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NASA NTRS2015

Climate Data Initiative: A Geocuration Effort to Support Climate Resilience

Curation is traditionally defined as the process of collecting and organizing information around a common subject matter or a topic of interest and typically occurs in museums, art galleries, and libraries. The task of organizing data around specific topics or themes is a vibrant and growing effort in the biological sciences but to date this effort has not been actively pursued in the Earth sciences. In this paper, we introduce the concept of geocuration and define it as the act of searching, selecting, and synthesizing Earth science data/metadata and information from across disciplines and repositories into a single, cohesive, and useful compendium We present the Climate Data Initiative (CDI) project as an exemplar example. The CDI project is a systematic effort to manually curate and share openly available climate data from various federal agencies. CDI is a broad multi-agency effort of the U.S. government and seeks to leverage the extensive existing federal climate-relevant data to stimulate innovation and private-sector entrepreneurship to support national climate-change preparedness. We describe the geocuration process used in CDI project, lessons learned, and suggestions to improve similar geocuration efforts in the future.

virtual collections↗
NASA NTRS2015

Geocuration Lessons Learned from the Climate Data Initiative Project

Curation is traditionally defined as the process of collecting and organizing information around a common subject matter or a topic of interest and typically occurs in museums, art galleries, and libraries. The task of organizing data around specific topics or themes is a vibrant and growing effort in the biological sciences but to date this effort has not been actively pursued in the Earth sciences. This presentation will introduce the concept of geocuration, which we define it as the act of searching, selecting, and synthesizing Earth science data/metadata and information from across disciplines and repositories into a single, cohesive, and useful compendium. We also present the Climate Data Initiative (CDI) project as an prototypical example. The CDI project is a systematic effort to manually curate and share openly available climate data from various federal agencies. CDI is a broad multi-agency effort of the U.S. government and seeks to leverage the extensive existing federal climate-relevant data to stimulate innovation and private-sector entrepreneurship to support national climate change preparedness. The geocuration process used in the CDI project, key lessons learned, and suggestions to improve similar geocuration efforts in the future will be part of this presentation.

climate↗
DOE OSTI2020

Activity profiling and crystal structures of inhibitor-bound SARS-CoV-2 papain-like protease: A framework for anti–COVID-19 drug design

Viral papain-like cysteine protease (PLpro, NSP3) is essential for SARS-CoV-2 replication and represents a promising target for the development of antiviral drugs. Here, we used a combinatorial substrate library and performed comprehensive activity profiling of SARS-CoV-2 PLpro. On the scaffold of the best hits from positional scanning, we designed optimal fluorogenic substrates and irreversible inhibitors with a high degree of selectivity for SARS PLpro. We determined crystal structures of two of these inhibitors in complex with SARS-CoV-2 PLpro that reveals their inhibitory mechanisms and provides a molecular basis for the observed substrate specificity profiles. Last, we demonstrate that SARS-CoV-2 PLpro harbors deISGylating activity similar to SARSCoV-1 PLpro but its ability to hydrolyze K48-linked Ub chains is diminished, which our sequence and structure analysis provides a basis for. Together, this work has revealed the molecular rules governing PLpro substrate specificity and provides a framework for development of inhibitors with potential therapeutic value or drug repurposing.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Visualizing Comparisons of Bill of Materials

