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At least 1,297 records · Page 72

A direct approach to estimate the anisotropy of protein structures from small-angle X-ray scattering

In the field of small-angle X-ray scattering (SAXS), the task of estimating the size of particles in solution is usually synonymous with the Guinier plot. The approximation behind this plot, developed by Guinier in 1939, provides a simple yet accurate characterization of the scattering behavior of particles at low scattering angle or momentum transfer q , together with a computationally efficient way of inferring their radii of gyration R G . Moreover, this approximation is valid beyond spherical scatterers, making its use ubiquitous in the SAXS world. However, when it is important to estimate further particle characteristics, such as the anisotropy of the scatterer's shape, no similar or extended approximations are available. Existing tools to characterize the shape of scatterers rely either on prior knowledge of the scatterers' geometry or on iterative procedures to infer the particle shape ab initio . In this work, a low-angle approximation of the scattering intensity I ( q ) for ellipsoids of revolution is developed and it is shown how the size and anisotropy information can be extracted from the parameters of that approximation. The goal of the approximation is not to estimate a particle's full structure in detail, and thus this approach will be less accurate than well known iterative and ab initio reconstruction tools available in the literature. However, it can be considered as an extension of the Guinier approximation and used to generate initial estimates for the aforementioned iterative techniques, which usually rely on R G and D max for initialization. This formulation also demonstrates that nonlinearity in the Guinier plot can arise from anisotropy in the scattering particles. Beyond ideal ellipsoids of revolution, it is shown that this approximation can be used to estimate the size and shape of molecules in solution, in both computational and experimental scenarios. The limits of the approach are discussed and the impact of a particle's anisotropy in the Guinier estimate of R G is assessed.

catalysis (homogeneous), catalysis (heterogeneous)↗

Efficient Reformulation of Linear and Nonlinear Solid-Phase Diffusion in Lithium-ion Battery Models using Symmetric Polynomials: Mass Conservation and Computational Efficiency

Lithium-ion batteries are typically modeled using porous electrode theory coupled with various transport and reaction mechanisms, along with suitable discretization or approximations for the solid-phase diffusion equation. The solid-phase diffusion equation represents the main computational burden for typical pseudo-2-dimensional (p2D) models since these equations in the pseudo r -dimension must be solved at each point in the computational grid. This substantially increases the complexity of the model as well as the computational time. Traditional approaches towards simplifying solid-phase diffusion possess certain significant limitations, especially in modeling emerging electrode materials which involve phase changes and variable diffusivities. A computationally efficient representation for solid-phase diffusion is discussed in this paper based on symmetric polynomials using Orthogonal Collocation and Galerkin formulation (weak form). A systematic approach is provided to increase the accuracy of the approximation (p form in finite element methods) to enable efficient simulation with a minimal number of semi-discretized equations, ensuring mass conservation even for non-linear diffusion problems involving variable diffusivities. These methods are then demonstrated by incorporation into the full p2D model, illustrating their advantages in simulating high C-rates and short-time dynamic operation of Lithium-ion batteries.

25 ENERGY STORAGE↗

An improved multipole approximation for self-gravity and its importance for core-collapse supernova simulations

Self-gravity computation by multipole expansion is a common approach in problems such as core-collapse and Type Ia supernovae, where single large condensations of mass must be treated. The standard formulation of multipole self-gravity in arbitrary coordinate systems suffers from two significant sources of error, which we correct in the formulation presented in this article. The first source of error is due to the numerical approximation that effectively places grid cell mass at the central point of the cell, then computes the gravitational potential at that point, resulting in a convergence failure of the multipole expansion. We describe a new scheme that avoids this problem by computing gravitational potential at cell faces. The second source of error is due to sub-optimal choice of location for the expansion center, which results in angular power at high multipole l values in the gravitational field, requiring a high—and expensive—value of multipole cutoff l {sub max}. By introducing a global measure of angular power in the gravitational field, we show that the optimal coordinate for the expansion is the square-density-weighted mean location. We subject our new multipole self-gravity algorithm, implemented in the FLASH simulation framework, to two rigorous test problems: MacLaurin spheroids for which exact analytic solutions are known, and core-collapse supernovae. We show that key observables of the core-collapse simulations, particularly shock expansion, proto-neutron star motion, and momentum conservation, are extremely sensitive to the accuracy of the multipole gravity, and the accuracy of their computation is greatly improved by our reformulated solver.

