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36 records · Page 2

PTM‐Psi : A python package to facilitate the computational investigation of p ost‐ t ranslational m odification on p rotein s tructures and their i mpacts on dynamics and functions

Abstract Post‐translational modification (PTM) of a protein occurs after it has been synthesized from its genetic template, and involves chemical modifications of the protein's specific amino acid residues. Despite of the central role played by PTM in regulating molecular interactions, particularly those driven by reversible redox reactions, it remains challenging to interpret PTMs in terms of protein dynamics and function because there are numerous combinatorially enormous means for modifying amino acids in response to changes in the protein environment. In this study, we provide a workflow that allows users to interpret how perturbations caused by PTMs affect a protein's properties, dynamics, and interactions with its binding partners based on inferred or experimentally determined protein structure. This Python‐based workflow, called PTM‐Psi , integrates several established open‐source software packages, thereby enabling the user to infer protein structure from sequence, develop force fields for non‐standard amino acids using quantum mechanics, calculate free energy perturbations through molecular dynamics simulations, and score the bound complexes via docking algorithms. Using the S ‐nitrosylation of several cysteines on the GAP2 protein as an example, we demonstrated the utility of PTM‐Psi for interpreting sequence–structure–function relationships derived from thiol redox proteomics data. We demonstrate that the S ‐nitrosylated cysteine that is exposed to the solvent indirectly affects the catalytic reaction of another buried cysteine over a distance in GAP2 protein through the movement of the two ligands. Our workflow tracks the PTMs on residues that are responsive to changes in the redox environment and lays the foundation for the automation of molecular and systems biology modeling.

59 BASIC BIOLOGICAL SCIENCES↗

Quandary

Quandary numerically simulates and optimizes the time-evolution of open quantum systems. The underlying dynamics are modelled by Lindblad's master equation, a linear ordinary differential equation (ODE) describing quantum systems interacting with the environment. Quandary solves this ODE numerically by applying a time-stepping integration scheme, and utilizes a gradient-based optimization approach to determine optimal control pulses that drive the quantum system to a desired target state. Two optimization objectives are considered: (a) Unitary gate optimization that finds controls to realize a unitary gate transformation, and (b) optimal reset that aims to drive the quantum system to the ground states. Gradient-based optimization schemes utilizing Petsc's Tao optimization package are applied to generate control pulses that minimize the respective measure. To evaluate the gradient of the objective function, the discrete adjoint method is used while leveraging techniques from Algorithmic Differentiation to produce exact and consistent gradients. To mitigate excessive execution run times, the software can be build together with the XBraid software library which provides a parallelization strategy to distribute the time-evolution of the underlying dynamics onto multiple processor.

Petersson, NilsA.↗

Perturbative second-order optical susceptibility of bulk materials: a symmetry-enforced return to non-orthogonal localized basis sets

The second-order optical susceptibility of semiconductors $\chi^{(2)}_{ijk}(-2\omega;\omega,\omega)$ finds application in metrology, spectroscopy, telecommunications, material characterization, and quantum information. Pioneering calculations of $\chi^{(2)}_{ijk}(-2\omega;\omega,\omega)$ utilized non-orthogonal Gaussian orbitals centered at atoms. That formulation transitioned into plane-wave-based algorithms as time went by. As of late, nevertheless, multiple tools for calculating optical susceptibilities have recast the problem using Wannier (i.e. localized) orbitals, making a comeback onto frameworks based on localized basis sets. Here, in this work, we present an approach for calculating $\chi^{(2)}_{ijk}(-2\omega;\omega,\omega)$ reliant on numerical pseudo-atomic orbitals (PAOs) within perturbation theory in the velocity gauge. Its salient feature is a calculation of ‘Slater–Koster-like’ two-center integrals of the momentum operator in between PAOs identified by symmetry. The approach was successfully tested on paradigmatic cubic silicon carbide (3C-SiC) and gallium arsenide, for which linear responses are contributed as well.