Protecting critical infrastructure from cyber attacks, natural disasters, and other disruptions is a priority of the U.S. Government. Critical infrastructure includes providing electricity to homes and businesses, supplying natural gas for heating, and producing renewable energy sources. A loss of these services, as seen in the Solarwinds supply chain attack in 2020 , Texas snowstorm of 2021, the Colonial Pipeline cyber incident of 2021, and the Washington power substation attacks in 2022 result in high costs to consumers, disruption of everyday life, and even death. To protect the infrastructure, we first have to know what equipment we are protecting. The complexity of distributed manufacturing and development coupled with the increasing prevalence of cyber and supply chain attacks necessitates a greater understanding of the hardware and software components that comprise equipment in critical infrastructure. When a vulnerability in a single software library can have disastrous consequences, it is vital to understand critical equipment and systems at a granular level. This need has led to increased energy around the development and incorporation of bill-of-materials (BOM) into existing asset management practices to aid in mitigating, and responding to future attacks \cite{noauthor_software_nodate}. While much of the current research is devoted to creating BOMs, it is equally important to develop methodologies for leveraging BOMs to answer questions, such as: How has my software changed? Are two pieces of equipment equivalent? Does this piece of equipment that just arrived match my historical information? In this work, we demonstrate how BOMs can be represented by graph structures. We then describe how these structures can be fed into a graph comparison algorithm to produce a novel interactive visualization that allows us to not only identify differences in BOMs, but show exactly where they are in the product.

Jones, Rebecca D.↗
DOE OSTI2023

The first two chromosome‐scale genome assemblies of American hazelnut enable comparative genomic analysis of the genus Corylus

Summary The native, perennial shrub American hazelnut ( Corylus americana ) is cultivated in the Midwestern United States for its significant ecological benefits, as well as its high‐value nut crop. Implementation of modern breeding methods and quantitative genetic analyses of C. americana requires high‐quality reference genomes, a resource that is currently lacking. We therefore developed the first chromosome‐scale assemblies for this species using the accessions ‘Rush’ and ‘Winkler’. Genomes were assembled using HiFi PacBio reads and Arima Hi‐C data, and Oxford Nanopore reads and a high‐density genetic map were used to perform error correction. N50 scores are 31.9 Mb and 35.3 Mb, with 90.2% and 97.1% of the total genome assembled into the 11 pseudomolecules, for ‘Rush’ and ‘Winkler’, respectively. Gene prediction was performed using custom RNAseq libraries and protein homology data. ‘Rush’ has a BUSCO score of 99.0 for its assembly and 99.0 for its annotation, while ‘Winkler’ had corresponding scores of 96.9 and 96.5, indicating high‐quality assemblies. These two independent assemblies enable unbiased assessment of structural variation within C. americana , as well as patterns of syntenic relationships across the Corylus genus. Furthermore, we identified high‐density SNP marker sets from genotyping‐by‐sequencing data using 1343 C. americana , C. avellana and C. americana × C. avellana hybrids, in order to assess population structure in natural and breeding populations. Finally, the transcriptomes of these assemblies, as well as several other recently published Corylus genomes, were utilized to perform phylogenetic analysis of sporophytic self‐incompatibility (SSI) in hazelnut, providing evidence of unique molecular pathways governing self‐incompatibility in Corylus .

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1977

Applications of remote-sensing data in Alaska

Public and private agencies were introduced to the use of remotely sensed data obtained by both satellite and aircraft, and benefitted from facilities for data processing enhancement and interpretation as well as from the institute's data library. Cooperative ventures involving the performance of operational activities included assistance to the Bureau of Land Management in the suppression of wildfires; the selection of sites for power line right-of-way; the mapping of leads in sea ice; determination of portions of public lands to be allocated for small scale farming; the identification of areas for large scale farming of barley; the observation of coastal processes and sediment transport near Prudhoe Bay; the establishment of a colar infrared file of the entire state; and photomapping for geological surveys. Monitoring of the outer continental shelf environment and reindeer herds was also conducted. Institutional constraints to full utilization of satellite remote sensing in the state are explored and plans for future activites include the generation of awareness by government agencies, the training of state personnel, and improving coordination and communication with users.

