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At least 1,225 records · Page 68

Dynamical downfolding for localized quantum states

We introduce an approach to treat localized correlated electronic states in the otherwise weakly correlated host medium. Here, the environment is dynamically downfolded on the correlated subspace. It is captured via renormalization of one and two quasiparticle interaction terms which are evaluated using many-body perturbation theory. We outline the strategy on how to take the dynamical effects into account by going beyond the static limit approximation. Further, we introduce an efficient stochastic implementation that enables treating the host environment with a large number of electrons at a minimal computational cost. For a small explicitly correlated subspace, the dynamical effects are critical. We demonstrate the methodology by reproducing optical excitations in the negatively charged NV center defect in diamond, that agree with experimental results.

36 MATERIALS SCIENCE↗

Multiscale Universal Interface: A concurrent framework for coupling heterogeneous solvers

Graphical abstract: - Abstract: Concurrently coupled numerical simulations using heterogeneous solvers are powerful tools for modeling multiscale phenomena. However, major modifications to existing codes are often required to enable such simulations, posing significant difficulties in practice. In this paper we present a C++ library, i.e. the Multiscale Universal Interface (MUI), which is capable of facilitating the coupling effort for a wide range of multiscale simulations. The library adopts a header-only form with minimal external dependency and hence can be easily dropped into existing codes. A data sampler concept is introduced, combined with a hybrid dynamic/static typing mechanism, to create an easily customizable framework for solver-independent data interpretation. The library integrates MPI MPMD support and an asynchronous communication protocol to handle inter-solver information exchange irrespective of the solvers' own MPI awareness. Template metaprogramming is heavily employed to simultaneously improve runtime performance and code flexibility. We validated the library by solving three different multiscale problems, which also serve to demonstrate the flexibility of the framework in handling heterogeneous models and solvers. In the first example, a Couette flow was simulated using two concurrently coupled Smoothed Particle Hydrodynamics (SPH) simulations of different spatial resolutions. In the second example, we coupled the deterministic SPH method with the stochastic Dissipative Particle Dynamics (DPD) method to study the effect of surface grafting on the hydrodynamics properties on the surface. In the third example, we consider conjugate heat transfer between a solid domain and a fluid domain by coupling the particle-based energy-conserving DPD (eDPD) method with the Finite Element Method (FEM)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

2022 INL Site Report

Visualization is key to the work we do at Idaho National Laboratory (INL). We support research computing, nuclear science, and educational outreach using both traditional and emerging visualization tools and technologies. In this presentation, we will introduce and summarize INL and its mission, describe some of the visualization resources INL provides, and present example applications from recent years.

97 MATHEMATICS AND COMPUTING↗

2024 INL Site Report

Visualization is key to the work we do at Idaho National Laboratory (INL). We support research computing, nuclear science, and educational outreach using both traditional and emerging visualization tools and technologies. In this presentation, we will introduce and summarize INL and its mission, describe some of the visualization resources INL provides, and present example applications from recent years.

97 - MATHEMATICS AND COMPUTING↗

Combined molecular and spin dynamics simulation of BCC iron with vacancy defects

Utilizing an atomistic computational model, which handles both translational and spin degrees of freedom, combined molecular and spin dynamics simulations have been performed to investigate the effect of vacancy defects on spin wave excitations in ferromagnetic iron. Fourier transforms of space- and time-displaced correlation functions yield the dynamic structure factor, providing characteristic frequencies and lifetimes of the spin wave modes. A comparison of the system with a 5% vacancy concentration with pure lattice data shows a decrease in frequency and a decrease in lifetime for all transverse spin wave excitations observed. In addition, the clearly defined transverse spin wave excitations are distorted with the introduction of vacancy defects, and we observe reduced excitation lifetimes due to increased magnon–magnon scattering. We observe further evidence of increased magnon–magnon scattering, as the peaks in the longitudinal spin wave spectrum become less distinct. Finally, similar impacts are observed in the vibrational subsystem, with a decrease in characteristic phonon frequency and flattening of lattice excitation signals due to vacancy defects.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Quantification of the transferability of a designed protein specificity switch reveals extensive epistasis in molecular recognition

