University of South Florida Showcase

Summary: This dataset contains molecular dynamics simulation inputs, outputs, and selected analysis data for an attractive Kremer-Grest bead-spring polymer glass-former. The simulations were first reported in: Hung, J.-H., Patra, T. K., Meenakshisundaram, V., Mangalara, J. H. & Simmons, D. S. Universal localization transition accompanying glass formation: insights from efficient molecular dynamics simulations of diverse supercooled liquids. Soft Matter 15, 1223-1242 (2018). That publication and this dataset should be cited in any publication using these data. Simulated system: The system is an attractive Kremer-Grest bead-spring polymer with 12-6 Lennard-Jones interactions truncated at 2.5 sigma, 8000 total beads, and 20 beads per chain, simulated at a constant pressure of 0. Simulations targeted alpha relaxation times approaching 10^7 Lennard-Jones time units. The thermal protocol was based on the Predictive Stepwise Quench Algorithm (PreSQ). This dataset merges elements of two independent runs of that protocol, denoted 000 and 001. Contents: The archive includes simulation inputs and outputs for generation, quench, equilibration, and production elements, together with selected analysis data. The simulations/ directory contains workflow subdirectories, Packmol inputs, and LAMMPS input templates. Production outputs are in simulations/production/ and include exponentially spaced custom LAMMPS trajectories collected during isothermal production simulations. Production trajectories are provided as a compressed tarball. For users wishing to simply make use of these trajectories to study the system's physics, these will be the most important files, together with the associated production log files specifying the time scheme. Trajectories from other simulation elements are provided in compressed LAMMPS xyz tarballs. Analysis results generated using AMDAT are in the analysis/ directory. The AMDAT analysis package, which can be readily used to further analyze these files, can be found here: https://github.com/dssimmons-codes/AMDAT. Temperatures are encoded in filenames as a 6- to 7-digit number following the capital letter T; the reduced Lennard-Jones temperature is obtained by dividing this number by 1,000,000. Additional documentation, including directory structure, file conventions, and interpretation of equilibrium status, is provided in the dataset README. Caution: Not all temperatures with archived outputs are necessarily in equilibrium. Temperatures identified by PreSQ as satisfying equilibrium criteria are listed in analysis/fit_data. For each replicate, the Regime8 file reports the temperatures and relaxation times accepted as in equilibrium.

This replication package reproduces all tables and figures in "Old But Gold: Historical Pathways and Path Dependence." It contains the analysis-ready datasets (municipality, mining census area, and census wage microdata panels, together with auxiliary historical series on population, GDP, crops, railroads, and roads), the digitized shapefiles for colonial gold roads, least-cost-path instruments, administrative boundaries, and highways, and the R and Julia scripts that build the tables, regression output, and maps from these inputs. Running MakeFiles.R executes the full pipeline and writes results to tables/ and figures/.

This repository contains the processed simulation data, selected trajectories, analysis outputs, and figure-generation scripts associated with the manuscript: Glassy interphases reinforce elastomeric nanocomposites by enhancing percolation-driven volume expansion under strain In filled elastomers, nanoparticle additives can dramatically increase stiffness and toughness, yet the molecular origins of this reinforcement have remained debated for decades. A prominent idea is that strong polymer–particle attractions create “glassy bridges” that directly cement particles into a load-bearing network. The data and scripts in this repository accompany a molecular simulation study showing a different picture: glassy interphases do not primarily reinforce by directly supplying elongational cohesion. Instead, they amplify a more fundamental mechanism in which competition between particulate and elastomeric networks increases volume expansion under strain, thereby activating large bulk-modulus contributions to the response. The repository is organized around two main directories. The `data/` directory contains processed simulation outputs, selected input files, and helper scripts for reproducing simulations and post-processing analyses. The `figures/` directory contains figure-specific plotting scripts and source files for all main-text and supporting-information figures. Simulation datasets are organized by filler structure, filler loading, and filler–polymer attraction strength. For full repository documentation, directory structure, software prerequisites, and detailed workflow instructions, see the top-level `README.md`. Associated manuscript: https://arxiv.org/abs/2509.04755