Miller, J. M.↗
DOE OSTI2024

GPU-enabled extreme-scale turbulence simulations: Fourier pseudo-spectral algorithms at the exascale using OpenMP offloading

Fourier pseudo-spectral methods for nonlinear partial differential equations are of wide interest in many areas of advanced computational science, including direct numerical simulation of three-dimensional (3-D) turbulence governed by the Navier-Stokes equations in fluid dynamics. This paper presents a new capability for simulating turbulence at a new record resolution up to 35 trillion grid points, on the world's first exascale computer, Frontier, comprising AMD MI250x GPUs with HPE's Slingshot interconnect and operated by the US Department of Energy's Oak Ridge Leadership Computing Facility (OLCF). Key programming strategies designed to take maximum advantage of the machine architecture involve performing almost all computations on the GPU which has the same memory capacity as the CPU, performing all-to-all communication among sets of parallel processes directly on the GPU, and targeting GPUs efficiently using OpenMP offloading for intensive number-crunching including 1-D Fast Fourier Transforms (FFT) performed using AMD ROCm library calls. With 99% of computing power on Frontier being on the GPU, leaving the CPU idle leads to a net performance gain via avoiding the overhead of data movement between host and device except when needed for some I/O purposes. Memory footprint including the size of communication buffers for MPI_ALLTOALL is managed carefully to maximize the largest problem size possible for a given node count. Detailed performance data including separate contributions from different categories of operations to the elapsed wall time per step are reported for five grid resolutions, from 2048 3 on a single node to 32768 3 on 4096 or 8192 nodes out of 9408 on the system. Both 1D and 2D domain decompositions which divide a 3D periodic domain into slabs and pencils respectively are implemented. The present code suite (labeled by the acronym GESTS, GPUs for Extreme Scale Turbulence Simulations) achieves a figure of merit (in grid points per second) exceeding goals set in the Center for Accelerated Application Readiness (CAAR) program for Frontier. The performance attained is highly favorable in both weak scaling and strong scaling, with notable departures only for 2048 3 where communication is entirely intra-node, and for 32768 3 , where a challenge due to small message sizes does arise. Communication performance is addressed further using a lightweight test code that performs all-to-all communication in a manner matching the full turbulence simulation code. Performance at large problem sizes is affected by both small message size due to high node counts as well as dragonfly network topology features on the machine, but is consistent with official expectations of sustained performance on Frontier. Overall, although not perfect, the scalability achieved at the extreme problem size of 32768 3 (and up to 8192 nodes — which corresponds to hardware rated at just under 1 exaflop/sec of theoretical peak computational performance) is arguably better than the scalability observed using prior state-of-the-art algorithms on Frontier's predecessor machine (Summit) at OLCF. New science results for the study of intermittency in turbulence enabled by this code and its extensions are to be reported separately in the near future.

3D fast Fourier transform↗
DOE OSTI2021

Core Analysis E-Reports Produced for the Southwest Regional Partnership on Carbon Sequestration for Wells 13-10A, 13-14, and 32-8 of the Farnsworth Unit, Texas

The submission is three electronic reports (e-reports) produced by Terra Tek, a former Schlumberger company, for and under the oversight of the Southwest Regional Partnership on Carbon Sequestration (SWP). The SWP designed and implemented a coring and core analysis program in conjunction with the previous field operator Chaparral Energy, L.L.C. The main SWP contacts who oversaw the coring and core analysis program, including geologic core descriptions and sample selection for testing by the Terra Tek, are listed below in the Authors section. The three reports are for Wells 13-10A, 13-14, and 32-8 of the Farnsworth Unit, TX, a site of the SWP's CO2 storage and enhanced oil recovery project. The e-reports include many data types that are not listed in full detail here, but may include: geomechanical, geochemical, and petrophysical measurements; white light and UV core photos; spectral gamma logs on the core; and Heterogeneous Rock Analysis logs. Fracture core review reports are included for Wells 13-14 and 32-8. The three e-reports each have many subfolders with the various types of data in spreadsheets, pdfs, image files, or other formats. The main e-reports for each well are listed by the well name. The sub-folder “E-Report” for each well has a Report.html file, which, when opened, will have hyperlinks to the various data sets and information. The files in the zipped folder will need to be extracted for the Report.html files to work properly. These authors thank Joseph Hall, a geologist formerly of Chaparral Energy, L.L.C., for assistance in designing the coring program, his geologic expertise of the Farnsworth Unit, and his assistance with characterizing the core. Christopher Gillespie, of Terra Tek at the time, managed the myriad geomechanical, geochemical, and petrophysical measurements provided by Terra Tek for this project. The core from which the samples were collected for this project are housed at the Subsurface Data and Core Libraries of the New Mexico Bureau of Geology and Mineral Resources, Socorro, New Mexico, USA. Funding for this project is provided by the U.S. Department of Energy's (DOE) National Energy Technology Laboratory (NETL) through the Southwest Regional Partnership on Carbon Sequestration (SWP) under Award No. DE-FC26-05NT42591. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525. These e-reports describe objective technical results and analysis. Any subjective views or opinions that might be expressed in the reports do not necessarily represent the views of the US Department of Energy or the United States Government.