Re-engineering protein–protein recognition is an important route to dissecting and controlling complex interaction networks. Experimental approaches have used the strategy of “second-site suppressors,” where a functional interaction is inferred between two proteins if a mutation in one protein can be compensated by a mutation in the second. Mimicking this strategy, computational design has been applied successfully to change protein recognition specificity by predicting such sets of compensatory mutations in protein–protein interfaces. To extend this approach, it would be advantageous to be able to “transplant” existing engineered and experimentally validated specificity changes to other homologous protein–protein complexes. Here, we test this strategy by designing a pair of mutations that modulates peptide recognition specificity in the Syntrophin PDZ domain, confirming the designed interaction biochemically and structurally, and then transplanting the mutations into the context of five related PDZ domain–peptide complexes. We find a wide range of energetic effects of identical mutations in structurally similar positions, revealing a dramatic context dependence (epistasis) of designed mutations in homologous protein–protein interactions. To better understand the structural basis of this context dependence, we apply a structure-based computational model that recapitulates these energetic effects and we use this model to make and validate forward predictions. The context dependence of these mutations is captured by computational predictions, our results both highlight the considerable difficulties in designing protein–protein interactions and provide challenging benchmark cases for the development of improved protein modeling and design methods that accurately account for the context.

59 BASIC BIOLOGICAL SCIENCES↗

Primitive to conventional geometry projection for efficient phonon transport calculations

Abstract The primitive Wigner-Seitz cell and corresponding first Brillouin zone (FBZ) are typically used in calculations of lattice vibrational and transport properties as they contain the smallest number of degrees of freedom and thus have the cheapest computational cost. However, in complex materials, the FBZ can take on irregular shapes where lattice symmetries are not apparent. Thus, conventional cells (with more atoms and regular shapes) are often used to describe materials, though dynamical and transport calculations are more expensive. Here we discuss an efficient anharmonic lattice dynamic method that maps conventional cell dynamics to primitive cell dynamics based on translational symmetries. Such symmetries have not been utilized in typical lattice dynamical calculations. This leads to phase interference conditions that act like conserved quantum numbers and a conservation rule for phonon scattering that is hidden in conventional dynamics which significantly reduces the computational cost. We demonstrate this method for phonon transport in a variety of materials with inputs from first-principles calculations and attribute its efficiency to reduced scattering phase space and fewer summations in scattering matrix element calculations.

36 MATERIALS SCIENCE↗

Accelerating computational modeling and design of high-entropy alloys

High-entropy alloys, with N elements and compositions {$c_{ν = 1,N}$} in competing crystal structures, have large design spaces for unique chemical and mechanical properties. In this work, to enable computational design, we use a metaheuristic hybrid Cuckoo search (CS) to construct alloy configurational models on the fly that have targeted atomic site and pair probabilities on arbitrary crystal lattices, given by supercell random approximates (SCRAPs) with S sites. Our Hybrid CS permits efficient global solutions for large, discrete combinatorial optimization that scale linearly in a number of parallel processors, and linearly in sites S for SCRAPs. For example, a four-element, 128-site SCRAP is found in seconds—a more than 13,000-fold reduction over current strategies. Our method thus enables computational alloy design that is currently impractical. We qualify the models and showcase application to real alloys with targeted atomic short-range order. Being problem-agnostic, our Hybrid CS offers potential applications in diverse fields.

36 MATERIALS SCIENCE↗

Special Topic on High Performance Computing in Chemical Physics

Computational modeling and simulation have become indispensable scientific tools in virtually all areas of chemical, biomolecular, and materials systems research. Computation can provide unique and detailed atomic level information that is difficult or impossible to obtain through analytical theories and experimental investigations. In addition, recent advances in micro-electronics have resulted in computer architectures with unprecedented computational capabilities, from the largest supercomputers to common desktop computers. In conclusion, combined with the development of new computational domain science methodologies and novel programming models and techniques, this has resulted in modeling and simulation resources capable of providing results at or better than experimental chemical accuracy and for systems in increasingly realistic chemical environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Deep learning symmetries and their Lie groups, algebras, and subalgebras from first principles

