Enhanced Exploration of Protein Conformational Space through Integration of Ultra-Coarse-Grained Models to Multiscale Workflows
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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
SEARCH · Engineering Papers
Results for “Coarse grained simulations”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Adaptive tau-leaping methods for microscopic-lattice kinetic Monte Carlo simulations
Traditional Kinetic Monte Carlo (KMC) approaches, rooted in Gillespie’s stochastic simulation algorithm, become computationally demanding in systems with a large range of timescales. The goal of this work is to propose and study new adaptive lattice-KMC time integration strategies for spatially non-uniform systems. To that end, two novel adaptive tau-leaping methods and their corresponding time integration strategies are developed based on the idea of the “n-fold” direct KMC method. These strategies allow for the simultaneous execution of multiple reactions, advancing time by adaptively selected coarse increments. We present numerical experiments comparing the proposed methods with existing approaches in a catalytic surface kinetics application involving ammonia decomposition.
Bimolecular reactions↗
Advancing material modeling in hydrocodes using a concurrent finite-element and molecular dynamics multiscale framework
We present a multiscale simulation framework that couples the finite-element method with molecular dynamics. Bypassing traditional equations of state (EOS) by using in-line atomistic simulations, the method offers the advantage of incorporating detailed microscale physics not easily represented with coarse-grained models. Coupling consistency with the continuum code is ensured through the use of lifting and restriction operators, in line with heterogeneous multiscale methods. The concurrent continuum-atomistic framework is validated through comparison with experimental results and conventional EOS models, and demonstrated in a shock-driven hydrodynamic flow simulation under extreme conditions. We further evaluate the framework's usability by comparing it to state-of-the-art EOS models of deuterium. A computational performance study reveals that the atomistic EOS evaluation is a feasible alternative to conventional approaches, and demonstrates a weak scaling of 99% efficiency. These results highlight the framework's potential for large-scale multiscale modeling across a broad range of materials and conditions.
Computer science↗
Development of a coarse-grained molecular dynamics model for poly(dimethyl- co -diphenyl)siloxane
Polydimethylsiloxane is an important polymeric material with a wide range of applications. However, environmental effects like low temperature can induce crystallization in this material with resulting changes in its structural and dynamic properties. The incorporation of phenyl-siloxane components, e.g., as in a poly(dimethyl-co-diphenyl)siloxane random copolymer, is known to suppress such crystallization. Molecular dynamics (MD) simulations can be a powerful tool to understand such effects in atomistic detail. Unfortunately, all-atomistic molecular dynamics (AAMD) is limited in both spatial dimensions and simulation times it can probe. Here, to overcome such constraints and to extend to more useful length- and time-scales, we systematically develop a coarse-grained molecular dynamics (CGMD) model for the poly(dimethyl-co-diphenyl)siloxane system with bonded and non-bonded interactions determined from all-atomistic simulations by the iterative Boltzmann inversion (IBI) method. Additionally, we propose a lever rule that can be useful to generate non-bonded potentials for such systems without reference to the all-atomistic ground truth. Our model captures the structural and dynamic properties of the copolymer material with quantitative accuracy and is useful to study long-time dynamics of highly-entangled systems, sequence-dependent properties, phase behaviour, etc.
36 MATERIALS SCIENCE↗
Coarse-Grain Bandwidth Estimation Techniques for Large-Scale Space Network
In this paper, we describe a top-down analysis and simulation approach to size the bandwidths of a store-andforward network for a given network topology, a mission traffic scenario, and a set of data types with different latency requirements. We use these techniques to estimate the wide area network (WAN) bandwidths of the ground links for different architecture options of the proposed Integrated Space Communication and Navigation (SCaN) Network.
Cheung, Kar-Ming↗
Equation-Free Coarse Control of Distributed Parameter Systems via Local Neural Operators
The control of high-dimensional distributed parameter systems (DPS) remains a challenge when explicit coarse-grained equations are unavailable. Classical equation-free (EF) approaches rely on fine-scale simulators treated as black-box timesteppers. However, repeated simulations for steady-state computation, linearization, and control design are often computationally prohibitive, or the microscopic timestepper may not even be available, leaving us with data as the only resource. We propose a data-driven alternative that uses local neural operators, trained on spatiotemporal microscopic/mesoscopic data, to obtain efficient short-time solution operators. These surrogates are employed within Krylov subspace methods to compute coarse steady and unsteady-states, while also providing Jacobian information in a matrix-free manner. Krylov-Arnoldi iterations then approximate the dominant eigenspectrum, yielding reduced models that capture the open-loop slow dynamics without explicit Jacobian assembly. Both discrete-time Linear Quadratic Regulator (dLQR) and pole-placement (PP) controllers are based on this reduced system and lifted back to the full nonlinear dynamics, thereby closing the feedback loop.
