Sialic acid identity modulates host tropism of sialoglycan-binding viridans group streptococci
Not provided.
Biochemistry & Molecular Biology↗
Engineering topics
Smith, Jeremy
Publications and source records attributed to Smith, Jeremy.
A Method to estimate the economy-wide consequences of widespread, long duration electric power interruptions
Not provided.
Science & Technology - Other Topics↗
Cyber-Informed Engineering Validation Methods and Guidance
Validation is an important step in any systems engineering process to ensure the correct system was made to fulfill stakeholders’ needs, goals, and expectations. In the context of Cyber-Informed Engineering (CIE), validation ensures cyber impact is reduced through implemented design choices and CIE requirements. This document details a process in validating CIE-based design choices relative to their effectiveness at mitigating high consequence events. The document includes a case study to illustrate the CIE validation process. The case study explores the implementation of CIE validation within the engineering lifecycle of a chemical mixing plant.
42 ENGINEERING↗
Integrating Cyber-Informed Engineering into Enterprise Risk Management
This document supports the application of Cyber-Informed Engineering (CIE) within the context of Enterprise Risk Management (ERM) to enhance cyber-resilience. It highlights that many critical infrastructure organizations use ERM to manage business risks and emphasizes the importance of evaluating critical systems and assets. The proposed approach can be adopted independently of formal ERM processes and offers a starting point for integrating CIE alongside existing or new ERM practices. Both CIE and ERM are iterative, and their alignment fosters continuous improvement and supports the engineering and operations cultures of an organization.
42 ENGINEERING↗
Oak Ridge National Laboratory's Strategic Research and Development Insights for Digital Twins
Oak Ridge National Laboratory (ORNL) is pleased to provide our response to the NITRD RFI on Digital Twins Research and Development. Digital twins are virtual representations of physical systems, leveraging real-time data to simulate and predict behaviors. ORNL is advancing digital twin technology across various disciplines, including neutron scattering, networking, science ecosystems, supercomputing, secure facilities, mobility technologies, materials design and discovery, power systems, fusion reactors, biological sciences, and earth observation. These efforts aim to enhance scientific research, operational efficiency, and decision-making processes. ORNL facilities, such as the High Flux Isotope Reactor (HFIR), Grid-C, Spallation Neutron Source (SNS), and Oak Ridge Leadership Computing Facility (OLCF), provide the infrastructure to develop and demonstrate these digital twin technologies. In this document, we lay out key challenges, research gaps, and future opportunities based on our experience with digital twins that aim to serve as useful contributions towards a National Digital Twins R&D Strategic Plan. In the remaining document, we address nine of the thirteen topic areas specified in the RFI.
97 MATHEMATICS AND COMPUTING↗
TReactMech v4.217
TReactMech couples geomechanical processes (poroelasticity, failure, and inelastic strain) with multiphase nonisothermal flow (derived from TOUGH2) and reactive geochemical transport. At its core is the reactive-transport code TOUGHREACT v4.13. TReactMech is an efficient hybrid parallel simulator, solving the geomechanics using finite elements and MPI/PetSc, the multiphase flow using integrated finite difference and MPI/PETSc, and the reactive chemistry using OpenMP. The advantages of TReactMech are in its multiphase flow capabilities (e.g., supercritical CO2, supercritical water, air) and parallel geomechanics including full 3-D stress tensor, shear and tensile failure, coupled to porosity and permeability changes. It is backwardly compatible with TOUGH2 and TOUGHREACT v4.13, allowing for easier transitions between the codes. TReactMech can be used to simulate many natural and engineered subsurface systems, including geothermal reservoirs, borehole heat exchangers, geologic carbon sequestration, geologic storage of nuclear waste, groundwater resources, weathering, sediment diagenesis, seafloor hydrothermal circulation, hydrofracturing in unconventional reservoirs, and injection/production-induced surface deformation.
Sonnenthal, Eric↗
Cyber-Informed Engineering Implementation Guide: Version 1.0 [Slides]
This Implementation Guide describes the principles of Cyber-Informed Engineering (CIE) and outlines questions that engineering teams should consider during each phase of a system's lifecycle to effectively employ these principles. It describes what it means to engineer systems in a cyber-informed way, rather than offering a comprehensive, step-by-step process or procedure for CIE implementation. This guide complements - but does not replace - the application of cybersecurity standards or practices currently in place within an organization. Engineers and technicians that design critical energy infrastructure installations can use this Implementation Guide to integrate the 12 principles of CIE into each phase of the engineering lifecycle, from concept to retirement. The guide is aimed at system or design engineers, rather than software engineers or operational cybersecurity practitioners. The engineers who design, build, operate, and maintain the physical infrastructure are best positioned to leverage a system's engineering design to diminish the severity of cyber attacks or digital technology failures. CIE expands cybersecurity decisions into the engineering space, not by asking engineers to become cyber experts, but by calling on engineers to apply engineering tools and make engineering decisions that improve cybersecurity outcomes. CIE examines the engineering consequences that a sophisticated cyber attacker could achieve and drives engineering changes that may provide deterministic mitigations to limit or eliminate those consequences.