Caprock↗
NASA NTRS2000

Infrastructure for Training and Partnershipes: California Water and Coastal Ocean Resources

The purpose of this project was to advance the existing ICESS/Bren School computing infrastructure to allow scientists, students, and research trainees the opportunity to interact with environmental data and simulations in near-real time. Improvements made with the funding from this project have helped to strengthen the research efforts within both units, fostered graduate research training, and helped fortify partnerships with government and industry. With this funding, we were able to expand our computational environment in which computer resources, software, and data sets are shared by ICESS/Bren School faculty researchers in all areas of Earth system science. All of the graduate and undergraduate students associated with the Donald Bren School of Environmental Science and Management and the Institute for Computational Earth System Science have benefited from the infrastructure upgrades accomplished by this project. Additionally, the upgrades fostered a significant number of research projects (attached is a list of the projects that benefited from the upgrades). As originally proposed, funding for this project provided the following infrastructure upgrades: 1) a modem file management system capable of interoperating UNIX and NT file systems that can scale to 6.7 TB, 2) a Qualstar 40-slot tape library with two AIT tape drives and Legato Networker backup/archive software, 3) previously unavailable import/export capability for data sets on Zip, Jaz, DAT, 8mm, CD, and DLT media in addition to a 622Mb/s Internet 2 connection, 4) network switches capable of 100 Mbps to 128 desktop workstations, 5) Portable Batch System (PBS) computational task scheduler, and vi) two Compaq/Digital Alpha XP1000 compute servers each with 1.5 GB of RAM along with an SGI Origin 2000 (purchased partially using funds from this project along with funding from various other sources) to be used for very large computations, as required for simulation of mesoscale meteorology or climate.

Siegel, David A.↗
NASA NTRS2022

VULCAN-CFD User Manual: Ver. 7.2.0

VULCAN-CFD offers a comprehensive set of capabilities to enable the simulation of continuum flowfields from subsonic to hypersonic conditions. The governing equations that are employed include allowances for both chemical and thermal nonequilibrium processes, coupled with a wide variety of turbulence models for both Reynolds-averaged and large eddy simulations. The software package can simulate two-dimensional, axisymmetric, or three-dimensional problems on structured multiblock meshes or fully unstructured meshes. A parabolic (i.e., space-marching) treatment can also be used for any subset of a structured mesh that can accommodate this solution strategy. The flow solver provides a significant level of geometric flexibility for structured grid simulations by allowing for arbitrary face-to-face C(0) continuous and non-C(0) continuous block interface connectivities. The unstructured grid paradigm allows for mixed element unstructured meshes that contain any combination of tetrahedral, prismatic, pyramidal, and hexahedral cell elements. The flow solver is also fully parallelized using MPI (Message Passing Interface) libraries in a data-parallel fashion, allowing for efficient simulations on modern High Performance Computing (HPC) systems. This document provides information related to the installation and execution of the VULCAN-CFD software package. A detailed description of the physical and numerical models available in the software are provided in the VULCAN-CFD Theory Manual.