93B52, 93C20, 47N70, 65J15, 65M32, 68T07, 68T20, 6↗
Onset of cavitation and vapor bubble development over hydrophilic and hydrophobic surfaces
Cavitation, the formation of vapor bubbles as the liquid pressure is reduced below the saturated vapor pressure, often requires a substantial negative relative pressure in a pure liquid. Classical nucleation theory (CNT) provides an estimate for the rate of cavitation but there is often a disconnect between the predictions at the molecular scale compared to observations at the macroscale. We report on mesoscale simulations of cavitation based on many-body dissipative particle dynamics (mDPD), a coarse-grained molecular dynamics (MD), which bridges the two scales. A liquid layer is confined between smooth planar walls at a constant temperature, while the pressure is reduced slowly by expanding the wall-bounded domain. The wetting properties of the liquid are determined by the parameters of the interaction potentials. With hydrophilic walls, homogeneous nucleation is observed in the liquid bulk. As a bubble forms and grows, it creates a strong pressure pulse and oscillations that cause other bubbles that may have formed slightly later to collapse. For a nearly neutral wall with a contact angle close to 90 ° , heterogeneous nucleation occurs at the walls at a smaller negative pressure and generates weaker pressure oscillations. With hydrophobic walls or seed particles, heterogeneous nucleation readily occurs, where fluctuations and the merger of transient surface bubbles are significant.
Science & Technology - Other Topics↗
Coarse Graining Discrete Element Method Information in Particle-in-Cell Length Scales Using a Machine Learning Approach
This report details the development of a machine learning (ML)-driven framework to coarse-grain inter-particle collision dynamics from high-fidelity Discrete Element Method (DEM) simulations to Particle-in-Cell (PIC) scales for gas-solid systems. Traditional PIC models, while computationally efficient, rely on empirical granular stress formulations that fail to capture the full complexity of collision physics, particularly the heterogeneity in particle dynamics. This study adopts a bottom-up approach, integrating insights from DEM simulations to improve the physical fidelity and interpretability of PIC-scale models.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Molecular dynamics study of hydrogen Cottrell atmosphere in aluminum: Influence of solute-solute interactions in the dislocation core
Cottrell atmospheres form when solute atoms segregate to dislocations, and is one of the most basic processes by which solutes alter mechanical properties of materials. In the case of hydrogen, Cottrell atmospheres are believed to contribute to hydrogen embrittlement. Here, in this study, we use direct molecular dynamics simulations to study the formation of hydrogen Cottrell atmospheres around edge dislocations in aluminum. Using coarse-graining techniques, we resolve the temporal and spatial evolution of the hydrogen concentration field. By comparing our results with theories of Cottrell atmosphere formation and thermodynamics, we show that a repulsive, concentration-dependent H-H interaction reduces the peak atmosphere concentration at the dislocation core. Furthermore, this interaction differs significantly from the H-H interaction that is experienced in the bulk away from a dislocation.
Aluminum↗
Origin of desert loess from some experimental observations
The aeolian attrition of angular quartz grains previously produced by weathering in deserts has been simulated, yielding abrasion products which show that both coarse and fine silt sizes are produced by this process. These results suggest that desert aeolian processes can produce loess, and it is speculated that while much of this material from many deserts has been deposited in the sea, the Chinese loess could have been produced in the Gobi desert. The finest of the particles produced by such attrition may serve as a source of silica for silcrete formation.
Whalley, W. B.↗
Molecular Simulations of Ultrafast Radiation Induced Melting at Metal-Semiconductor Interfaces
Understanding radiation induced ultrafast melting at material interfaces is essential in designing robust electronic devices for aviation/space applications and in laser machining. While it is difficult to achieve the spatial and temporal resolution required to quantify the phenomenon experimentally, simulations can provide the detailed mechanisms of the structural changes that happen during phase transition. In this work, we use molecular simulations to study the effect of radiation damage on silicon carbide (SiC) - tungsten (W) interfaces which is of interest in high power electronics. A multi-scale approach is involved wherein the reactions at the interfaces are quantified using ab-initio molecular dynamics (MD) simulations and classical MD simulations are employed to understand the structural and diffusional changes across the material interface. Finally, coarse-grained Lennard-Jones type models are used to study the larger scale mechanisms and structures obtained due to the induced damages. We show that the response of the material to radiation damage depends on factors such as energy of the incident radiation, thermal properties, and molecular structure of the material.
