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At least 559 records · Page 31

Multiscale Molecular Dynamics Simulations: Accelerating Conformational Sampling of Biomolecular Systems by Iterating All-Atom and Coarse-Grained Simulations

We developed the atomistic-coarse-grained multiscale MD simulation method in the OpenMM simulation package by iterating between the all-atom (AA) and coarse-grained (CG) MD simulations to enhance the sampling of biomolecular conformations. As the free energy surfaces are flattened during CG MD simulations, we can accelerate the transitions between different low-energy conformations. The AA-CG-AA cycles are repeated, facilitating the accelerated sampling of biomolecular conformations at a CG level, while the finer atomistic interactions are refined with AA simulators.

Do, Hung Nguyen↗

ExaCA grain structure predictions for laser powder bed fusion processing

This dataset contains simulated cross-sections of laser powder bed fusion grain structures produced using the microstructure model ExaCA, in turn using time-temperature history data produced using the heat transport model AdditiveFOAM. These predictions show the grain structure using various permutations of hatch spacing and nucleation density. Also contained in the dataset are the input files necessary to reproduce the results. AdditiveFOAM (https://github.com/ORNL/AdditiveFOAM) and ExaCA (https://github.com/LLNL/ExaCA), both open source software, are required to reproduce the results in this dataset using the given input files. This DOI was updated 12/09/2025.

36 MATERIALS SCIENCE↗

AmeriFlux FLUXNET-1F US-WT1 Kress, TX no-till cotton and grain sorghum production

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site US-WT1 Kress, TX no-till cotton and grain sorghum production. This is the FLUXNET version of the carbon flux data for the site US-WT1 Kress, TX no-till cotton and grain sorghum production produced by applying the standard ONEFlux (1F) software. Site Description - Non irrigated cotton and gain sorghum production

Bednarz, Craig [West Texas A&M University]↗

Peridynamic Model for Single-Layer Graphene Obtained from Coarse Grained Bond Forces

An ordinary state-based peridynamic material model is proposed for single sheet graphene. The model is calibrated using coarse grained molecular dynamics simulations. The coarse graining method allows the dependence of bond force on bond length to be determined, including the horizon. The peridynamic model allows the horizon to be rescaled, providing a multiscale capability and allowing for substantial reductions in computational cost compared with molecular dynamics. The calibrated peridynamic model is compared to experimental data on the deflection and perforation of a graphene monolayer by an atomic force microscope probe.

36 MATERIALS SCIENCE↗

Research Plan and Preliminary Results in Developing the Fabrication Parameters for Alloy 709 in Different Product Forms―Grain Coarsening Temperature Evaluation

The Advanced Reactor Technologies (ART) Program has established a multi-year plan to develop Alloy 709 advanced stainless steel (A709), generate the data package and develop material-specific design parameters in qualifying it as a new structural material for Class A component design in the American Society of Mechanical Engineers (ASME) Boiler and Pressure Vessel Code, Section III, Division 5, High Temperature Reactors. In collaboration with material vendors, the Advanced Materials Development activities under ART have successfully scaled the A709 plate form production from a laboratory heat of 500 pounds to commercial heats totaling 133,000 pounds of A709 plate fabricated from three heats. The goal of the overall A709 development program is to establish the necessary microstructural and mechanical properties relationship for A709 to ultimately develop fabrication parameters for other product forms such as bars, piping and forging using the available ART A709 materials. The objective of this A709 development work at ORNL in FY2023 is to experimentally determine grain coarsening behavior for the A709 heats and to experimentally generate the continuous cooling precipitation (CCP) diagram for A709 using the as-rolled commercial heat plate materials. Integral to this work is the characterization of the as-rolled materials and the determination of an effective solution annealing process. This report summarizes the work performed to identify the grain coarsening temperature for commercial heat 58776-3RB fabricated by G. O. Carlson and heat 529900-02 fabricated by Allegheny Technologies Incorporated (ATI) Flat Rolled Products.