79 ASTRONOMY AND ASTROPHYSICS↗

Surface hopping with a manifold of electronic states. I. Incorporating surface-leaking to capture lifetimes

We investigate the incorporation of the surface-leaking (SL) algorithm into Tully’s fewest-switches surface hopping (FSSH) algorithm to simulate some electronic relaxation induced by an electronic bath in conjunction with some electronic transitions between discrete states. The resulting SL-FSSH algorithm is benchmarked against exact quantum scattering calculations for three one-dimensional model problems. The results show excellent agreement between SL-FSSH and exact quantum dynamics in the wide band limit, suggesting the potential for a SL-FSSH algorithm. Discrepancies and failures are investigated in detail to understand the factors that will limit the reliability of SL-FSSH, especially the wide band approximation. Considering the easiness of implementation and the low computational cost, we expect this method to be useful in studying processes involving both a continuum of electronic states (where electronic dynamics are probabilistic) and processes involving only a few electronic states (where non-adiabatic processes cannot ignore short-time coherence)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Stochastic GW -GPU: Rapid Quasi-Particle Energies for Molecules beyond 10,000 Atoms

StochasticGW is a code for computing accurate quasi-particle (QP) energies of molecules and material systems in the GW approximation. StochasticGW utilizes the stochastic Resolution of the Identity (sROI) technique to enable a massively parallel implementation with computational costs that scale semilinearly with system size, allowing the method to access systems with tens of thousands of electrons. Here, we introduce a new implementation, StochasticGW-GPU, for which the main bottleneck steps have been ported to GPUs and give substantial performance improvements over previous versions of the code. We showcase the new code by computing band gaps of hydrogenated silicon clusters (Si x H y ) containing up to 10,001 atoms and 35,144 electrons, and we obtain individual QP energies with a statistical precision of better than ±0.03 eV with times-to-solution of less than 1 h.

Thomas, Phillip S. [Lawrence Berkeley National Lab↗

Large Deviations for Gaussian Diffusions with Delay

Dynamical systems driven by nonlinear delay SDEs with small noise can exhibit important rare events on long timescales. When there is no delay, classical large deviations theory quantifies rare events such as escapes from metastable fixed points. Near such fixed points, one can approximate nonlinear delay SDEs by linear delay SDEs. Here, we develop a fully explicit large deviations framework for (necessarily Gaussian) processes X{sub t} driven by linear delay SDEs with small diffusion coefficients. Our approach enables fast numerical computation of the action functional controlling rare events for X{sub t} and of the most likely paths transiting from X{sub 0}=p to X{sub T}=q. Via linear noise local approximations, we can then compute most likely routes of escape from metastable states for nonlinear delay SDEs. We apply our methodology to the detailed dynamics of a genetic regulatory circuit, namely the co-repressive toggle switch, which may be described by a nonlinear chemical Langevin SDE with delay.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Feynman diagrams for matter wave interferometry

We introduce a new theoretical framework based on Feynman diagrams to compute phase shifts in matter wave interferometry. The method allows for analytic computation of higher order quantum corrections, beyond the traditional semi-classical approximation. These additional terms depend on the finite size of the initial matter wavefunction and/or have higher order dependence on ℏ. We apply the method to compute the response of matter wave interferometers to power law potentials and potentials with an arbitrary spatial dependence. The analytic expressions are validated by comparing to numerical simulations, and estimates are provided for the scale of the quantum corrections to the phase shift response to the gravitational field of the earth, anharmonic trapping potentials, and gravitational fields from local proof masses. We also find that for certain experimentally feasible parameters, these corrections are large enough to be measured and could lead to systematic errors if they are not mitigated. We find that to first order in a spatially dependent potential, quantum corrections vanish when the initial matter wavepacket has spherical symmetry and the potential satisfies Laplace's equation. We anticipate these quantum corrections will be especially important for trapped matter wave interferometers and for free-space matter wave interferometers in the presence of proof masses. These interferometers are becoming increasingly sensitive tools for mobile inertial sensing, gravity surveying, tests of gravity and its interplay with quantum mechanics, and searches for dark energy.

