloma-Enabled Reproducible Workflows
Validating Structural Predictions of Conjugated Macromolecules in Espaloma-Enabled Reproducible Workflows Open
We incorporated Espaloma forcefield parameterization into MoSDeF tools for performing molecular dynamics simulations of organic molecules with HOOMD-Blue. We compared equilibrium morphologies predicted for perylene and poly-3-hexylthiophen…
View article: Representing Structural Isomer Effects in a Coarse-Grain Model of Poly(Ether Ketone Ketone)
Representing Structural Isomer Effects in a Coarse-Grain Model of Poly(Ether Ketone Ketone) Open
Carbon-fiber composites with thermoplastic matrices offer many processing and performance benefits in aerospace applications, but the long relaxation times of polymers make it difficult to predict how the structure of the matrix depends on…
View article: Board 380: Self-storytelling Interventions to Promote Engineering Student Success
Board 380: Self-storytelling Interventions to Promote Engineering Student Success Open
This IUSE project focuses on the development, implementation, and evaluation of the impact of a unique storytelling intervention to enhance the self-view of undergraduate engineering students. It explores how telling personal narratives ab…
View article: FlowerMD: Flexible Library of Organic Workflows andExtensible Recipes for Molecular Dynamics
FlowerMD: Flexible Library of Organic Workflows andExtensible Recipes for Molecular Dynamics Open
Albooyeh et al., (2023). FlowerMD: Flexible Library of Organic Workflows and Extensible Recipes for Molecular Dynamics. Journal of Open Source Software, 8(92), 5989, https://doi.org/10.21105/joss.05989
View article: MORG1—A Negative Modulator of Renal Lipid Metabolism in Murine Diabetes
MORG1—A Negative Modulator of Renal Lipid Metabolism in Murine Diabetes Open
Renal fatty acid (FA) metabolism is severely altered in type 1 and 2 diabetes mellitus (T1DM and T2DM). Increasing evidence suggests that altered lipid metabolism is linked to tubulointerstitial fibrosis (TIF). Our previous work has demons…
View article: Open‐source molecular modeling software in chemical engineering focusing on the Molecular Simulation Design Framework
Open‐source molecular modeling software in chemical engineering focusing on the Molecular Simulation Design Framework Open
Peer Reviewed
View article: signac: Data Management and Workflows for Computational Researchers
signac: Data Management and Workflows for Computational Researchers Open
The signac data management framework (https://signac.io) helps researchers execute reproducible computational studies, scales workflows from laptops to supercomputers, and emphasizes portability and fast prototyping. With signac, users can…
View article: Validating Structural and Thermodynamic Properties of Nonfullerene Acceptors for Organic Photovoltaics
Validating Structural and Thermodynamic Properties of Nonfullerene Acceptors for Organic Photovoltaics Open
A single junction solar cell can possess a theoretical maximum efficiency of 33.7%; the closer solar cells are to this value, the harder it is to improve efficiency. Organic photovoltaics (OPVs)—solar materials made from organic compounds—…
View article: Molecular Simulations for Understanding the Stabilization of Fullerenes in Water
Molecular Simulations for Understanding the Stabilization of Fullerenes in Water Open
Making materials out of buckminsterfullerene is challenging, because it requires first dispersing the molecules in a solvent, and then getting the molecules to assemble in the desired arrangements.In this computational work, we focus on th…
View article: Using Computational Tools to Accelerate Discovery of High-Efficiency Solar Cell Materials
Using Computational Tools to Accelerate Discovery of High-Efficiency Solar Cell Materials Open
High-efficiency organic photovoltaic (OPV) materials made with non-fullerene electron acceptors are exciting because of their potential for realizing solar power that pays for its capital cost in weeks rather than decades. Optimizing these…
View article: Open-Source Molecular Modeling Software in Chemical Engineering Focusing on the Molecular Simulation Design Framework
Open-Source Molecular Modeling Software in Chemical Engineering Focusing on the Molecular Simulation Design Framework Open
Molecular simulation has emerged as an important sub-field of chemical engineering, due in no small part to the leadership of Keith Gubbins. A characteristic of the chemical engineering molecular simulation community is the commitment to f…
View article: General-Purpose Coarse-Grained Toughened Thermoset Model for 44DDS/DGEBA/PES
General-Purpose Coarse-Grained Toughened Thermoset Model for 44DDS/DGEBA/PES Open
The objective of this work is to predict the morphology and material properties of crosslinking polymers used in aerospace applications. We extend the open-source dybond plugin for HOOMD-Blue to implement a new coarse-grained model of reac…
View article: Perspective on coarse-graining, cognitive load, and materials simulation
Perspective on coarse-graining, cognitive load, and materials simulation Open
The predictive capabilities of computational materials science today derive from overlapping advances in simulation tools, modeling techniques, and best practices. We outline this ecosystem of molecular simulations by explaining how import…
View article: Machine learning predictions of electronic couplings for charge transport calculations of P3HT
Machine learning predictions of electronic couplings for charge transport calculations of P3HT Open
The purpose of this work is to lower the computational cost of predicting charge mobilities in organic semiconductors, which will benefit the screening of candidates for inexpensive solar power generation. We characterize efforts to minimi…
View article: swcarpentry/shell-novice: Software Carpentry: the UNIX shell, June 2019
swcarpentry/shell-novice: Software Carpentry: the UNIX shell, June 2019 Open
Software Carpentry lesson on how to use the shell to navigate the filesystem and write simple loops and scripts.
