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Foldy: An open-source web application for interactive protein structure analysis
Foldy is a cloud-based application that allows non-computational biologists to easily utilize advanced AI-based structural biology tools, including AlphaFold and DiffDock. With many deployment options, it can be employed by individuals, labs, universities, and companies in the cloud without requiring hardware resources, but it can also be configured to utilize locally available computers. Foldy enables scientists to predict the structure of proteins and complexes up to 6000 amino acids with AlphaFold, visualize Pfam annotations, and dock ligands with AutoDock Vina and DiffDock. In our manuscript, we detail Foldy’s interface design, deployment strategies, and optimization for various user scenarios. We demonstrate its application through case studies including rational enzyme design and analyzing proteins with domains of unknown function. Furthermore, we compare Foldy’s interface and management capabilities with other open and closed source tools in the field, illustrating its practicality in managing complex data and computation tasks. Our manuscript underlines the benefits of Foldy as a day-to-day tool for life science researchers, and shows how Foldy can make modern tools more accessible and efficient.
Collaborative Computing Support for Analysis Facilities Exploiting Software as Infrastructure Techniques
Prior to the public release of Kubernetes it was difficult to conduct joint development of elaborate analysis facilities due to the highly non-homogeneous nature of hardware and network topology across compute facilities. However, since the advent of systems like Kubernetes and OpenShift, which provide declarative interfaces for building fault-tolerant and self-healing deployments of networked software, it is possible for multiple institutes to collaborate more effectively since resource details are abstracted away through various forms of hardware and software virtualization. In this whitepaper we will outline the development of two analysis facilities: "Coffea-casa" at University of Nebraska Lincoln and the "Elastic Analysis Facility" at Fermilab, and how utilizing platform abstraction has improved the development of common software for each of these facilities, and future development plans made possible by this methodology.
The Portals 4.0.2 Networking Programming Interface
This report presents a specification for the Portals 4 network programming interface. Portals 4 is intended to allow scalable, high-performance network communication between nodes of a parallel computing system. Portals 4 is well suited to massively parallel processing and embedded systems. Portals 4 represents an adaption of the data movement layer developed for massively parallel processing platforms, such as the 4500-node Intel TeraFLOPS machine. Sandia's Cplant cluster project motivated the development of Version 3.0, which was later extended to Version 3.3 as part of the Cray Red Storm machine and XT line. Version 4 is targeted to the next generation of machines employing advanced network interface architectures that support enhanced offload capabilities.
The Portals 4.3 Network Programming Interface
This report presents a specification for the Portals 4 network programming interface. Portals 4 is intended to allow scalable, high-performance network communication between nodes of a parallel computing system. Portals 4 is well suited to massively parallel processing and embedded systems. Portals 4 represents an adaption of the data movement layer developed for massively parallel processing platforms, such as the 4500-node Intel TeraFLOPS machine. Sandia's Cplant cluster project motivated the development of Version 3.0, which was later extended to Version 3.3 as part of the Cray Red Storm machine and XT line. Version 4 is targeted to the next generation of machines employing advanced network interface architectures that support enhanced offload capabilities.
CFD Evaluation of Pressure Change Along Coolant Passages in Sodium-Cooled Fast Reactor with Nek5000
To support the design efforts of advanced sodium-cooled fast reactors (SFRs), a series of computational fluid dynamics (CFD) simulations are performed to investigate the pressure change along various flow passages in the proposed SFR system. The simulations are carried out with the state-of-the-art spectral element flow solver, Nek5000. Two specific case studies are presented in this paper: the flow exiting the axial neutron reflector channels and the flow entering the fuel pin bundle. Due to the high Reynolds numbers expected, a Reynolds-averaged Navier-Stokes (RANS) approach is necessary to model the turbulence. A newly developed regularized k-omega RANS model is adopted in the related CFD calculations. The first case study explores the effect of Reynolds number on the pressure change when flow exits the reflector channels. The pressure change in this case has two major contributors: the change due to wall friction and the Bernoulli effect. It is noted that the nondimensional pressure loss follows a log-linear trend up to Re = 10 5 , and then the trend is flattened. In the second case study, the advanced NekNek coupling capability is tested where an integral domain can be divided into multiple subdomains with coupling interfaces, which would greatly ease the meshing process of complex engineering geometries and potentially save computational resources. The preliminary results obtained so far confirm the consistency between the NekNek results and those produced by regular Nek5000 simulation. The presented work demonstrates the readiness and flexibility of the related CFD techniques, which is part of the broader effort to leverage cutting-edge CFD to inform the advanced nuclear reactor designs.