VULCAN-CFD User Manual↗
DOE OSTI2022

Taylor wave solution for a general equation of state

This document describes a solution procedure for calculating the Taylor wave behind an unsupported Chapman–Jouguet (CJ) detonation in planar, cylindrical, and spherical geometries given a general equation of state. The resulting semi-analytic solution can be utilized to examine new equation of state models for detonation products and during the verification of hydrodynamic codes. The governing partial differential equations are reduced to ordinary differential equations in both characteristic and self-similar forms. The first-order systems corresponding to each geometry are amenable to solution numerically using commonly available methods. A difficulty arises at the CJ point in radial coordinates where the similarity equations become singular. Two separate strategies are proposed to integrate the first-order system. The first one uses an asymptotic approximation near the CJ point that can be used to perturb the boundary conditions. The second one applies a change of variables which removes the singularity at the expense of an additional equation to be integrated. A test problem is provided for the Davis products equation of state to illustrate the qualitative features of the Taylor wave in each geometric configuration and compared with a Lagrangian hydrodynamics research code. A Python code listing gives an implementation using the SciPy library to assists users in generating the results.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

hIPPYlib-MUQ: A Bayesian Inference Software Framework for Integration of Data with Complex Predictive Models under Uncertainty

Bayesian inference provides a systematic framework for integration of data with mathematical models to quantify the uncertainty in the solution of the inverse problem. However, the solution of Bayesian inverse problems governed by complex forward models described by partial differential equations (PDEs) remains prohibitive with black-box Markov chain Monte Carlo (MCMC) methods. We present hIPPYlib-MUQ, an extensible and scalable software framework that contains implementations of state-of-the art algorithms aimed to overcome the challenges of high-dimensional, PDE-constrained Bayesian inverse problems. These algorithms accelerate MCMC sampling by exploiting the geometry and intrinsic low-dimensionality of parameter space via derivative information and low rank approximation. The software integrates two complementary open-source software packages, hIPPYlib and MUQ. hIPPYlib solves PDE-constrained inverse problems using automatically-generated adjoint-based derivatives, but it lacks full Bayesian capabilities. MUQ provides a spectrum of powerful Bayesian inversion models and algorithms, but expects forward models to come equipped with gradients and Hessians to permit large-scale solution. By combining these two complementary libraries, we created a robust, scalable, and efficient software framework that realizes the benefits of each and allows us to tackle complex large-scale Bayesian inverse problems across a broad spectrum of scientific and engineering disciplines. To illustrate the capabilities of hIPPYlib-MUQ, we present a comparison of a number of MCMC methods available in the integrated software on several high-dimensional Bayesian inverse problems. These include problems characterized by both linear and nonlinear PDEs, various noise models, and different parameter dimensions. The results demonstrate that large (~ 50×) speedups over conventional black box and gradient-based MCMC algorithms can be obtained by exploiting Hessian information (from the log-posterior), underscoring the power of the integrated hIPPYlib-MUQ framework.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Innovating the next generation of commercial smart building software

Nearly 30% of commercial building energy use is wasted due to equipment faults and HVAC controls problems. The result is increased emissions, compromised comfort and productivity, and less reliable coordination of building power needs with a clean grid. The energy impact alone represents $17 billion in potential savings. Today’s smart building software provides a robust solution to address these operational deficiencies. Energy management and information systems (EMIS) are saving up to 9% on average, with two-year paybacks. They are being incorporated into energy management processes, commissioning services, and utility programs. As effective as they are, two barriers prevent even deeper benefits; limited personnel to fix problems once they are identified, and the expense and time to manually implement changes in control systems. In partnership with the research community, the EMIS industry is developing new capabilities to overcome these barriers. Moving beyond siloed products for either fault detection and diagnostics, or optimal control, these new capabilities empower users to not only automatically identify faults, but also to push corrective action, and control improvements to their buildings. In this paper, several areas for enhancements are documented: ‘one-time’ correction of faults such as setpoints, schedules, and economizer lockouts; short-term active testing for automated proportional integral derivative (PID) loop tuning and functional testing; and continuous supervisory control for demand flexibility and year-round efficiency. Results are presented from a pair of partner implementations out of a dozen providers integrating these enhancements into their products, including field tests from across the country, and insights into operator acceptance and integration into operations and maintenance practices.