Huamán, Angiolo [Univ. of Arkansas, Fayetteville, ↗

Nyström type exponential integrators for strongly magnetized charged particle dynamics

Solving for charged particle motion in electromagnetic fields (i.e. the particle pushing problem) is a computationally intensive component of particle-in-cell (PIC) methods for plasma physics simulations. This task is especially challenging when the plasma is strongly magnetized due numerical stiffness arising from the wide range of time scales between highly oscillatory gyromotion and long term macroscopic behavior. A promising approach to solve these problems is by a class of methods known as exponential integrators that can solve linear problems exactly and are A-stable. This work extends the standard exponential integration framework to derive Nyström-type exponential integrators that integrates the Newtonian equations of motion as a second-order differential equation directly. In particular, we derive second-order and third-order Nyström-type exponential integrators for strongly magnetized particle pushing problems. Numerical experiments show that the Nyström-type exponential integrators exhibit significant improvement in computation speed over the standard exponential integrators.

general physics↗

Approximating the linear response of physical chaos

Abstract Parametric derivatives of statistics are highly desired quantities in prediction, design optimization and uncertainty quantification. In the presence of chaos, the rigorous computation of these quantities is certainly possible, but mathematically complicated and computationally expensive. Based on Ruelle’s formalism, this paper shows that the sophisticated linear response algorithm can be dramatically simplified in higher-dimensional systems featuring statistical homogeneity in the physical space. We argue that the contribution of the SRB (Sinai–Ruelle–Bowen) measure gradient, which is an integral yet the most cumbersome part of the full algorithm, is negligible if the objective function is appropriately aligned with unstable manifolds. This abstract condition could potentially be satisfied by a vast family of real-world chaotic systems, regardless of the physical meaning and mathematical form of the objective function and perturbed parameter. We demonstrate several numerical examples that support these conclusions and that present the use and performance of a simplified linear response algorithm. In the numerical experiments, we consider physical models described by differential equations, including Lorenz 96 and Kuramoto–Sivashinsky.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Matrix-Model Simulations Using Quantum Computing, Deep Learning, and Lattice Monte Carlo

Matrix quantum mechanics plays various important roles in theoretical physics, such as a holographic description of quantum black holes, and it underpins the only practical numerical approach to the study of complex high-dimensional supergravity theories. Understanding quantum black holes and the role of entanglement in a holographic setup is of paramount importance for the realization of a quantum theory of gravity. Moreover, a complete numerical understanding of the holographic duality and the emergence of geometric space-time features from microscopic degrees of freedom could pave the way for new discoveries in quantum information science. Euclidean lattice Monte Carlo simulations are the de facto numerical tool for understanding the spectrum of large matrix models and have been used to test the holographic duality. However, they are not tailored to extract dynamical properties or even the quantum wave function of the ground state of matrix models. Quantum computing and deep learning provide potentially useful approaches to study the dynamics of matrix quantum mechanics. If successful in the context of matrix models, these rapidly improving numerical techniques could become the new Swiss army knife of quantum gravity practitioners. In this paper, we perform the first systematic survey for quantum computing and deep-learning approaches to matrix quantum mechanics, comparing them to lattice Monte Carlo simulations. These provide baseline benchmarks before addressing more complicated problems. In particular, we test the performance of each method by calculating the low-energy spectrum.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Anisotropic fluid dynamical simulations of heavy-ion collisions

We present VAH, a (3+1)–dimensional simulation that evolves the far-from-equilibrium quark-gluon plasma produced in ultrarelativistic heavy-ion collisions with anisotropic fluid dynamics. We solve the hydrodynamic equations on an Eulerian grid using the Kurganov–Tadmor algorithm in combination with a new adaptive Runge–Kutta method. Our numerical scheme allows us to start the simulation soon after the nuclear collision, largely avoiding the need to integrate it with a separate pre-equilibrium dynamics module. We test the code's performance by simulating on the Eulerian grid conformal and non-conformal Bjorken flow as well as conformal Gubser flow, whose (0+1)–dimensional solutions are precisely known. Finally, we compare non-conformal anisotropic hydrodynamics to second-order viscous hydrodynamics in central Pb+Pb collisions and find that the former's longitudinal flow profile responds more consistently to the fluid's gradients along the spacetime rapidity direction.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Ab Initio Direct Dynamics