36 MATERIALS SCIENCE↗

Establishing Validation Sites for Field-Level Emissions Quantification from Grain Sorghum in Southern Great Plains

Establish publicly available open-source, high-resolution datasets of greenhouse gas (GHG) emissions, meteorology, soil, and vegetation to support testing and validation of emerging biofuel production monitoring technologies. The project team deployed latest technologies to collect “Gold Standard” data for field- level fluxes of CO 2 , N 2 O, CH 4 and H 2 O in grain sorghum production systems in Texas, Oklahoma, and Kansas. The Oklahoma State University led SMARTFARM was initiated on Oct 1, 2020, due to COVID-19 pandemic delay. We installed closed-path dual laser Eddy Covariance (EC) flux measurement system along with a well-established open-path EC system for simultaneously measuring field-level fluxes of CO 2 , N 2 O, CH 4 , and H2O. The eddy flux data are combined with sub-acre soil moisture and temperature measurements, plant and soil analysis data (nutrient, composition, carbon, growth, and phenology), spatial surveys of soil EC, and pH. Grain sorghum crop was managed including planting and harvesting by producers. All teams recruited postdocs and students for the project and submitted purchase orders for field equipment. The team has developed a draft impact sheet and finalized the advisory board for the project.

09 BIOMASS FUELS↗

Development of a concurrent coupled Atomistic - Continuum model to predict the defect and grain structure for Additive Manufacturing process [Slides]

Development of a coupled atomistic-continuum model for metal AM process. Two-way coupling between atomistic (heat flux) and continuum (temperature) domain. Identification of grain and dislocation structure at the atomistic domain. Conversion of dislocation data from discrete atomistic to density form at the continuum. Obtain the spatial distribution of grain structure and dislocation density in additively manufactured metal polycrystal material.

36 MATERIALS SCIENCE↗

Fundamental Study of Fatigue Crack Initiation at Grain and Twin Boundaries in Austentic Stainless Steel (Final Technical Report)

The overarching goal of this project was to understand the dislocation-based mechanisms driving fatigue crack initiation at grain and twin boundaries. The hypothesis of the work is that dislocation structures equivalent to persistent slip bands (PSBs) form in the boundaries, leading to local stress concentrations and fatigue crack initiation. The sub-goals associated with this work include: • Understanding the evolution of the dynamic stress state and dislocation density surrounding PSB/grain boundary interactions. This will require the development of new techniques that couple high resolution electron backscatter diffraction (HREBSD) with in situ scanning electron microscopy (SEM) deformation. • Uncover the mechanisms by which dislocations are accommodated in grain and twin boundaries during fatigue. The proposed approach here is to conduct in situ transmission electron microscopy (TEM) deformation experiments on fatigued samples. • Establish correlations between microstructure, deformation accommodation, and crack initiation across time and length scales. This work primarily focuses on understanding fatigue crack initiation in austenitic stainless steels, though promising work by an undergraduate researcher extended the work to high purity Al.

42 ENGINEERING↗

Temporal Coarse Graining for Classical Stochastic Noise in Quantum Systems

Simulations of quantum systems with Hamiltonian classical stochastic noise can be challenging when the noise exhibits temporal correlations over a multitude of time scales, such as for 1/f noise in solid-state quantum information processors. Here we present an approach for simulating Hamiltonian classical stochastic noise that performs temporal coarse-graining by effectively integrating out the high-frequency components of the noise. We focus on the case where the stochastic noise can be expressed as a sum of Ornstein-Uhlenbeck processes. Temporal coarse-graining is then achieved by conditioning the stochastic process on a coarse realization of the noise, expressing the conditioned stochastic process in terms of a sum of smooth, deterministic functions and bridge processes with boundaries fixed at zero, and performing the ensemble average over the bridge processes. For Ornstein-Uhlenbeck processes, the deterministic components capture all dependence on the coarse realization, and the stochastic bridge processes are not only independent but taken from the same distribution with correlators that can be expressed analytically, allowing the associated noise propagators to be precomputed once for all simulations. This combination of noise trajectories on a coarse time grid and ensemble averaging over bridge processes has practical advantages, such as a simple concatenation rule, that we highlight with numerical examples.