24 POWER TRANSMISSION AND DISTRIBUTION↗
Modeling the partitioning of amphiphilic molecules and co-solvents in biomembranes
We report amphiphilic co-solvents can have a significant impact on the structure, organization and physical properties of lipid bilayers. Describing the mutual impact of partitioning and induced structure changes is therefore a crucial consideration for a range of topics such as anesthesia and other pharmacokinetic effects, as well as microbial solvent tolerance in the production of biofuels and other fermentation products, where molecules such as ethanol, butanol or acetic acid might be generated. Small-angle neutron scattering (SANS) is a key method for studying lipid and polymer bilayer structures, with many models for extracting bilayer structure (thickness, area per lipid etc.) from scattering data in use today. However, the molecular details of co-solvent partitioning are conflated with induced changes to bilayer structure, making interpretation and modeling of the scattering curves a challenge with the existing set of models. To address this, a model of a bilayer structure is presented which invokes a two-term partition constant accounting for the localization of the co-solvent within the bilayer. This model was validated using a series of SANS measurements of lipid vesicles in the presence of the co-solvent tetrahydrofuran (THF), showing several strategies of how to deploy the two-parameter partition constant model to describe scattering data and extract both structure and partitioning information from the data. Molecular dynamics simulations are then used to evaluate assumptions of the model, provide additional molecular scale details and illustrate its complementary nature to the data fitting procedure. This approach results in estimates of the partition coefficient for THF in 1,2-dimyristoyl-sn-glycero-3-phosphocholine at 35°C, along with an estimate of the fraction of THF residing in the hydrophobic core of the membrane. The authors envision that this model will be applicable to a wide range of other bilayer/amphiphile interactions and provide the associated code needed to implement this model as a fitting algorithm for scattering data in the SasView suite.
59 BASIC BIOLOGICAL SCIENCES↗
Hit Expansion of a Noncovalent SARS-CoV-2 Main Protease Inhibitor
Inhibition of the SARS-CoV-2 main protease (M pro ) is a major focus of drug discovery efforts against COVID-19. Here we report a hit expansion of non-covalent inhibitors of M pro . Starting from a recently discovered scaffold (The COVID Moonshot Consortium. Open Science Discovery of Oral Non-Covalent SARS-CoV-2 Main Protease Inhibitor Therapeutics. bioRxiv 2020.10.29.339317) represented by an isoquinoline series, we searched a database of over a billion compounds using a cheminformatics molecular fingerprinting approach. We identified and tested 48 compounds in enzyme inhibition assays, of which 21 exhibited inhibitory activity above 50% at 20 μM. Among these, four compounds with IC 50 values around 1 μM were found. Interestingly, despite the large search space, the isoquinolone motif was conserved in each of these four strongest binders. Room-temperature X-ray structures of co-crystallized protein–inhibitor complexes were determined up to 1.9 Å resolution for two of these compounds as well as one of the stronger inhibitors in the original isoquinoline series, revealing essential interactions with the binding site and water molecules. Molecular dynamics simulations and quantum chemical calculations further elucidate the binding interactions as well as electrostatic effects on ligand binding. The results help explain the strength of this new non-covalent scaffold for M pro inhibition and inform lead optimization efforts for this series, while demonstrating the effectiveness of a high-throughput computational approach to expanding a pharmacophore library.
60 APPLIED LIFE SCIENCES↗
Microbial Membranes: A Challenge for Bioenergy
The production of bioenergy and bioproducts from lignocellulosic biomass promises to contribute significantly to the establishment of a clean, green economy. However, obstacles remain to making this industry economically viable. Among these is achieving high production rates and titers of target molecules through fermentation: microorganisms used in bioprocesses are inhibited by the toxic effects of biomass pretreatment and biofuel solvents which degrade the overall function of biological membranes. Here, we review historical research on the structure of the plasma membrane before detailing some progress on understanding the effects of amphiphilic solvents relevant to biofuel production on microbial membranes at the nanoscale.
09 BIOMASS FUELS↗
SARS-CoV2 Docking Dataset
Description: Small-molecule conformations and docking scores for 1.4 billion molecules docked against 6 protein targets from SARS-CoV2: MPro 5R84, MPro 6WQF, NSP15 6WLC, PLPro 7JIR, Spike 6M0J, and a hand-optimized model of the RNA-dependent RNA polymerase. Docking was carried out using the Autodock-GPU program performing 20 independent structure minimizations per dock - saving 3 results per molecule. Scores reported include the Autodock free energy estimate as well as RF3 and VS-DUD-E v2 machine-learned rescoring models. Protein structure files and maps in the format input to Autodock-GPU are included. Literature Ref: Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19, J. Chem. Inf. Model. 2020, 60(12): 5832–5852.