Glick, Jonah [Northwestern U.; Fermilab] (ORCID:00↗

DiaMonD: An Integrated Multifaceted Approach to Mathematics at the Interfaces of Data, Models, and Decisions

The major goal of the project was to invent, analyze, implement, and apply new algorithms to speed up the computational simulation of complex systems in settings in which multiple simulations are needed. The main efforts we undertook are as follows: 1. Develop novel reduced order methods to reduce the costs of simulations, especially in settings (e.g., UQ, inference, optimization and control) for which numerous simulation are needed and also for nonlocal problems (e.g., fractional derivative, anomalous diffusion, nonlocal mechanics) for which lack of sparsity results in more expensive full-order simulation than encountered in partial differential equations settings; rigorous analyses as well as computational tests were carried out, 2. Develop multifidelity methods based on the usage of a variety of models having different fidelities and different costs to accelerate simulations again in settings where numerous simulations are needed or are especially expensive; rigorous analyses as well as computational tests were carried out, 3. Develop ensemble methods to reduced the costs of simulations again in settings where numerous simulations are needed or are especially expensive; rigorous analyses as well as computational tests were carried out, and 4. Analyze a model for Richardson pair dispersion in turbulent flows and develop discretization methods for the efficient and accurate approximations of the solution of the model; rigorous analyses as well as computational tests were carried out.

97 MATHEMATICS AND COMPUTING↗

Boltzmann-conserving classical dynamics in quantum time-correlation functions: “Matsubara dynamics”

We show that a single change in the derivation of the linearized semiclassical-initial value representation (LSC-IVR or “classical Wigner approximation”) results in a classical dynamics which conserves the quantum Boltzmann distribution. We rederive the (standard) LSC-IVR approach by writing the (exact) quantum time-correlation function in terms of the normal modes of a free ring-polymer (i.e., a discrete imaginary-time Feynman path), taking the limit that the number of polymer beads N → ∞, such that the lowest normal-mode frequencies take their “Matsubara” values. The change we propose is to truncate the quantum Liouvillian, not explicitly in powers of ħ{sup 2} at ħ{sup 0} (which gives back the standard LSC-IVR approximation), but in the normal-mode derivatives corresponding to the lowest Matsubara frequencies. The resulting “Matsubara” dynamics is inherently classical (since all terms O(ħ{sup 2}) disappear from the Matsubara Liouvillian in the limit N → ∞) and conserves the quantum Boltzmann distribution because the Matsubara Hamiltonian is symmetric with respect to imaginary-time translation. Numerical tests show that the Matsubara approximation to the quantum time-correlation function converges with respect to the number of modes and gives better agreement than LSC-IVR with the exact quantum result. Matsubara dynamics is too computationally expensive to be applied to complex systems, but its further approximation may lead to practical methods.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Linear-scaling time-dependent density-functional theory beyond the Tamm-Dancoff approximation: Obtaining efficiency and accuracy with in situ optimised local orbitals

We present a solution of the full time-dependent density-functional theory (TDDFT) eigenvalue equation in the linear response formalism exhibiting a linear-scaling computational complexity with system size, without relying on the simplifying Tamm-Dancoff approximation (TDA). The implementation relies on representing the occupied and unoccupied subspaces with two different sets of in situ optimised localised functions, yielding a very compact and efficient representation of the transition density matrix of the excitation with the accuracy associated with a systematic basis set. The TDDFT eigenvalue equation is solved using a preconditioned conjugate gradient algorithm that is very memory-efficient. The algorithm is validated on a small test molecule and a good agreement with results obtained from standard quantum chemistry packages is found, with the preconditioner yielding a significant improvement in convergence rates. The method developed in this work is then used to reproduce experimental results of the absorption spectrum of bacteriochlorophyll in an organic solvent, where it is demonstrated that the TDA fails to reproduce the main features of the low energy spectrum, while the full TDDFT equation yields results in good qualitative agreement with experimental data. Furthermore, the need for explicitly including parts of the solvent into the TDDFT calculations is highlighted, making the treatment of large system sizes necessary that are well within reach of the capabilities of the algorithm introduced here. Finally, the linear-scaling properties of the algorithm are demonstrated by computing the lowest excitation energy of bacteriochlorophyll in solution. The largest systems considered in this work are of the same order of magnitude as a variety of widely studied pigment-protein complexes, opening up the possibility of studying their properties without having to resort to any semiclassical approximations to parts of the protein environment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Hybrid framework for the simulation of stochastic chemical kinetics