Ravichandran, Ashwin↗
Seamlessly joining length scales: From atomistic thermal graphs to anisotropic continuum conductivity
Thermal transport in complex solids is governed by local structure, defects, and anisotropy, yet most continuum models still rely on oversimplified and homogenized conductivities. Here, we bridge atomistic and continuum descriptions by building finite element (FE) models directly from the site-projected thermal conductivity (SPTC), an atomic-level decomposition of the Green–Kubo thermal conductivity. We introduce a toolkit, the “Simulator Collection for Atomic-to-Continuum Scales (SCACS)”, which uses a graph neural network to predict SPTC on large atomic structures, coarse-grains these fields into anisotropic conductivity tensors, and embeds them into the heat-flow FE equation with a customized, anisotropy-aware adaptive mesh refinement scheme. Applied to silicon nanostructures, the resulting FE models act as representative volume elements, reproduce bulk conductivities, and capture interfacial and defect-driven anisotropy while maintaining thermodynamic consistency. Additionally, SCACS predicts experimental conductance trends and fields. This work demonstrates a general route for transferring atomistic transport information into device-scale thermal simulations with physics-based approximations.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Simulations of transition and turbulence on the Navier-Stokes computer
The Navier-Stokes Computer (NSC) consists of multiple local memory parallel processors interconnected in a hypercube network. Efficient implementation of algorithms on the NSC thus requires the effective utilization of both the coarse and fine grain paralelism inherent in the architectural design. The basic approach to implementing an algorithm on the NSC is presented herein. The particular finite-difference algorithm considered was developed for performing transition and turbulence simulations by direct solution of the time-dependent incompressible Navier-Stokes equations. The suitability of this algorithm for performing simulations of the isotropic turbulence problem is verified from computations performed on a Cray 2. Projected timing results for the algorithm on the NSC itself are presented for both the isotropic turbulence and laminar turbulent transition problems.
Krist, S. E.↗
Development of Standardized Lunar Regolith Simulant Materials
Lunar exploration requires scientific and engineering studies using standardized testing procedures that ultimately support flight certification of technologies and hardware. It is necessary to anticipate the range of source materials and environmental constraints that are expected on the Moon and Mars, and to evaluate in-situ resource utilization (ISRU) coupled with testing and development. We describe here the development of standardized lunar regolith simulant (SLRS) materials that are traceable inter-laboratory standards for testing and technology development. These SLRS materials must simulate the lunar regolith in terms of physical, chemical, and mineralogical properties. A summary of these issues is contained in the 2005 Workshop on Lunar Regolith Simulant Materials [l]. Lunar mare basalt simulants MLS-1 and JSC-1 were developed in the late 1980s. MLS-1 approximates an Apollo 11 high-Ti basalt, and was produced by milling of a holocrystalline, coarse-grained intrusive gabbro (Fig. 1). JSC-1 approximates an Apollo 14 basalt with a relatively low-Ti content, and was obtained from a glassy volcanic ash (Fig. 2). Supplies of MLS-1 and JSC-1 have been exhausted and these materials are no longer available. No highland anorthosite simulant was previously developed. Upcoming lunar polar missions thus require the identification, assessment, and development of both mare and highland simulants. A lunar regolith simulant is manufactured from terrestrial components for the purpose of simulating the physical and chemical properties of the lunar regolith. Significant challenges exist in the identification of appropriate terrestrial source materials. Lunar materials formed under comparatively reducing conditions in the absence of water, and were modified by meteorite impact events. Terrestrial materials formed under more oxidizing conditions with significantly greater access to water, and were modified by a wide range of weathering processes. The composition space of lunar materials can be modeled by mixing programs utilizing a low-Ti basalt, ilmenite, KREEP component, high-Ca anorthosite, and meteoritic components. This approach has been used for genetic studies of lunar samples via chemical and modal analysis. A reduced composition space may be appropriate for simulant development, but it is necessary to determine the controlling properties that affect the physical, chemical and mineralogical components of the simulant.