Abstract We design a deep-learning algorithm for the discovery and identification of the continuous group of symmetries present in a labeled dataset. We use fully connected neural networks to model the symmetry transformations and the corresponding generators. The constructed loss functions ensure that the applied transformations are symmetries and the corresponding set of generators forms a closed (sub)algebra. Our procedure is validated with several examples illustrating different types of conserved quantities preserved by symmetry. In the process of deriving the full set of symmetries, we analyze the complete subgroup structure of the rotation groups SO (2), SO (3), and SO (4), and of the Lorentz group S O ( 1 , 3 ) . Other examples include squeeze mapping, piecewise discontinuous labels, and SO (10), demonstrating that our method is completely general, with many possible applications in physics and data science. Our study also opens the door for using a machine learning approach in the mathematical study of Lie groups and their properties.

97 MATHEMATICS AND COMPUTING↗

SU-D-BRD-02: A Web-Based Image Processing and Plan Evaluation Platform (WIPPEP) for Future Cloud-Based Radiotherapy

Purpose: Visualization and processing of medical images and radiation treatment plan evaluation have traditionally been constrained to local workstations with limited computation power and ability of data sharing and software update. We present a web-based image processing and planning evaluation platform (WIPPEP) for radiotherapy applications with high efficiency, ubiquitous web access, and real-time data sharing. Methods: This software platform consists of three parts: web server, image server and computation server. Each independent server communicates with each other through HTTP requests. The web server is the key component that provides visualizations and user interface through front-end web browsers and relay information to the backend to process user requests. The image server serves as a PACS system. The computation server performs the actual image processing and dose calculation. The web server backend is developed using Java Servlets and the frontend is developed using HTML5, Javascript, and jQuery. The image server is based on open source DCME4CHEE PACS system. The computation server can be written in any programming language as long as it can send/receive HTTP requests. Our computation server was implemented in Delphi, Python and PHP, which can process data directly or via a C++ program DLL. Results: This software platform is running on a 32-core CPU server virtually hosting the web server, image server, and computation servers separately. Users can visit our internal website with Chrome browser, select a specific patient, visualize image and RT structures belonging to this patient and perform image segmentation running Delphi computation server and Monte Carlo dose calculation on Python or PHP computation server. Conclusion: We have developed a webbased image processing and plan evaluation platform prototype for radiotherapy. This system has clearly demonstrated the feasibility of performing image processing and plan evaluation platform through a web browser and exhibited potential for future cloud based radiotherapy.

60 APPLIED LIFE SCIENCES↗

Investigating Deformation and Failure Mechanisms in Nanoscale Multilayer Metallic Composites

Over the history of materials science there are many examples of materials discoveries that have made superlative materials; the strongest, lightest, or toughest material is almost always a goal when we invent new materials. However, often these have been a result of enormous trial and error approaches. A new methodology, one in which researchers design, from the atoms up, new ultra-strong materials for use in energy applications, is taking hold within the science and engineering community. This project focused on one particular new classification of materials; nanolaminate metallic composites. These materials, where two metallic materials are intimately bonded and layered over and over to form sheets or coatings, have been shown over the past decade to reach strengths over 10 times that of their constituents. However, they are not yet widely used in part because while extremely strong (they don’t permanently bend), they are also not particularly tough (they break relatively easily when notched). Our program took a coupled approach to investigating new materials systems within the laminate field. We used computational materials science to explore ways to institute new deformation mechanisms that occurred when a tri-layer, rather than the more common bi-layer system was created. Our predictions suggested that copper-nickel or copper-niobium composites (two very common bi-layer systems) with layer thicknesses on the order of 20 nm and then layered 100’s of times, would be less tough than a copper-nickel-niobium metallic composite of similar thicknesses. In particular, a particular mode of permanent deformation, cross-slip, could be activated only in the tri-layer system; the crystal structure of the other bi-layers would prohibit this particular mode of deformation. We then experimentally validated this predication using a wide range of tools. We utilized a DOE user facility, the Center for Integrated Nanotechnology (CINT), to fabricate, for the first time, these tri-layer composites. CINT formed nanolaminate composites were tested in tension, with bulge testing, using nanoindentation, and using micro-compression testing to demonstrate that the tri-layer films were indeed tougher and hardened more during deformation (they got stronger as we deformed them) than equivalent bi-layers. The seven graduate students, 4 post-docs and research faculty, and the two faculty co-PI’s were able to create a collaborated computational prediction and experimental validation team to demonstrate the benefits of this class of materials to the community. The computational work crossed from atomistic to bulk simulations, and the experiments coupled form nm-scale to the mm scale; closely matching the simulations. The simulations provided viable mechanisms that explained the observed results, and new experimental results were used to push the boundaries of the simulation tools. Over the life of the 7 years of this program we proved that tri-layer nanolaminate metallic composite systems exceeded the mechanical performance of bi-layer systems if the right materials were chosen, and that the mechanism responsible for this was tied to the cross slip of dislocations. With 30 journal publications resulting from this work we have broadly disseminated this family of results to the scientific community.