Stochasticity plays a fundamental role in various biochemical processes, such as cell regulatory networks and enzyme cascades. Isothermal, well-mixed systems can be modelled as Markov processes, typically simulated using the Gillespie Stochastic Simulation Algorithm (SSA) [25]. While easy to implement and exact, the computational cost of using the Gillespie SSA to simulate such systems can become prohibitive as the frequency of reaction events increases. This has motivated numerous coarse-grained schemes, where the “fast” reactions are approximated either using Langevin dynamics or deterministically. While such approaches provide a good approximation when all reactants are abundant, the approximation breaks down when one or more species exist only in small concentrations and the fluctuations arising from the discrete nature of the reactions become significant. This is particularly problematic when using such methods to compute statistics of extinction times for chemical species, as well as simulating non-equilibrium systems such as cell-cycle models in which a single species can cycle between abundance and scarcity. In this paper, a hybrid jump-diffusion model for simulating well-mixed stochastic kinetics is derived. It acts as a bridge between the Gillespie SSA and the chemical Langevin equation. For low reactant reactions the underlying behaviour is purely discrete, while purely diffusive when the concentrations of all species are large, with the two different behaviours coexisting in the intermediate region. A bound on the weak error in the classical large volume scaling limit is obtained, and three different numerical discretisations of the jump-diffusion model are described. The benefits of such a formalism are illustrated using computational examples.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Rosseland and Flux Mean Opacities for Compton Scattering

Rosseland mean opacity plays an important role in theories of stellar evolution and X-ray burst models. In the high-temperature regime, when most of the gas is completely ionized, the opacity is dominated by Compton scattering. Our aim here is to critically evaluate previous works on this subject and to compute the exact Rosseland mean opacity for Compton scattering over a broad range of temperature and electron degeneracy parameter. We use relativistic kinetic equations for Compton scattering and compute the photon mean free path as a function of photon energy by solving the corresponding integral equation in the diffusion limit. As a byproduct we also demonstrate the way to compute photon redistribution functions in the case of degenerate electrons. We then compute the Rosseland mean opacity as a function of temperature and electron degeneracy and present useful approximate expressions. We compare our results to previous calculations and find a significant difference in the low-temperature regime and strong degeneracy. We then proceed to compute the flux mean opacity in both free-streaming and diffusion approximations, and show that the latter is nearly identical to the Rosseland mean opacity. We also provide a simple way to account for the true absorption in evaluating the Rosseland and flux mean opacities.

79 ASTRONOMY AND ASTROPHYSICS↗

Bayesian Monte-Carlo Evaluation Framework of Differential and Integral Data [Slides]

This presentation discusses the Bayesian Monte Carlo evaluation framework of differential and integral data, specifically in relation to two methods that are based on Bayes theorem, which assumes that all PDFs are normal (Gaussian) and that they use a linear approximation for IBEs. The presentation states that basic components of the MC evaluation framework include the computation of random MC ensemble from ENDF File 32, the simulation of IBEs and R-matrix cross section compared to experimental data, and the computation of weighted averages. It also states that the application to U-233 indicates deviation from the conventional linear approximation. In conclusion, evaluation framework will require MCMC method e.g., Metropolis-Hastings (M.-H.).