Carpenter, P.↗
Scalable parallel communications
Coarse-grain parallelism in networking (that is, the use of multiple protocol processors running replicated software sending over several physical channels) can be used to provide gigabit communications for a single application. Since parallel network performance is highly dependent on real issues such as hardware properties (e.g., memory speeds and cache hit rates), operating system overhead (e.g., interrupt handling), and protocol performance (e.g., effect of timeouts), we have performed detailed simulations studies of both a bus-based multiprocessor workstation node (based on the Sun Galaxy MP multiprocessor) and a distributed-memory parallel computer node (based on the Touchstone DELTA) to evaluate the behavior of coarse-grain parallelism. Our results indicate: (1) coarse-grain parallelism can deliver multiple 100 Mbps with currently available hardware platforms and existing networking protocols (such as Transmission Control Protocol/Internet Protocol (TCP/IP) and parallel Fiber Distributed Data Interface (FDDI) rings); (2) scale-up is near linear in n, the number of protocol processors, and channels (for small n and up to a few hundred Mbps); and (3) since these results are based on existing hardware without specialized devices (except perhaps for some simple modifications of the FDDI boards), this is a low cost solution to providing multiple 100 Mbps on current machines. In addition, from both the performance analysis and the properties of these architectures, we conclude: (1) multiple processors providing identical services and the use of space division multiplexing for the physical channels can provide better reliability than monolithic approaches (it also provides graceful degradation and low-cost load balancing); (2) coarse-grain parallelism supports running several transport protocols in parallel to provide different types of service (for example, one TCP handles small messages for many users, other TCP's running in parallel provide high bandwidth service to a single application); and (3) coarse grain parallelism will be able to incorporate many future improvements from related work (e.g., reduced data movement, fast TCP, fine-grain parallelism) also with near linear speed-ups.
Maly, K.↗
Dissipative ground state preparation in ab initio electronic structure theory
Dissipative engineering is a powerful tool for quantum state preparation, and has drawn significant attention in quantum algorithms and quantum many-body physics in recent years. In this work, we introduce a novel approach using the Lindblad dynamics to efficiently prepare the ground state for general ab initio electronic structure problems on quantum computers, without variational parameters. These problems often involve Hamiltonians that lack geometric locality or sparsity structures, which we address by proposing two generic types of jump operators for the Lindblad dynamics. Type-I jump operators break the particle number symmetry and should be simulated in the Fock space. Type-II jump operators preserves the particle number symmetry and can be simulated more efficiently in the full configuration interaction space. For both types of jump operators, we prove that in a simplified Hartree-Fock framework, the spectral gap of our Lindbladian is lower bounded by a universal constant. For physical observables such as energy and reduced density matrices, the convergence rate of our Lindblad dynamics with Type-I jump operators remains universal, while the convergence rate with Type-II jump operators only depends on coarse grained information such as the number of orbitals and the number of electrons. To validate our approach, we employ a Monte Carlo trajectory-based algorithm for simulating the Lindblad dynamics for full ab initio Hamiltonians, demonstrating its effectiveness on molecular systems amenable to exact wavefunction treatment.
Quantum chemistry↗
A compartmentalized model of multiphase chemical kinetics
There are significant challenges in predicting multiphase chemical kinetics due to the complex coupling of reaction and mass transport across a phase boundary (i.e., interface). Here, we describe a framework for predicting multiphase kinetics that embeds the elementary kinetic steps of reaction, solvation, and diffusion into a coarse grain spatial description of two phases. The model is constructed to bridge the short-timescale interfacial dynamics observed in molecular simulations with the longer timescales observed in kinetic experiments. A simple set of governing differential equations is derived, which, when solved numerically or analytically, yield accurate predictions of multiphase kinetics in microdroplets. Although the equations are formulated for gas-liquid reactions, the underlying conceptual framework is general and can be applied to transformations in other two-phase systems (solid-liquid, liquid-liquid, etc.).
Chemical kinetics and dynamics↗
The dimension of attractors underlying periodic turbulent Poiseuille flow
A lower bound on the Liapunov dimenison, D-lambda, of the attractor underlying turbulent, periodic Poiseuille flow at a pressure-gradient Reynolds number of 3200 is calculated, on the basis of a coarse-grained (16x33x8) numerical solution, to be approximately 352. Comparison of Liapunov exponent spectra from this and a higher-resolution (16x33x16) simulation on the same spatial domain shows these spectra to have a universal shape when properly scaled. On the basis of these scaling properties, and a partial exponent spectrum from a still higher-resolution (32x33x32) simulation, it is argued that the actual dimension of the attractor underlying motion of the given computational domain is approximately 780. It is suggested that this periodic turbulent shear flow is deterministic chaos, and that a strange attractor does underly solutions to the Navier-Stokes equations in such flows.
Keefe, Laurence↗