Flexible and Modular Simultaneous Modeling of Flow and Reactive Transport in Rivers and Hyporheic Zones
Investigations of coupled multiphysics processes in rivers and hyporheic zones have extensively used numerical models. Most existing models use a sequential, one-way coupling between the surface and subsurface domains. Such one-way coupling potentially introduces error. To overcome this, a fully coupled model, hyporheicFoam, was developed using the open-source computational platform OpenFOAM. It captures the coupled flow and multicomponent reactive transport processes within both surface and subsurface domains and across their interface. The coupling between two domains is implemented by mapping conservative flux boundary conditions at the interface through an iterative algorithm. Reactive transport is enabled by specifying a reaction network. To start, we have implemented reaction kinetics following the double Monod-type model with inhibition. The model capability is illustrated through modeling of both conservative and reactive hyporheic flow and transport through dune bedforms. With the novel coupled model, it is now possible to quantify reactions wherein the reactants and products are constantly exchanging between domains and have feedbacks. hyporheicFoam can simulate large, three-dimensional cases owing to the computational flexibility and power offered by the code structure and parallel design of OpenFOAM.
Intermetallic phase formation in Al-Si-Zr alloys during hot isostatic pressing revealed by experiments and molecular dynamics
Understanding phase transformations at alloy interfaces is critical for the design of advanced structural materials. Here, in this study, we investigate the formation mechanisms of the Al 2 SiZr intermetallic phase in the Al-Si-Zr system under hot isostatic pressing (HIP) using molecular dynamics (MD) simulations and thermodynamic analysis. A unique aspect of our approach in MD involves the replacement of a disordered Al 2 SiZr stoichiometry with an ordered phase at the Al-Zr interface once HIP results in the desired Al 2 SiZr stoichiometry, allowing us to compute the total energetic cost of transformation by accounting for both formation energies and diffusion barriers. Diffusion coefficients and activation energies, extracted across a range of temperatures, reveal that HIP substantially enhances atomic mobility, creating favorable stoichiometry for phase evolution. Our results show that Al 2 SiZr phase formation is kinetically unfavorable at lower temperatures but becomes feasible when the thermodynamic driving energy surpass a critical energy threshold.
First-Principles Approach for Assessing Cold Electron Injection Efficiency of Dye-Sensitized Solar Cell: Elucidation of Mechanism of Charge Injection and Recombination
The adequacy of the inclusion of spacer units in the metal-free D-π–A organic dyes pertaining to the augmentation of dye-sensitized solar cell (DSSC) efficiency has been examined through the excited-state simulations of the charge injection and recombination processes at the dye–semiconductor interface. Within the framework of the time-dependent density functional theory, the proposed computational studies focus on the precise evaluation of pivotal factors controlling the rates of photoinduced charge-transfer and energy-transfer processes, including electronic coupling, reorganization energy, and threshold energy barrier in the semiclassical Marcus formalism. The estimation of the fluorescent state appears to be the crucial step while explaining the ultrafast electron injection process and the charge recombination at the Marcus inverted region, as revealed by the obtained results. The retardation of charge recombination is facilitated by the insertion of a thiophene moiety between the π-bridge and the acceptor units. The estimated cold electron injection efficiencies deploying the Onsager–Braun theory, that rely on the computations of cold electron injection lifetime and cold electron lifetime, show a linear correlation with the experimental photovoltaic parameters of the DSSC comprising short-circuit current density, open-circuit voltage, and power conversion efficiency. The outcomes of the present investigation establish a basis for unraveling the mechanism of intricate dynamical processes upon photoexcitation of the sensitizers, as well as devising plausible routes for functional DSSC materials.
