Molecular investigation of polypyrrole and surface recognition by affinity peptides

textSuccessful tissue engineering strategies in the nervous system must be carefully crafted to interact favorably with the complex biochemical signals of the native environment. To date, all chronic implants incorporating electrical conductivity degrade in performance over time as the foreign body reaction and subsequent fibrous encapsulation isolate them from the host tissue. Our goal is to develop a peptide-based interfacial biomaterial that will non-covalently coat the surface of the conducting polymer polypyrrole, allowing the implant to interact with the nervous system through both electrical and chemical cues. Starting with a candidate peptide sequence discovered through phage display, we used computational simulations of the peptide on polypyrrole to describe the bound peptide structure, explore the mechanism of binding, and suggest new, better binding peptide sequences. After experimentally characterizing the polymer, we created a molecular mechanics model of polypyrrole using quantum mechanics calculations and compared its in silico properties to experimental observables such as density and chain packing. Using replica exchange molecular dynamics, we then modeled the behavior of affinity binding peptides on the surface of polypyrrole in explicit water and saline environments. Relative measurements of the contributions of each amino acid were made using distance measurements and computational alanine scanning.Biomedical Engineerin

Containerization on Petascale HPC Clusters

Containerization technologies provide a mechanism to encapsulate applications and many of their dependencies, facilitating software portability and reproducibility on HPC systems. However, in order to access many of the architectural features that enable HPC system performance, compatibility between certain components of the container and host are required, resulting in a trade-off between portability and performance. In this work, we discuss our early experiences running three state-of-the-art containerization technologies on the petascale Frontera system. We present how we build the containers to ensure performance and security and their performance at scale.We ran microbenchmarks at a scale of 4,096 nodes and demonstrate the near-native performance and minimal memory overheads by the containerized environments at 70,000 processes on 1,296 nodes with a scientific application MILC - a quantum chromodynamics code.UT Austin-Portugal Program, a collaboration between the Portuguese Foundation of Science and Technology and the University of Texas at Austin, award UTA18-001217Texas Advanced Computing Center (TACC

Workshop Report: Container Based Analysis Environments for Research Data Access and Computing

Report of the first workshop on Container Based Analysis Environments for Research Data Access and Computing supported by the National Data Service and Data Exploration Lab and held at the National Center for Supercomputing Applications (NCSA) at the University of Illinois at Urbana-Champaign

UT-MeteoGAN: A Next-Generation AI Model for High-Resolution Numerical Weather Prediction

We introduce UT-MeteoGAN, a cutting-edge, AI-driven model for high-resolution numerical weather prediction. UT-MeteoGAN enhances prediction accuracy and resolution by transitioning from Super Resolution Convolutional Neural Networks to the Swin Transformer, leveraging adversarial loss to refine its outputs. The model integrates data assimilation techniques, directly incorporating station observations into the training process, which significantly boosts forecast reliability. By utilizing a global model as input and targeting high-resolution gridded ground truth observations, UT-MeteoGAN excels in generating high-resolution gridded products, even in the absence of detailed high-resolution data. We conducted a comprehensive case study over the continental United States, when UT-MeteoGAN provided 36-hour lead forecasts at 1-km spatial and 1-hour temporal resolution. The global model Graphcast served as the input, with the National Oceanic and Atmospheric Administration (NOAA) Analysis of Record for Calibration (AORC) as the high-resolution target and NOAA’s Global Historical Climatological Network hourly (GHCNh) for station observations. UT-MeteoGAN consistently delivered forecasts that were comparable to or exceeded those of other models, offering rapid predictions with high accuracy. The development and operational deployment of UT-MeteoGAN are supported by the advanced NVIDIA H100 GPUs available through the Texas Advanced Computing Center. UT-MeteoGAN represents a significant advancement in numerical weather prediction, providing a robust and scalable solution for precise and timely weather forecasts. Its successful application in the continental United States case study highlights its potential for broader adoption in meteorological forecasting.Texas Advanced Computing Center (TACC

Attenuated Glial Reactivity on Topographically Functionalized Poly(3,4-Ethylenedioxythiophene):P-Toluene Sulfonate (PEDOT:PTS) Neuroelectrodes Fabricated by Microimprint Lithography

Following implantation, neuroelectrode functionality is susceptible to deterioration via reactive host cell response and glial scar-induced encapsulation. Within the neuroengineering community, there is a consensus that the induction of selective adhesion and regulated cellular interaction at the tissue–electrode interface can significantly enhance device interfacing and functionality in vivo. In particular, topographical modification holds promise for the development of functionalized neural interfaces to mediate initial cell adhesion and the subsequent evolution of gliosis, minimizing the onset of a proinflammatory glial phenotype, to provide long-term stability. Herein, a low-temperature microimprint-lithography technique for the development of micro-topographically functionalized neuroelectrode interfaces in electrodeposited poly(3,4-ethylenedioxythiophene):p-toluene sulfonate (PEDOT:PTS) is described and assessed in vitro. Platinum (Pt) microelectrodes are subjected to electrodeposition of a PEDOT:PTS microcoating, which is subsequently topographically functionalized with an ordered array of micropits, inducing a significant reduction in electrode electrical impedance and an increase in charge storage capacity. Furthermore, topographically functionalized electrodes reduce the adhesion of reactive astrocytes in vitro, evident from morphological changes in cell area, focal adhesion formation, and the synthesis of proinflammatory cytokines and chemokine factors. This study contributes to the understanding of gliosis in complex primary mixed cell cultures, and describes the role of micro-topographically modified neural interfaces in the development of stable microelectrode interfaces

Using the Agave API and Jupyter to Run Simulations, Monitor Events, and Share and Visualize Scientific Results

As science becomes increasingly digital, researchers face new challenges and opportunities to analyze, share, and understand large volumes of data more effectively. Gateways are at the forefront of this challenge, and the Agave Platform has been at the forefront of the gateway movement. Over the last 6 years, the authors have been working to develop this Science-as-a-Service platform, making it possible for users to go from the desktop, to their local data center, to the cloud.But Agave isn’t simply a tool for building web portals–it is, first and foremost, a sophisticated tool chain that enables developers to run jobs, monitor them, collaborate, and share data. As such, it is versatile and adaptable to new environments and interfaces. One such new and innovative variation on the web application is the Jupyter notebook, which combines the best elements of both the command line and the graphical interface

Lightning Talk - The Agave Platform: An Open Science-As-A-Service Cloud Platform for Reproducible Science

<p>The Agave Platform (Agave) is an open source, standards-based platform delivering Science-as-a-Service to the open science community. Agave uses standards-based technologies and community promoted best practices to enable users to run code, manage data, collaborate meaningfully, and integrate anywhere.</p><div>Chances are, Agave already works with the academic and commercial infrastructure you are already using, in the languages and frameworks you love, with zero installation required.</div