36 MATERIALS SCIENCE↗

Strength can be controlled by edge dislocations in refractory high-entropy alloys

Energy efficiency is motivating the search for new high-temperature (high-T) metals. Some new body-centered-cubic (BCC) random multicomponent “high-entropy alloys (HEAs)” based on refractory elements (Cr-Mo-Nb-Ta-V-W-Hf-Ti-Zr) possess exceptional strengths at high temperatures but the physical origins of this outstanding behavior are not known. Here we show, using integrated in-situ neutron-diffraction (ND), high-resolution transmission electron microscopy (HRTEM), and recent theory, that the high strength and strength retention of a NbTaTiV alloy and a high-strength/low-density CrMoNbV alloy are attributable to edge dislocations. This finding is surprising because plastic flows in BCC elemental metals and dilute alloys are generally controlled by screw dislocations. We use the insight and theory to perform a computationally-guided search over 10 7 BCC HEAs and identify over 10 6 possible ultra-strong high-T alloy compositions for future exploration.

36 MATERIALS SCIENCE↗

Scalable 3D reconstruction for X-ray single particle imaging with online machine learning

X-ray free-electron lasers offer unique capabilities for measuring the structure and dynamics of biomolecules, helping us understand the basic building blocks of life. Notably, high-repetition-rate free-electron lasers enable single particle imaging, where individual, weakly scattering biomolecules are imaged under near-physiological conditions with the opportunity to access fleeting states that cannot be captured in cryogenic or crystallized conditions. Existing X-ray single particle reconstruction algorithms, which estimate the particle orientation for each image independently, are slow and memory-intensive when handling the massive datasets generated by emerging free-electron lasers. Here, we introduce X-RAI (X-Ray single particle imaging with Amortized Inference), an online reconstruction framework that estimates the structure of 3D macromolecules from large X-ray single particle datasets. X-RAI consists of a convolutional encoder, which amortizes pose estimation over large datasets, as well as a physics-based decoder, which employs an implicit neural representation to enable high-quality 3D reconstruction in an end-to-end, self-supervised manner. We demonstrate that X-RAI achieves state-of-the-art performance for small-scale datasets in simulation and challenging experimental settings and demonstrate its unprecedented ability to process large datasets containing millions of diffraction images in an online fashion. These abilities signify a paradigm shift in X-ray single particle imaging towards real-time reconstruction.

Computer science↗

HamLib: A Library of Hamiltonians for Benchmarking Quantum Algorithms and Hardware

For a considerable time, large datasets containing problem instances have proven valuable for analyzing computer hardware, software, and algorithms. One notable example of the value of large datasets is ImageNet [1], a vast repository of images that has been instrumental in testing numerous deep learning packages. Similarly, in the domain of computational chemistry and materials science, the availability of extensive datasets such as the Protein Data Bank [2], the Materials Project [3], and QM9 [4] has greatly facilitated the evaluation of new algorithms and software approaches, while also promoting standardization within the field. These well-defined datasets and problem instances, in turn, serve as the foundation for creating benchmarking suites like MLPerf [5] and LINPACK [6], [7]. These suites enable fair and rigorous comparisons of different methodologies and solutions, fostering continuous advancements in various areas of computer science and beyond.