36 MATERIALS SCIENCE↗
GPU-Accelerated Drug Discovery with Docking on the Summit Supercomputer: Porting, Optimization, and Application to COVID-19 Research
Protein-ligand docking is an in silico tool used to screen potential drug compounds for their ability to bind to a given protein receptor within a drug-discovery campaign. Experimental drug screening is expensive and time consuming, and it is desirable to carry out large scale docking calculations in a high-throughput manner to narrow the experimental search space. Few of the existing computational docking tools were designed with high performance computing in mind. Therefore, optimizations to maximize use of high-performance computational resources available at leadership-class computing facilities enables these facilities to be leveraged for drug discovery. Here we present the porting, optimization, and validation of the AutoDock-GPU program for the Summit supercomputer, and its application to initial compound screening efforts to target proteins of the SARS-CoV-2 virus responsible for the current COVID-19 pandemic.
LeGrand, Scott↗
Porting Adaptive Ensemble Molecular Dynamics Workflows to the Summit Supercomputer
Molecular dynamics (MD) simulations must take very small (femtosecond) integration steps in simulation-time to avoid numerical errors. Efficient use of parallel programming models and accelerators in state-of-the art MD programs now is pushing Moore’s limit for time-per-MD step. As a result, directly simulating timescales beyond milliseconds will not be attainable directly, even at exascale. However, concepts from statistical physics can be used to combine many parallel simulations to provide information about longer timescales and to adequately sample the simulation space, while preserving details about the dynamics of the system. Implementing such an approach requires a workflow program that allows adaptable steering of task assignments based on extensive statistical analysis of intermediate results. Here we report the implementation of such an adaptable workflow program to drive simulations on the Summit IBM Power System AC922, a pre-exascale supercomputer at the Oak Ridge Leadership Computing Facility (OLCF). We compare to experiences on Titan, Summit’s predecessor, report the performance of the workflow and its components, and describe the porting process. We find that using a workflow program managed by a Mongo database can provide the fault tolerance, scalable performance, task dispatch rate, and reconfigurability required for robust and portable implementation of ensemble simulations such as are used in enhanced-sampling molecular dynamics. This type of workflow generator can also be used to provide adaptive steering of ensemble simulations for other applications in addition to MD.
Ossyra, John R.↗
Highly interactive, steered scientific workflows on HPC systems: optimizing design solutions
Scientific workflows are becoming increasingly important in high performance computing (HPC) settings, as the feasibility and appeal of many simultaneous heterogeneous tasks increases with increasing hardware capabilities. Currently no HPC-based workflow platform supports a dynamically adaptable workflow with interactive steering and analysis at run-time. Furthermore, for most workflow programs, compute resources are fixed for a given instance, resulting in a possible waste of expensive allocation resources when tasks are spawned and killed. Here we describe the design and testing of a run-time-interactive, adaptable, steered workflow tool capable of executing thousands of parallel tasks without an MPI programming model, using a database management system to facilitate task management through multiple live connections. We find that on the Oak Ridge Leadership Computing Facility pre-exascale Summit supercomputer it is possible to launch and interactively steer workflows with thousands of simultaneous tasks with negligible latency. For the case of particle simulation and analysis tasks that run for minutes to hours, this paradigm offers the prospect of a robust and efficient means to perform simulation-space exploration with on-the-fly analysis and adaptation.