View article: Tying Together Multiscale Calculations for Charge Transport in P3HT: Structural Descriptors, Morphology, and Tie-Chains
Tying Together Multiscale Calculations for Charge Transport in P3HT: Structural Descriptors, Morphology, and Tie-Chains Open
Evaluating new, promising organic molecules to make next-generation organic optoelectronic devices necessitates the evaluation of charge carrier transport performance through the semi-conducting medium. In this work, we utilize quantum che…
View article: Optimization and Validation of Efficient Models for Predicting Polythiophene Self-Assembly
Optimization and Validation of Efficient Models for Predicting Polythiophene Self-Assembly Open
We develop an optimized force-field for poly(3-hexylthiophene) (P3HT) and demonstrate its utility for predicting thermodynamic self-assembly. In particular, we consider short oligomer chains, model electrostatics and solvent implicitly, an…
View article: Tying Together Multiscale Calculations for Charge Transport in P3HT: Structural Descriptors, Morphology, and Tie-Chains
Tying Together Multiscale Calculations for Charge Transport in P3HT: Structural Descriptors, Morphology, and Tie-Chains Open
Evaluating new, promising organic molecules to make next-generation organic optoelectronic devices necessitates the evaluation of charge carrier transport performance through the semi-conducting medium. In this work, we utilize quantum che…
View article: Optimization and Validation of Efficient Models for Predicting Polythiophene Self-Assembly
Optimization and Validation of Efficient Models for Predicting Polythiophene Self-Assembly Open
We develop an optimized force-field for poly(3-hexylthiophene) (P3HT) and demonstrate its utility for predicting thermodynamic self-assembly. In particular, we consider short oligomer chains, model electrostatics and solvent implicitly, an…
View article: Molecular Dynamics Data for Optimization and Validation of Modeling Techniques for Predicting Structures and Charge Mobilities of P3HT
Molecular Dynamics Data for Optimization and Validation of Modeling Techniques for Predicting Structures and Charge Mobilities of P3HT Open
The self-assembled active layer morphology strongly affects the performance of organic electronic devices. In this work, we present the development of an optimized OPLS-UA force-field for the benchmark donor polymer poly(3 -hexylthiophene)…
View article: Data for Simplified Models for Accelerated Structural Prediction of Conjugated Semiconducting Polymers
Data for Simplified Models for Accelerated Structural Prediction of Conjugated Semiconducting Polymers Open
We perform molecular dynamics simulations of poly(benzodithiophene-thienopyrrolodione) (BDT-TPD) oligomers in order to evaluate the accuracy with which unoptimized molecular models can predict experimentally characterized morphologies. The…
View article: Molecular Interactions of Polydimethylsiloxane and Ni-Mn-Ga
Molecular Interactions of Polydimethylsiloxane and Ni-Mn-Ga Open
Tiny pumps that can deliver microliters of fluid against high back-pressures can be made from Ni-Mn-Ga alloys. The fluid is transported in a movable pocket made between the alloy and a surrounding seal material, enabled by the magnetic sha…
View article: Simplified Models for Accelerated Structural Prediction of Conjugated Semiconducting Polymers
Simplified Models for Accelerated Structural Prediction of Conjugated Semiconducting Polymers Open
We perform molecular dynamics simulations of poly(benzodithiophene-thienopyrrolodione) (BDT-TPD) oligomers in order to evaluate the accuracy with which unoptimized molecular models can predict experimentally characterized morphologies. The…
View article: Application of artificial neural networks to identify equilibration in computer simulations
Application of artificial neural networks to identify equilibration in computer simulations Open
Determining which microstates generated by a thermodynamic simulation are representative of the ensemble for which sampling is desired is a ubiquitous, underspecified problem. Artificial neural networks are one type of machine learning alg…
View article: Enhanced Computational Sampling of Perylene and Perylothiophene Packing with Rigid-Body Models
Enhanced Computational Sampling of Perylene and Perylothiophene Packing with Rigid-Body Models Open
Molecular simulations have the potential to advance the understanding of how the structure of organic materials can be engineered through the choice of chemical components but are limited by computational costs. The computational costs can…