The reactivity and dynamics of molecular systems can be explored computationally by classical trajectory calculations. The traditional approach involves fitting a functional form of a potential energy surface (PES) to the energies from a large number of electronic structure calculations and then integrating numerous trajectories on this fitted PES to model the molecular dynamics. The ever-decreasing cost of computing and continuing advances in computational chemistry software have made it possible to use electronic structure calculations directly in molecular dynamics simulations without first having to construct a fitted PES. In this “on-the-fly” approach, every time the energy and its derivatives are needed for the integration of the equations of motion, they are obtained directly from quantum chemical calculations. This approach started to become practical in the mid-1990s as a result of increased availability of inexpensive computer resources and improved computational chemistry software. The application of direct dynamics calculations has grown rapidly over the last 25 years and would require a lengthy review article. The present Account is limited to some of our contributions to methods development and various applications. To improve the efficiency of direct dynamics calculations, we developed a Hessian-based predictor-corrector algorithm for integrating classical trajectories. Hessian updating made this even more efficient. Furthermore, this approach was also used to improve algorithms for following the steepest descent reaction paths. For larger molecular systems, we developed an extended Lagrangian approach in which the electronic structure is propagated along with the molecular structure. Strong field chemistry is a rapidly growing area, and to improve the accuracy of molecular dynamics in intense laser fields, we included the time-varying electric field in a novel predictor-corrector trajectory integration algorithm. Since intense laser fields can excite and ionize molecules, we extended our studies to include electron dynamics. Specifically, we developed code for time-dependent configuration interaction electron dynamics to simulate strong field ionization by intense laser pulses. Our initial application of ab initio direct dynamics in 1994 was to CH 2 O → H 2 + CO; the calculated vibrational distributions in the products were in very good agreement with experiment. In the intervening years, we have used direct dynamics to explore energy partitioning in various dissociation reactions, unimolecular dissociations yielding three fragments, reactions with branching after the transition state, nonstatistical dynamics of chemically activated molecules, dynamics of molecular fragmentation by intense infrared laser pulses, selective activation of specific dissociation channels by aligned intense infrared laser fields, angular dependence of strong field ionization, and simulation of sequential double ionization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Tensor network representation of non-abelian gauge theory coupled to reduced staggered fermions

We show how to construct a tensor network representation of the path integral for reduced staggered fermions coupled to a non-abelian gauge field in two dimensions. The resulting formulation is both memory and computation efficient because reduced staggered fermions can be represented in terms of a minimal number of tensor indices while the gauge sector can be approximated using Gaussian quadrature with a truncation. Numerical results obtained using the Grassmann TRG algorithm are shown for the case of SU(2) lattice gauge theory and compared to Monte Carlo results.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

A machine learning approach for efficient multi-dimensional integration

Many physics problems involve integration in multi-dimensional space whose analytic solution is not available. The integrals can be evaluated using numerical integration methods, but it requires a large computational cost in some cases, so an efficient algorithm plays an important role in solving the physics problems. We propose a novel numerical multi-dimensional integration algorithm using machine learning (ML). After training a ML regression model to mimic a target integrand, the regression model is used to evaluate an approximation of the integral. Then, the difference between the approximation and the true answer is calculated to correct the bias in the approximation of the integral induced by ML prediction errors. Because of the bias correction, the final estimate of the integral is unbiased and has a statistically correct error estimation. Three ML models of multi-layer perceptron, gradient boosting decision tree, and Gaussian process regression algorithms are investigated. The performance of the proposed algorithm is demonstrated on six different families of integrands that typically appear in physics problems at various dimensions and integrand difficulties. The results show that, for the same total number of integrand evaluations, the new algorithm provides integral estimates with more than an order of magnitude smaller uncertainties than those of the VEGAS algorithm in most of the test cases.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Emergence of a Spin Microemulsion in Spin-Orbit Coupled Bose-Einstein Condensates