Ossyra, John R↗
Quantum Mechanical/Molecular Mechanical Analysis of the Catalytic Mechanism of Phosphoserine Phosphatase
Phosphoserine phosphatase (PSP), a member of the haloacid dehalogenase (HAD) superfamily that comprises the vast majority of phosphotransferases, is likely a steady-state regulator of the level of d-serine in the brain. The introduced catalytic cycle of PSP consists of a two-step mechanism: formation of a phospho-enzyme intermediate by phosphate transfer to Asp11 and its subsequent hydrolysis. Our combined quantum mechanical/molecular mechanical (QM/MM) calculations of the reaction pathways favour a dissociative mechanism of nucleophilic substitution via a trigonal-planar metaphosphate-like configuration for both steps, associated with proton transfer to the leaving group or from the nucleophile. This proton transfer is facilitated by active site residue Asp13 that acts as both a general base and a general acid. Free energy calculation on the reaction pathways further support the structural role of the enzymatic environment and the active site architecture. The choice of a proper reaction coordinate along which to bias the free energy calculations can be guided by a projection of the canonical reaction coordinate obtained from a chain-of-state optimisation onto important internal coordinates.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Molecular Communication over Gas Stream Channels using Portable Mass Spectrometry
The synthetic generation/coding and transmission of olfactory information over a gas stream or an odor network is a new and unexplored field. Application areas vary from the entertainment or advertisement industry to security and telemedicine. However, current technological limitations frustrate the accurate reproduction of decoded and transmitted olfactory data. This study describes the development, testing, and characterization of a novel odor emitter (OE) that is used to investigate the generation-encoding of gaseous standards with odorous characteristics with a regulatable way, for scent transmission purposes. The calibration and the responses of a developed OE were examined using a portable quadrupole mass spectrometer (MS). Experiments were undertaken for a range of volatile organic compounds (VOCs) at different temperatures and flow rates. Individual compounds and mixtures were tested to investigate periodic and dynamic transmission characteristics within two different size tubular containers for distances up to 3 m. Olfactory information transmission is demonstrated using MS as the main molecular sensor for odor detection and monitoring and for the first time spatial encryption of olfactory information is shown. .
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
Systematic evaluation of structure–property relationships in heteroacene – diketopyrrolopyrrole molecular donors for organic solar cells
Improved understanding of fundamental structure–property relationships, particularly the effects of molecular shape and intermolecular packing on film morphology and active layer charge transport characteristics, enables more rational synthesis of new p-type small molecules. Here we investigate a series of small molecules consisting of an acene-based electron-rich core flanked by one or two electron-deficient diketopyrrolopyrrole (DPP) moieties. Through minor changes in the molecule structures, measurable variations in the crystal structure and sizable differences in macroscopic properties are achieved. The molecular symmetry as well as the conformation of the side chains affects the unit cell packing density and strength of the intermolecular electronic coupling in single crystals of all molecules in this series. Here, the addition of a second DPP unit to the benzodithiophene (BDT) core increases molecular planarity leading to decreased reorganization energy, strong cofacial coupling, and moderate hole mobility (2.7 × 10 –4 cm 2 V –1 s –1 ). Increasing the length of the acene core from benzodithiophene to naphthodithiophene (NDT) results in a further reduction in reorganization energy and formation of smaller crystalline domains (~11 nm) when mixed with PCBM. Decreasing the aspect ratio of the core using a “zig-zag” naphthodithiophene (zNDT) isomer results in the highest hole mobility of 1.3 × 10 –3 cm 2 V –1 s –1 due in part to tight lamellar (d = 13.5 Å) and π–π stacking (d = 3.9 Å). The hole mobility is directly correlated with the short-circuit current (11.7 mA cm –2 ) and solar cell efficiency (4.4%) of the highest performing zNDT:PCBM device. For each of these small molecules the calculated π-coupling constant is correlated with the hole mobility as a function of crystal structure and orientation indicating the importance of designing molecules that create extended crystalline networks with maximal π-orbital overlap.
36 MATERIALS SCIENCE↗
Buta-1,3-diyne-Based π-Conjugated Polymers for Organic Transistors and Solar Cells
We report the synthesis and characterization of new alkyl-substituted 1,4-di(thiophen-2-yl)buta-1,3-diyne (R-DTB) donor building blocks, based on the -C≡C-C≡C- conjugative pathway, and their incorporation with thienyl-diketopyrrolopyrrole (R'-TDPP) acceptor units into π-conjugated PTDPP-DTB polymers (P1-P4). The solubility of the new polymers strongly depends on the DTB and DPP solubilizing (R and R', respectively) substituents. Thus, solution processable and high molecular weight PDPP-DTB polymers are achieved for P3 (R = n-C12H25, R' = 2- butyloctyl) and P4 (R = 2-ethylhexyl, R' = 2-butyloctyl). Systematic studies of P3 and P4 physicochemical properties are carried using optical spectroscopy, cyclic voltammetry, and thermal analysis, revealing characteristic features of the dialkynyl motif. For the first time, optoelectronic devices (OFETs, OPVs) are fabricated with 1,3-butadiyne containing organic semiconductors. OFET hole mobilities and record OPV power conversion efficiencies for acetylenic organic materials approach 0.1 cm2/(V s) and 4%, respectively, which can be understood from detailed thin-film morphology and microstructural characterization using AFM, TEM, XRD, and GIWAXS methodologies. Importantly, DTB-based polymers (P3 and P4) exhibit, in addition to stabilization of frontier molecular orbitals and to -C≡C-C≡C- relief of steric torsions, discrete morphological pliability through thermal annealing and processing additives. The advantageous materials properties and preliminary device performance reported here demonstrate the promise of 1,3-butadiyne-based semiconducting polymers.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