Albash, Tameem [Sandia National Lab. (SNL-NM), Alb↗

On the Prospect of Chemically Transferable Coarse-Grained Electronic Models for Soft Materials

Electronic coarse-graining (ECG) methods predict quantum-mechanical electronic properties directly from coarse-grained (CG) molecular configurations, enabling electronic predictions at mesoscale length scales. Here, we present a diagnostic assessment of the feasibility of chemically transferable ECG models across a broad polymer-relevant chemical space using all-atom, united-atom, and Martini-scale representations. While high-resolution ECG models achieve near-quantitative accuracy, we show that chemically transferable ECG at the Martini resolution fails because the CG force field does not sample the same configurational distribution of local molecular structure as that underlying the DFT-parameterized ECG model. We demonstrate that our proposed Element-Count-Label (ECL) representation, which augments Martini beads with explicit stoichiometric data, significantly improves chemical generalization across diverse polymer chemistries. However, we find that even with improved chemical resolution, the model cannot recover electronic property distributions that are absent from the configurational space sampled by the CG force field. These results demonstrate that chemically transferable ECG requires future Martini-like force fields to explicitly preserve quantum chemistry–compatible local molecular structure in addition to thermodynamic and structural fidelity.

Kidder, Katherine M [Department of Chemistry; Univ↗

Effect of Grain Boundary Misorientation on Spall Strength in Ta via Shock-Free Simulations with Relatively Few Atoms

A suite of 37 molecular dynamics simulations is conducted at two system sizes to systematically characterize the role of grain boundary (GB) misorientation on spall strength in pure BCC tantalum (Ta). The systems studied consist of bicrystals with a single [110] symmetric tilt grain boundary. Two loading conditions are compared: (i) homogeneous extension under uniaxial strain simulated in this study and (ii) piston/flyer impact of sample, which induces heterogeneous deformation via shockwave propagation along the length of the sample. The piston/flyer impact is taken from the literature and run on the same set of GB misorientation angles using LAMMPS. The major finding here is that both methods result in similar spall strength predictions, but the homogeneous extension method generally requires two to three orders of magnitude fewer atoms and similar reductions in computational costs. Spall strength results systematically overpredict using this method, by about 10% for the dataset three orders of magnitude smaller than piston/flyer simulations, and 5% for the dataset two orders of magnitude smaller. Lastly, the effect of system size and pre-compression magnitude on spall strength is systematically characterized.

36 MATERIALS SCIENCE↗

ezAlign: A Tool for Converting Coarse-Grained Molecular Dynamics Structures to Atomistic Resolution for Multiscale Modeling

Soft condensed matter is challenging to study due to the vast time and length scales that are necessary to accurately represent complex systems and capture their underlying physics. Multiscale simulations are necessary to study processes that have disparate time and/or length scales, which abound throughout biology and other complex systems. Herein we present ezAlign, an open-source software for converting coarse-grained molecular dynamics structures to atomistic representation, allowing multiscale modeling of biomolecular systems. The ezAlign v1.1 software package is publicly available for download at github.com/LLNL/ezAlign. Its underlying methodology is based on a simple alignment of an atomistic template molecule, followed by position-restraint energy minimization, which forces the atomistic molecule to adopt a conformation consistent with the coarse-grained molecule. The molecules are then combined, solvated, minimized, and equilibrated with position restraints. Validation of the process was conducted on a pure POPC membrane and compared with other popular methods to construct atomistic membranes. Additional examples, including surfactant self-assembly, membrane proteins, and more complex bacterial and human plasma membrane models, are also presented. By providing these examples, parameter files, code, and an easy-to-follow recipe to add new molecules, this work will aid future multiscale modeling efforts.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Interstellar Extinction, Polarization, and Grain Alignment in the Sh 2-185 (IC 59 and IC 63) Region

Optical and infrared continuum polarization from the interstellar medium is driven by radiative processes aligning the grains with the magnetic field. While a quantitative, predictive theory of radiative alignment torques (RATs) exists and has been extensively tested, several parameters of the theory remain to be fully constrained. In a recent paper, Medan & Andersson showed that the polarization efficiency (and therefore grain alignment efficiency) at different locations in the wall of the Local Bubble (LB) could be modeled as proportional to the integrated light intensity from the surrounding stars and OB associations. Here we probe that relationship at high radiation field intensities by studying the extinction and polarization in the two reflection nebulae IC 59 and IC 63 in the Sh 2-185 H ii region, illuminated by the B0 IV star γ Cassiopeia. We combine archival visual polarimetry with new seven-band photometry in the Vilnius system, to derive the polarization efficiency from the material. We find that the same linear relationship seen in the LB wall also applies to the Sh 2-185 region, strengthening the conclusion from the earlier study.