We report the first numerical prediction of a “spin microemulsion”—a phase with undulating spin domains resembling classical bicontinuous oil-water-surfactant emulsions—in two-dimensional systems of spinor Bose-Einstein condensates with isotropic Rashba spin-orbit coupling. Using field-theoretic numerical simulations, we investigated the melting of a low-temperature stripe phase with supersolid character and find that the stripes lose their superfluidity at elevated temperature and undergo a Kosterlitz-Thouless-like transition into a spin microemulsion. Momentum distribution calculations highlight a thermally broadened occupation of the Rashba circle of low-energy states with macroscopic and isotropic occupation around the ring. Here, we provide a finite-temperature phase diagram that positions the emulsion as an intermediate, structured isotropic phase with residual quantum character before transitioning at higher temperature into a structureless normal fluid.

Finite temperature field theory↗

Fast and Universal Kohn-Sham Density Functional Theory Algorithm for Warm Dense Matter to Hot Dense Plasma

Understanding many processes, e.g., fusion experiments, planetary interiors, and dwarf stars, depends strongly on microscopic physics modeling of warm dense matter and hot dense plasma. This complex state of matter consists of a transient mixture of degenerate and nearly free electrons, molecules, and ions. This regime challenges both experiment and analytical modeling, necessitating predictive ab initio atomistic computation, typically based on quantum mechanical Kohn-Sham density functional theory (KS-DFT). However, cubic computational scaling with temperature and system size prohibits the use of DFT through much of the warm dense matter regime. A recently developed stochastic approach to KS-DFT can be used at high temperatures, with the exact same accuracy as the deterministic approach, but the stochastic error can converge slowly and it remains expensive for intermediate temperatures (< 50 eV). Here we have developed a universal mixed stochastic-deterministic algorithm for DFT at any temperature. This approach leverages the physics of KS-DFT to seamlessly integrate the best aspects of these different approaches. We demonstrate that this method significantly accelerated self-consistent field calculations for temperatures from 3 to 50 eV, while producing stable molecular dynamics and accurate diffusion coefficients.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Accurately simulating nine-dimensional phase space of relativistic particles in strong fields

Next-generation high-power laser systems that can be focused to ultra-high intensities exceeding 10 23 W/cm 2 are enabling new physics regimes and applications. The physics of how these lasers interact with matter is highly nonlinear, relativistic, and can involve lowest-order quantum effects. The current tool of choice for modeling these interactions is the particle-in-cell (PIC) method. In the presence of strong electromagnetic fields, the motion of charged particles and their spin is affected by radiation reaction (either the semi-classical or the quantum limit). Standard (PIC) codes usually use Boris or similar operator-splitting methods to advance the particles in standard phase space. These methods have been shown to require very small time steps in the strong-field regime in order to obtain accurate results. In addition, some problems require tracking the spin of particles, which creates a nine-dimensional (9D) particle phase space, i.e., (x, u, s). Therefore, numerical algorithms that enable high-fidelity modeling of the 9D phase space in the strong-field regime (where both the spin and momentum evolution are affected by radiation reaction) are desired. Here we present a new particle pusher that works in 9D and 6D phase space (i.e., with and without spin) based on analytical rather than leapfrog solutions to the momentum and spin advance from the Lorentz force, together with the semi-classical form of radiation reaction in the Landau-Lifshitz equation and spin evolution given by the Bargmann-Michel-Telegdi equation. Analytical solutions for the position advance are also obtained, but these are not amenable to the staggering of space and time in standard PIC codes. These analytical solutions are obtained by assuming a locally uniform and constant electromagnetic field during a time step. The solutions provide the 9D phase space advance in terms of a particle's proper time, and a mapping is used to determine the proper time step duration for each particle as a function of the lab frame time step. Due to the analytical integration of particle trajectory and spin orbit, the constraint on the time step needed to resolve trajectories in ultra-high fields can be greatly reduced. The time step required in a PIC code for accurately advancing the fields may provide additional constraints. We present single-particle simulations to show that the proposed particle pusher can greatly improve the accuracy of particle trajectories in 6D or 9D phase space for given laser fields. We have implemented the new pusher into the PIC code Osiris. Example simulations show that the proposed pusher provides improvement for a given time step. A discussion on the numerical efficiency of the proposed pusher is also provided.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Small arms suppression project (LLNL final report)