Curvature Memory in Electrically Stimulated Lipid Membranes
Here, we demonstrate, using non-equilibrium molecular dynamics simulations, that lipid membrane capacitance varies with surface charge accumulation linked to membrane shape and curvature changes. Specifically, we show that lipid membranes exhibit a hysteretic response when exposed to oscillatory electric fields. The electromechanical coupling in these membranes leads to hysteretic buckling, in which the membrane can spontaneously buckle in one of two distinct directions along the electric field, even for the same ionic charge accumulation at the water–membrane interface. In this regard, these binary buckled membrane states suggest potential applications in neuromorphic computing. Their bistable nature, characterized by two distinct and stable configurations, could serve as a foundation for implementing memory storage systems and logic operations. Furthermore, we introduce a circuit model that captures these dynamic effects, offering insights into emergent memory effects in electrically stimulated lipid membranes. Finally, this work presents lipid bilayers as dynamic, adaptable elements and suggests a new platform for exploring energy storage, information processing, and memory encoding at the lipid membrane level.
Continuum model for hydrogen pickup in zirconium alloys of LWR fuel cladding
A continuum model for calculating the time-dependent hydrogen pickup fractions in various Zirconium alloys under steam and pressured water oxidation has been developed in this paper. Using only one fitting parameter, the effective hydrogen gas partial pressure at the oxide surface, a qualitative agreement is obtained between the predicted and previously measured hydrogen pickup fractions. The calculation results therefore demonstrate that H diffusion through the dense oxide layer plays an important role in the hydrogen pickup process. Finally, the limitations and possible improvement of the model are also discussed.
An open source analysis framework for large-scale building energy modeling
Full integration of building energy modelling into the design and retrofit process has long been a goal of building scientists and practitioners. However, significant barriers still exist. Among them are the lack of available: (1) configurable technology stacks for performing both small- and large-scale analyses, (2) different classes of algorithms compatible with common design workflows, and (3) analysis tools for effectively visualizing large-scale simulation results. This article discusses the OpenStudio® Analysis Framework: a scalable analysis framework for building energy modelling that was developed to overcome the three barriers listed above. The framework is open-source and scalable to facilitate wider adoption and has a clearly defined application programming interface upon which other applications can be built. It runs on high-performance computing systems, within cloud infrastructure, and on laptops, and uses a common workflow to enable different classes of algorithms. Lessons learned from previous development efforts are also discussed.
Neutron-Friendly Li-Ion Battery Coin Cell for In Situ 3D Visualization of Li Plating
Advanced battery characterization using in situ/operando neutron imaging is critical for uncovering degradation modes such as lithium (Li) plating in Li-ion batteries (LIBs). However, conventional LIBs hinder operando neutron radiography (NR) and in situ neutron micro-computed tomography (N-μCT) for visualizing Li plating near the graphite-separator interface due to strong attenuation from hydrogen-rich components like PP–PE–PP separators, electrolyte, and Fe-based spacers. In this work, we designed and tested a neutron-friendly battery (NFB) optimized for in situ Li detection during extreme fast charging (XFC). Guided by neutron attenuation cross-sections and material transmission, the NFB enables clear visualization at the graphite–separator interface, which is typically opaque in standard LIBs. Electrochemical tests show the NFB exhibits voltage/current responses like standard cells for up to 50 XFC cycles. However, its lower reversibility and capacity are likely due to Cu-coated Al spacer degradation from delamination or corrosion. We propose titanium spacers as a more stable alternative, albeit requiring custom machining. Using this optimized cell, we achieved simultaneous neutron tomography of multiple cells, capturing in situ 3D images of dead Li accumulation, particularly near graphite edges. These heterogeneous deposits and disconnected Li clusters suggest localized current density hotspots during XFC.