Sawaya, Nicolas PD↗

Collaborative Project: Building improved optimized parameter estimation algorithms to improve methane and nitrogen fluxes in a climate model

Soils in natural and managed ecosystems and wetlands are well known sources of methane, nitrous oxides, and reactive nitrogen gases, but the magnitudes of gas flux to the atmosphere are still poorly constrained. Thus, the reasons for the large increases in atmospheric concentrations of methane and nitrous oxide since the preindustrial time period are not well understood. The low atmospheric concentrations of methane and nitrous oxide, despite being more potent greenhouse gases than carbon dioxide, complicate empirical studies to provide explanations. In addition to climate concerns, the emissions of reactive nitrogen gases from soils are important to the changing nitrogen balance in the earth system, subject to human management, and may change substantially in the future. Thus improved modeling of the emission fluxes of these species from the land surface is important. Currently, there are emission modules for methane and some nitrogen species in the Community Earth System Model’s Community Land Model (CLM-ME/N); however, there are large uncertainties and problems in the simulations, resulting in coarse estimates. In this proposal, we seek to improve these emission modules by combining state-of-the-art process modules for emissions, available data, and new optimization methods. In earth science problems, we often have substantial data and knowledge of processes in disparate systems, and thus we need to combine data and a general process level understanding into a model for projections of future climate that are as accurate as possible. The best methodologies for optimization of parameters in earth system models are still being developed. In this proposal we will develop and apply surrogate algorithms that a) were especially developed for computationally expensive simulations like CLM-ME/N models; b) were (in the earlier surrogate optimization Stochastic RBF) demonstrated to perform very well on computationally expensive complex partial differential equations in earth science with limited numbers of simulations; and, c) will be (as part of the proposed research) significantly improved both by adding asynchronous parallelism, early truncation of unsuccessful simulations, and the improvement of both serial and parallel performance by the use of derivative and sensitivity information from global and local surrogate approximations S(x) . The algorithm development and testing will be focused on the CLM-ME/N model application, but the methods are general and are expected to also perform well on optimization for parameter estimation of other climate models and other classes of continuous multimodal optimization problems arising from complex simulation models. In addition, this proposal will compile available datasets of emissions of methane, nitrous oxides and reactive nitrogen species and develop protocols for site level comparisons with the CLM-ME/N. Once the model parameters are optimized against site level data, the model will be simulated at the global level and compared to atmospheric concentration measurements for the current climate, and future emissions will be estimated using climate change as simulated by the CESM. This proposal combines experts in earth system modeling, optimization, computer science, and process level understanding of soil gas emissions in an interdisciplinary team in order to improve the modeling of methane and nitrogen gas emissions. This proposal thus meets the requirements of the SciDAC RFP, by integrating state-of-the-art computer science and earth system to build an improved earth system model.

54 ENVIRONMENTAL SCIENCES↗

Integration of Russian Tier-1 Grid Center with High Performance Computers at NRC-KI for LHC experiments and beyond HENP

The LHC experiments are preparing for the precision measurements and further discoveries that will be made possible by higher LHC energies from April 2015 (LHC Run2). The need for simulation, data processing and analysis would overwhelm the expected capacity of grid infrastructure computing facilities deployed by the Worldwide LHC Computing Grid (WLCG). To meet this challenge the integration of the opportunistic resources into LHC computing model is highly important. The Tier-1 facility at Kurchatov Institute (NRC-KI) in Moscow is a part of WLCG and it will process, simulate and store up to 10% of total data obtained from ALICE, ATLAS and LHCb experiments. In addition Kurchatov Institute has supercomputers with peak performance 0.12 PFLOPS. The delegation of even a fraction of supercomputing resources to the LHC Computing will notably increase total capacity. In 2014 the development a portal combining a Tier-1 and a supercomputer in Kurchatov Institute was started to provide common interfaces and storage. The portal will be used not only for HENP experiments, but also by other data- and compute-intensive sciences like biology with genome sequencing analysis; astrophysics with cosmic rays analysis, antimatter and dark matter search, etc.

97 MATHEMATICS AND COMPUTING↗

Ontologies for Intelligent Data Science

As anyone even vaguely aware of current technology can tell you, machine learning (ML) and artificial intelligence (AI) have made exceptional breakthroughs in recent years. Generative artificial intelligence (GAI) emerged circa 2022 dominated by Large Language Models (LLMs) and generative tools for images emerged at about the same time.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