47 OTHER INSTRUMENTATION↗

Production of Radioactive 22 Na in Core-collapse Supernovae: The Ne-E(L) Component in Presolar Grains and Its Possible Consequences on Supernova Observations

Presolar graphite grains carry the isotopic signatures of their parent stars. A significant fraction of presolar graphites show isotopic abundance anomalies relative to solar for elements such as O, Si, Mg, and Ca, which are compatible with nucleosynthesis in core-collapse supernovae (CCSNe). Therefore, they must have condensed from CCSN ejecta before the formation of the Sun. Their most puzzling abundance signature is the 22 Ne-enriched component Ne-E(L), interpreted as the effect of the radioactive decay of 22 Na (T 1/2 = 2.6 yr). Previous works have shown that if H is ingested into the He shell and not fully destroyed before the explosion, the CCSN shock in the He-shell material produces large amounts of 22 Na. Here we focus on such CCSN models, showing a radioactive 26 Al production compatible with grain measurements, and analyze the conditions of 22Na nucleosynthesis. In these models, 22 Na is mostly made in the He shell, with a total ejected mass varying between 2.6 × 10 −3 M ⊙ and 1.9 × 10 −6 M ⊙ . We show that such 22 Na may already impact the CCSN light curve 500 days after the explosion, and at later stages it can be the main source powering the CCSN light curve for up to a few years before 44 Ti decay becomes dominant. Based on the CCSN yields above, the 1274.53 keV γ-ray flux due to 22 Na decay could be observable for years after the first CCSN light is detected, depending on the distance. This makes CCSNe possible sites to detect a 22 Na γ-ray signature consistently with the Ne-E(L) component found in presolar graphites. Finally, we discuss the potential contribution from 22 Na decay to the Galactic positron annihilation rate.

79 ASTRONOMY AND ASTROPHYSICS↗

Atomic structures for studying elemental segregation at garnet grain boundaries

This is a dataset containing atomic structures of bulk and grain boundaries of doped/undoped Li7La3Zr2O12 solid electrolytes, which were obtained from atomic simulations in a journal paper "Elemental Segregation at Garnet Grain Boundaries: Eliminating Its Detrimental Role in Conductivity and Lithium Nucleation" by Kai Yao et al.

Kim, Kwangnam [Lawrence Livermore National Laborat↗

Electric component including custom metal grain orientation

An electrical device includes an electromagnetic component configured to generate a magnetic flux. The electromagnetic component includes a soft magnetically-conductive material configured to pass magnetic flux therethrough along a flux path. The soft magnetically-conductive material includes at least one grain oriented portion having metal grains that are oriented parallel with respect to the magnetic flux.

42 ENGINEERING↗

Grain boundary engineering for additive manufacturing

In one embodiment, a method of manufacturing a metal part using a laser or electron beam during a powder bed additive manufacturing process includes melting each of a number of layers of metal powder of the metal part with an effective amount of energy using the laser or electron beam to form the metal part such that at least one or more portions of the metal part have a critical amount of residual strain. The method also includes performing a heat treatment on the metal part that transforms the residual strain into substantially distributed coincidence site lattice (CSL) grain boundaries, low angle grain boundaries, or both in the metal part.

36 MATERIALS SCIENCE↗

AURORA: Automated Refinement of Coarse-Grained Reconfigurable Accelerators

Coarse-grained reconfigurable arrays (CGRAs), loosely defined as arrays of functional units interconnected through a network-on-chip (NoC), provide higher flexibility than domain-specific ASIC accelerators while offering increased hardware efficiency with respect to fine-grained reconfigurable devices, such as Field Programmable Gate Arrays (FPGAs). Un-fortunately, designing a CGRA for a specific application domain involves enormous software/hardware engineering effort (e.g., designing the CGRA, map operations onto the CGRA, etc) and requires the exploration on a large design space (e.g., applying appropriate loop transformation on each application, specializing the reconfigurable processing elements of the CGRA, refining the network topology, deciding the size of the data memory, etc). Int his paper, we propose AURORA – a software/hardware co-design framework to automatically synthesize optimal CGRA given a set of applications of interest

Tan, Cheng↗