Casillas, Armando↗
NASA NTRS2004

U.S. Centennial of Flight Commision: Born of Dreams - Inspired by Freedom

The U.S. Centennial of Flight Commission developed and maintained a public web site that included activities related to the centennial of flight celebration and the history of aviation. The web site, www.centennialofflight.gov, was continually updated with educational and historical information, events, sights and sounds, and Commission information from its inception to June 2004. This DVD contains a 'snap shot' of the web site as of April 2004. The Web site on this DVD can be enjoyed without an Internet connection although in some places, you will be given links to online content. DVD content includes: 1) About the Commission - Information on the legislation, the Commissioners and Advisory Board members, news, the National Plans, meeting minutes and status reports; 2) Calendar of Events - A comprehensive list of activities, symposiums, exhibits, air shows, educational activities and more that took place through March 2004; 3) Wright Brothers History - The Library of Congress bibliography of Wright-related resources as well as the Chronology and Flight Log; the Brunsman articles; interactive learning modules from The Wright Experience; short informative essays and a series of links to other Wright brothers information sources. 4) History of Flight - Essays and images on the history of flight; 5) Sights and Sounds - Images, movies and special collections that capture the accomplishments of the Wright brothers and others who made significant contributions throughout the history of aviation and aerospace. As part of the NASA Art Program, a centennial song, 'Way Up There,' was commissioned; 6) Licensed Products - View collections of souvenirs and gift items to commemorate the 100th anniversary of the first powered flight; 7) Education - Resources that will help educators and their students celebrate 100 years of flight. Teachers can download Wright brothers posters and a Centennial of Flight bookmark, view live Web casts, and access an Educational Resources Center Matrix representing more than 50 government, industry and labor organizations promoting aviation and aerospace education.

Source record↗
DOE OSTI2026

Two-Level Sketching Alternating Anderson Acceleration for Complex Physics Applications

We present a novel two-level sketching extension of the Alternating Anderson–Picard (AAP) method for accelerating fixed-point iterations in challenging single- and multiphysics simulations governed by discretized PDEs. Our approach combines a static, physics-based projection that reduces the least-squares (LS) problem to the most informative field (e.g., via Schur-complement insight) with a dynamic, algebraic sketching stage driven by a backward stability analysis under Lipschitz continuity. We introduce inexpensive estimators for stability thresholds and cache-aware randomized selection strategies to balance computational cost against memory access overhead. The resulting algorithm solves reduced LS systems in place, minimizes memory footprints, and seamlessly alternates between low-cost Picard updates and Anderson mixing. Implemented in Julia, our two-level sketching AAP achieves up to 50% time-to-solution reductions compared to standard Anderson acceleration—without degrading convergence rates—on benchmark problems including Stokes, 𝑝-Laplacian, bidomain, and Navier–Stokes formulations at varying problem sizes. These results demonstrate the method’s robustness, scalability, and potential for integration into high-performance scientific computing frameworks. Our implementation is available open source in the AAP.jl library.