Study remote organ injury(liver) by AKI

Using mutant mice with laminin-γ1 deficiency in PDGFRβ+ cells, we investigated the functions of PDGFRβ+ cell-derived laminin-γ1 in blood-brain barrier integrity maintenance, pericyte number, basal lamina thickness, brain stiffness, CSF influx/brain clearance, synaptic loss, and cognitive function in an age-dependent manner. The raw data and unprocessed Western Blot images are provided here.

Bulk modulus versus temperature data from equilibrium molecular dynamics simulations of a model neat elastomer. Dataset for Kawak, Bhapkar, Simmons. Origin of Heating-Induced Softening and Enthalpic Reinforcement in Elastomeric Nanocomposites. ACS Macro Letters 2025, 14, 12, 1867–1873 DOI:10.1021/acsmacrolett.5c00442

Young's modulus and Poisson's ratio versus temperature data from uniaxial extension molecular dynamics simulations of model neat and filled elastomers. Dataset for Kawak, Bhapkar, Simmons. Origin of Heating-Induced Softening and Enthalpic Reinforcement in Elastomeric Nanocomposites. ACS Macro Letters 2025, 14, 12, 1867–1873 DOI:10.1021/acsmacrolett.5c00442

(a) Young's modulus E versus temperature T in LJ units for model neat elastomers and filled elastomers at 150 parts per hundred rubber (PHR) loading or 0.415 filler volume fraction calculated using finite difference of extensional stress between strains of 4.5% and 5.5%. The solid green curve is the prediction of the composite modulus temperature dependence from Equation (5), with f =1.19. The solid blue curve is the prediction of the neat modulus temperature dependence from classical theory of rubber elasticity (i.e., proportionality to temperature) (b) Bulk modulus Ke versus T in LJ units for a model neat elastomer at zero pressure. Ke is computed via the fluctuation-dissipation relation as T〈V〉/〈δV2〉, where V is the volume, 〈V〉 is the NPT ensemble average of the volume, and 〈δV2〉 is the NPT ensemble variance of the volume. The solid curve is a fit to the Tait equation (Equation (2)). (c) Poisson’s ratio ν versus T computed by finite difference of extensional strain to normal strain between 4.5% and 5.5% extensional strain. d) Ec from panel a) versus theoretical prediction from Equation (1). Error bars reflect standard errors of the mean over 100 (a), 5 (b), and 100 (c) independent replicates. Dataset for Kawak, Bhapkar, Simmons. Origin of Heating-Induced Softening and Enthalpic Reinforcement in Elastomeric Nanocomposites. ACS Macro Letters 2025, 14, 12, 1867–1873 DOI:10.1021/acsmacrolett.5c00442

Relaxation times of interfacial and bulk polymer segments (distance less than 1 σ and greater than 3 σ away from filler surface, respectively) versus temperature in Lennard-Jones (LJ) units (εLJ is LJ energy scale and kB is the Boltzmann constant). Dataset for Kawak, Bhapkar, Simmons. Origin of Heating-Induced Softening and Enthalpic Reinforcement in Elastomeric Nanocomposites. ACS Macro Letters 2025, 14, 12, 1867–1873 DOI:10.1021/acsmacrolett.5c00442

Rendering of a configuration of model filled elastomer with loading of 150 parts per hundred rubber (PHR) or 0.415 filler volume fraction. Polymers are rendered in green (with bonds shown); beads that comprise filler particles are rendered in pale yellow. Rendered by OVITO. Dataset for Kawak, Bhapkar, Simmons. Origin of Heating-Induced Softening and Enthalpic Reinforcement in Elastomeric Nanocomposites. ACS Macro Letters 2025, 14, 12, 1867–1873 DOI:10.1021/acsmacrolett.5c00442