US Special Operations Command (USSOCOM) was seeking a technological leap in small firearms weapon suppressor technology, because anticipated enemy capabilities are requiring the operators to have smaller detection cross sections to ensure the safe execution of missions. Suppressors have been developed almost exclusively through trial-and-error methods since the time of the original design by Hiram Maxim over one hundred years ago. Consequently USSOCOM deemed it prudent to perform a physicsbased study of weapon suppression to understand performance limits and possibly identify breakthrough technologies. Lawrence Livermore National Laboratory’s (LLNL’s) high performance production level computational tool called ALE3D (Arbitrary Lagrangian-Eulerian 3D and 2D) has unique physics models and numerical algorithms for modeling suppressor dynamics. The flexible and extendable code framework supports fully integrated hydrodynamics, heat transfer, solid and fluid dynamics, and chemistry that can be applied to simulating propellant-driven motion of a bullet down a gun barrel, the transfer of heat from the burning propellant to the barrel and suppressor, the chemistry of muzzle flash, and the shock/acoustic/optical signatures in the near-field. LLNL’s originally anticipated role was to augment ALE3D for this task, by developing the software and analysis methodologies specific to the simulation of blast and muzzle flash phenomena. It was believed that insights provided by our ALE3D simulations in tandem with a coordinated experimental component by our other team members from Oak Ridge National Laboratory (ORNL) and the U. S. Army Armament, Research, Development and Engineering Center (ARDEC), would have excellent prospects of yielding useful suppressor design improvements that could be transitioned to industry and utilized by US Special Operations Command. The three year effort has come to fruition with the development of revolutionary suppressor designs that far outperform any previous or current design by anyone outside this multi-lab team.

42 ENGINEERING↗

Numerical Evidence for Many-Body Localization in Two and Three Dimensions

Disorder and interactions can lead to the breakdown of statistical mechanics in certain quantum systems, a phenomenon known as many-body localization (MBL). Much of the phenomenology of MBL emerges from the existence of localized-bits, or l-bits, a set of conserved quantities that are spatially localized and binary (i.e., possess only ±1 eigenvalues). While MBL and l-bits are known to exist in one-dimensional systems, their existence in dimensions greater than one is a key open question. To tackle this question, we develop an algorithm that can find approximate binary l-bits in arbitrary dimensions by adaptively generating a basis of operators in which to represent the l-bit. We use the algorithm to study four models: the one-, two-, and three-dimensional disordered Heisenberg models and the two-dimensional disordered hard-core Bose-Hubbard model. For all four of the models studied, our algorithm finds high-quality l-bits at large disorder strength and rapid qualitative changes in the distributions of l-bits in particular ranges of disorder strengths, suggesting the existence of MBL transitions. Furthermore, these transitions in the one-dimensional Heisenberg model and two-dimensional Bose-Hubbard model coincide well with past estimates of the critical disorder strengths in these models which further validates the evidence of MBL-like behavior in the other two and three-dimensional models we examine. In addition to finding MBL-like behavior in higher dimensions, our algorithm can be used to probe MBL in various geometries and dimensionality.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Sparsity of the electron repulsion integral tensor using different localized virtual orbital representations in local second-order Møller–Plesset theory