KiteFAST
KiteFAST is a simulator for airborne wind energy systems based on NREL's OpenFAST whole turbine simulator. KiteFAST is a multi-physics engineering tool for modeling the coupled aero-servo-elastic dynamics of airborne wind energy systems i.e. a wind-energy kite. The engineering model is like NREL's OpenFAST tool for land-based or offshore horizontal-axis wind turbines atop towers, in that KiteFAST models the important physical phenomena and system couplings, including the wind/aerodynamic excitation and full-system dynamics response (fuselage, wings, tail, stabilizers, pylons, nacelles, rotors, tether, ground station, control surfaces, and controller) under both normal (for fatigue) and extreme (for ultimate) loading conditions. The configuration of the wind-energy kite is assumed to have one fuselage; two wings (starboard, port) attached to the fuselage; one vertical stabilizer attached the fuselage; two horizontal stabilizers (starboard, port) attached to the vertical stabilizer; one or more pylons per wing, each with two rotors (top, bottom); one ground-station-fixed tether with a bridal connection to the wings, and nominal circular motion of the energy kite in the port (left) direction. The general configuration of the control surfaces assumes one or more flaps per wing, two rudders on the vertical stabilizer, two elevators per horizontal stabilizer, and rotors with variable speed and rotor-collective blade pitch. KiteFAST was developed from (1) the existing MBDyn open-source multi-body dynamics code; (2) the existing/modified OpenFAST modules NWTC Subroutine Library, AirfoilInfo, InflowWind, MoorDyn, and TurbSim; and (3) new source code for a) generating MBDyn models of the energy kite (KiteMBDyn Preprocessor), b) computing quasi-steady energy-kite aerodynamics (KiteAeroDyn, KiteAeroDyn Driver, KiteVSM, ActuatorDisk), c) interfacing an energy-kite controller, and d) coupling the various KiteFAST modules together (KiteFASTMBD).
pnnl/arena
CFA ARENA is a novel programming model with the support of a runtime targeting asynchronous data-centric execution paradigm in a distributed system. All the machine nodes in ARENA are connected by a ring network to bring the specialized computation to the data rather than the reverse to minimize data movement. The programming interfaces are implemented using C++
TChem-atm v1.0
SAND2024-11300O TChem-atm is a software library that was developed to solve complex kinetic models for atmospheric chemistry applications. TChem-atm interface employs a hierarchical parallelism design to exploit the massive parallelism available from modern computing platforms. It also supports gas atmospheric chemistry applications, e.g., the energy exascale earth system model. TChem can be used as a box model or coupled with a climate model to compute the time evolution of gas tracer species. 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.
Virtual Design and Analysis of the Balancing Element of an External Gear Machine Considering Cavitation and Mixed Lubrication Effects
This report presents a simulation based approach for sizing the axial balance elements of a pressure compensated external gear machine. The reference hydraulic unit must be able to guarantee operation in two quadrants, as either a pump or a motor. It also needs to operate in a wide operating range of speed and pressure, as it is to be used as primary hydraulic unit for an electro-hydraulic actuator (EHA). The design procedure builds upon past work at the author’s center, but it extends it to the case of multiple quadrant units. Also, a unique method for modeling of both mixed lubrication and cavitation that might occur in the lubricating film is used. After describing the design procedure, the paper discusses the features of the balancing of a reference unit, along with the effects of both cavitation and mixed lubrication.
Platform for efficient large-scale storage and analysis of multi-omics data in plant and microbial systems (Final Technical Report)
Genomic variation at the sequence level fundamentally affects the phenotypic state of all organisms at all stages of development, while dynamic processes such as changes in the epigenome (e.g. DNA methylation state) and transcriptome regulate the specific phenotype expressed at any given state of development based upon that genomic variation. In plants, DNA methylation is a particularly important mechanism for both regulating transcriptomic expression and for management of genomic variations that could be deleterious to the organism due to the presence of active retrotransposons in plant genomes. While DNA methylation is heritable, it is also dynamic through a given plant’s development and life cycle, particularly during the development from seed to mature specimen suggesting variations in DNA methylation could be critical regulators of biologically and commercially important phenotypes such as time to flowering; in addition, plant DNA methylation is more complex than that of animals, with methylation of CHG and CHH trinucleotides evident in addition to the better-known CG methylation. The complexity of plant DNA methylation and its interplay with genomic sequence variation, transcriptomics and other epigenomic factors demand a storage and analysis framework that can cope with the complexity both within a single specimen and with analyses that span many individuals and even many species, such as attempts to extend models from model organisms to commercially relevant species. In addition to complexity, the rapid development and proliferation of sequencing technology has led to an explosion of data volume that conventional storage and analysis solutions will likely be unable to cope with in the long run. We proposed to study these with suitable distributed storage and computation and therefore for the application of cloud computing to biological analyses; integrate with existing data sources and compatible with virtually any interface use case, from fully automated shell scripts to notebooks and do all these at scale in this STTR grant.