Barnafi, Nicolas [University of Chile, Santiago]↗
NASA NTRS2021

BUMPER: A Tool for Analyzing Spacecraft Micrometeoroid and Orbital Debris Risk

“Bumper” is a computer program for analyzing spacecraft micrometeoroid and orbital debris (MMOD) risk. Bumper was developed in the late-1980s and has been continuously maintained and used since. The user base has grown from a few government entities now include numerous commercial entities as well. The National Aeronautics and Space Administration (NASA) Johnson Space Center (JSC) Hypervelocity Impact Technology (HVIT) group is responsible for all aspects of the Bumper software. Bumper has been used to characterize MMOD risk on many spacecraft. All of the International Space Station (ISS) modules, visiting vehicles and numerous external components and systems have been analyzed. Bumper was used to analyze the Space Shuttle, Orion, and many space probes, telescopes and satellites. Bumper is also being used to analyze future spacecraft such as the Deep Space Gateway (DSG) and Mars Sample Return (MSR) missions. The Bumper Configuration Control Board (CCB) ensures that all changes to the code are approved, reviewed, and documented. The current Bumper version – “Bumper 3” – is a Fortran executable that utilizes a 64-bit architecture. Bumper has numerous features that make it a powerful tool for analyzing spacecraft MMOD risk. Bumper uses the latest orbital debris and meteoroidenvironment models. Bumper also has a large library of ballistic limit “damage” equations available that can be used for a wide variety of MMOD shielding configurations. Bumper can also handle large spacecraft finite elementmodels (FEMs) and conducts checks of the model. This paper introduces Bumper and the MMOD risk analysis process using a simplified cube-shaped spacecraft model

hypervelocity↗
DOE OSTI2026

Single-Molecule Electron Transport in Peptoids

Peptoids are structural analogs of peptides in which side chains are appended to the backbone nitrogen rather than the α-carbon. The sequence-defined modularity of peptoids enables precise control over structure−function relationships, enabling applications in energy storage and biomedical materials. Despite recent progress, the role of sequence and conformation on electron transport in peptoid molecules is not fully understood. Here, we synthesize a library of peptoid oligomers and characterize their molecular electronic properties using the scanning tunneling microscope-break junction (STM-BJ) technique. Our results show well-defined electron transport behavior for peptoid sequences containing aromatic side groups lacking hydrogen bonds (H-bonds) and without chemical substitutions at the N−C α position. This behavior fundamentally differs from electron transport in peptides, where H-bond interactions give rise to higher conductance states. All-atom molecular dynamics (MD) simulations are used to understand the conformational heterogeneity of peptoids, and molecular conformations obtained from MD simulations are used in quantum mechanical calculations based on the nonequilibrium Green’s function−density functional theory (NEGF-DFT) formalism. In all cases, computational results are in reasonable qualitative agreement with experiments. Our work demonstrates that the conductance behavior of peptoids depends on monomer identity, including side-chain aromaticity and substitution at the N−C α position. Overall, this work provides new insights into the structure−function relationships governing electron transport in peptoid-based materials and establishes design rules for peptoid-based molecular junctions.

Charge transport↗
DOE OSTI2021

Zinc binding alters the conformational dynamics and drives the transport cycle of the cation diffusion facilitator YiiP

YiiP is a secondary transporter that couples Zn 2+ transport to the proton motive force. Structural studies of YiiP from prokaryotes and Znt8 from humans have revealed three different Zn 2+ sites and a conserved homodimeric architecture. These structures define the inward-facing and outward-facing states that characterize the archetypal alternating access mechanism of transport. To study the effects of Zn 2+ binding on the conformational transition, we use cryo-EM together with molecular dynamics simulation to compare structures of YiiP from Shewanella oneidensis in the presence and absence of Zn 2+ . To enable single-particle cryo-EM, we used a phage-display library to develop a Fab antibody fragment with high affinity for YiiP, thus producing a YiiP/Fab complex. To perform MD simulations, we developed a nonbonded dummy model for Zn 2+ and validated its performance with known Zn 2+ -binding proteins. Using these tools, we find that, in the presence of Zn 2+ , YiiP adopts an inward-facing conformation consistent with that previously seen in tubular crystals. After removal of Zn 2+ with high-affinity chelators, YiiP exhibits enhanced flexibility and adopts a novel conformation that appears to be intermediate between inward-facing and outward-facing states. This conformation involves closure of a hydrophobic gate that has been postulated to control access to the primary transport site. Comparison of several independent cryo-EM maps suggests that the transition from the inward-facing state is controlled by occupancy of a secondary Zn 2+ site at the cytoplasmic membrane interface. This work enhances our understanding of individual Zn 2+ binding sites and their role in the conformational dynamics that govern the transport cycle.

59 BASIC BIOLOGICAL SCIENCES↗