Utilizing localized orbitals, local correlation theory can reduce the unphysically high system-size scaling of post-Hartree–Fock (post-HF) methods to linear scaling in insulating molecules. The sparsity of the four-index electron repulsion integral (ERI) tensor is central to achieving this reduction. For second-order Møller–Plesset theory (MP2), one of the simplest post-HF methods, only the (ia|jb) ERIs are needed, coupling occupied orbitals i, j and virtuals a, b. In this paper, we compare the numerical sparsity (called the “ragged list”) and two other approaches revealing the low-rank sparsity of the ERI. The ragged list requires only one set of (localized) virtual orbitals, and we find that the orthogonal valence virtual-hard virtual set of virtuals originally proposed by Subotnik et al. gives the sparsest ERI tensor. To further compress the ERI tensor, the pair natural orbital (PNO) type representation uses different sets of virtual orbitals for different occupied orbital pairs, while the occupied-specific virtual (OSV) approach uses different virtuals for each occupied orbital. Here, our results indicate that while the low-rank PNO representation achieves significant rank reduction, it also requires more memory than the ragged list. The OSV approach requires similar memory to that of the ragged list, but it involves greater algorithmic complexity. An approximation (called the “fixed sparsity pattern”) for solving the local MP2 equations using the numerically sparse ERI tensor is proposed and tested to be sufficiently accurate and to have highly controllable error. A low-scaling local MP2 algorithm based on the ragged list and the fixed sparsity pattern is therefore promising.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

nPINNs: nonlocal Physics-Informed Neural Networks for a parametrized nonlocal universal Laplacian operator. Algorithms and Applications

Physics-informed neural networks (PINNs) are effective in solving inverse problems based on differential and integro-differential equations with sparse, noisy, unstructured, and multifidelity data. PINNs incorporate all available information, including governing equations (reflecting physical laws), initial-boundary conditions, and observations of quantities of interest, into a loss function to be minimized, thus recasting the original problem into an optimization problem. In this paper, we extend PINNs to parameter and function inference for integral equations such as nonlocal Poisson and nonlocal turbulence models, and we refer to them as nonlocal PINNs (nPINNs). The contribution of the paper is three-fold. First, we propose a unified nonlocal Laplace operator, which converges to the classical Laplacian as one of the operator parameters, the nonlocal interaction radius δ goes to zero, and to the fractional Laplacian as δ goes to infinity. This universal operator forms a super-set of classical Laplacian and fractional Laplacian operators and, thus, has the potential to fit a broad spectrum of data sets. We provide theoretical convergence rates with respect to δ and verify them via numerical experiments. Second, we use nPINNs to estimate the two parameters, δ and α, characterizing the kernel of the unified operator. The strong non-convexity of the loss function yielding multiple (good) local minima reveals the occurrence of the operator mimicking phenomenon, that is, different pairs of estimated parameters could produce multiple solutions of comparable accuracy. Third, we propose another nonlocal operator with spatially variable order α(γ), which is more suitable for modeling turbulent Couette flow. Our results show that nPINNs can jointly infer this function as well as δ. More importantly, these parameters exhibit a universal behavior with respect to the Reynolds number, a finding that contributes to our understanding of nonlocal interactions in wall-bounded turbulence.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Semi-implicit method to solve compressible multiphase fluid flows without acoustic time step restrictions

A new 3D multiphase numerical capability is presented here for simulating multiphase flow regimes at all Mach numbers (M). The new method is a semi-implicit extension of the finite volume discrete equation method (DEM) of Chinnaya et al. (2004), which originally used explicit time-stepping. The capability is also developed to work with another extension of the DEM to moving grids for arbitrary Lagrangian-Eularian (ALE) methods detailed in Dunn (2011). Rather than solving all phase equations simultaneously, the DEM reduces the equations to a system of single-phase Riemann solves, where each phase has its own velocity and thermodynamic state. Exchanges between the phases are modeled through source terms accounting for the phase interactions. Furthermore, since the original multiphase scheme uses an explicit time-advancement scheme, it has time step restrictions dictated by the speed of sound, which limits the model's ability to simulate weakly compressible flows which typically need to be integrated for longer time periods. Here, we extend the current multiphase formulation by implementing a pressure-correcting step to enable implicit calculations and remove acoustic time step limitations. The new semi-implicit algorithm allows use of relatively large time steps compared to an explicit method. Validation and benefits of the new implicit time-step method are illustrated using several examples including weakly compressible flows and strong shock waves. The scheme presented here is general and may be used for a variety of applications which require capabilities for handling multiphase flow at a wide range of Mach numbers. However, the goal of this research is to simulate all stages of high energy explosions, including the shock formation (high Mach numbers) and evolution of the buoyant cloud (low Mach numbers).

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