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Generation and focusing of electron beams with initial transverse-longitudinal correlation

In charged particle beams, one of the roles played by space charge is to couple the transverse and longitudinal dynamics of the beam. This can lead to very complex phenomena which are generally studied using computer simulations. However, in some cases models based on phenomenological or analytic approximations can provide valuable insight into the system behavior. In this paper, we employ such approximations to investigate the conditions under which all the slices of a space charge dominated electron beam with slowly varying current could be focused to a waist with the same radius and at the same location, independent of slice current, and show that this can be accomplished approximately if the initial transverse-longitudinal correlation introduced onto the beam by the electron gun is chosen to compensate for the transverse-longitudinal correlation introduced onto the beam in the drift section. The validity of our approximations is assessed by use of progressively more realistic calculations. We also consider several design elements of electron guns that affect the initial correlations in the beams they generate.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Linear embedding of nonlinear dynamical systems and prospects for efficient quantum algorithms

The simulation of large nonlinear dynamical systems, including systems generated by discretization of hyperbolic partial differential equations, can be computationally demanding. Such systems are important in both fluid and kinetic computational plasma physics. This motivates exploring whether a future error-corrected quantum computer could perform these simulations more efficiently than any classical computer. In this work, we describe a method for mapping any finite nonlinear dynamical system to an infinite linear dynamical system (embedding) and detail three specific cases of this method that correspond to previously studied mappings. Then we explore an approach for approximating the resulting infinite linear system with finite linear systems (truncation). Using a number of qubits only logarithmic in the number of variables of the nonlinear system, a quantum computer could simulate truncated systems to approximate output quantities if the nonlinearity is sufficiently weak. Other aspects of the computational efficiency of the three detailed embedding strategies are also discussed.

97 MATHEMATICS AND COMPUTING↗

FINITE-ELEMENT DISTORED WAVE BORN APPROXIMATION FOR SURFACE SCATTERING

FE-DWBA is a software package that computes the x-ray scattering patterns of objects that locate on a surface or buried next to a surface, such as the nano-circuits and nano-patterns of the mask used in the extreme ultraviolet lithography. It can incorporate the dynamical scattering effect (photons scattered multiple times), which is predominant in surface scattering and yield high-fidelity scattering patterns. The application includes surface imaging using x-rays, and critical dimension determination for semiconductor manufacturing.

HU, MAIOQI↗

Thermal Effects on Far-Field Distributed Acoustic Strain-Rate Sensors

Summary Fiber-optic cables cemented outside of the casing of an unconventional well measure crosswell strain changes during fracturing of neighboring wells with low-frequency distributed acoustic sensing (LF-DAS). As a hydraulic fracture intersects an observation well instrumented with fiber-optic cables, the fracture fluid injected at ambient temperatures can cool a section of the sensing fiber. Often, LF-DAS and distributed temperature sensing (DTS) cables are run in tandem, enabling the detection of such cooling events. The increasing use of LF-DAS for characterizing unconventional hydraulic fracture completions demands an investigation of the effects of temperature on the measured strain response by LF-DAS. Researchers have demonstrated that LF-DAS can be used to extract the temporal derivative of temperature for use as a differential-temperature-gradient sensor. However, differential-temperature-gradient sensing is predicated on the ability to filter strain components out of the optical signal. In this work, beginning with an equation for optical phase shift of LF-DAS signals, a model relating strain, temperature, and optical phase shift is explicitly developed. The formula provides insights into the relative strength of strain and temperature effects on the phase shift. The uncertainty in the strain-rate measurements due to thermal effects is estimated. The relationship can also be used to quantify uncertainties in differential-temperature-gradient sensors due to strain perturbations. Additionally, a workflow is presented to simulate the LF-DAS response accounting for both strain and temperature effects. Hydraulic fracture geometries are generated with a 3D fracture simulator for a multistage unconventional completion. The fracture width distributions are imported by a displacement discontinuity method (DDM) program to compute the strain rates along an observation well. An analytic model is used to approximate the temperature in the fracture. Using the derived formulae for optical phase shift, the model outputs are then used to compute the LF-DAS response at a fiber-optic cable, enabling the generation of waterfall plots including both strain and thermal effects. The model results suggest that before, during, and immediately following a fracture intersecting a well instrumented with fiber, the strain on the fiber drives the LF-DAS signal. However, at later times, as completion fluid cools the observation well, the temperature component of the LF-DAS signal can be equal to or exceed the strain component. The modeled results are compared to a published field case in an attempt to enhance the interpretation of LF-DAS waterfall plots. Finally, we propose a sensing configuration to identify the events when “wet fractures” (fractures with fluids) intersect the observation well.

Engineering↗