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At least 1,603 records · Page 89

An adaptive multi-level simulation algorithm for stochastic biological systems

Discrete-state, continuous-time Markov models are widely used in the modeling of biochemical reaction networks. Their complexity often precludes analytic solution, and we rely on stochastic simulation algorithms (SSA) to estimate system statistics. The Gillespie algorithm is exact, but computationally costly as it simulates every single reaction. As such, approximate stochastic simulation algorithms such as the tau-leap algorithm are often used. Potentially computationally more efficient, the system statistics generated suffer from significant bias unless tau is relatively small, in which case the computational time can be comparable to that of the Gillespie algorithm. The multi-level method [Anderson and Higham, “Multi-level Monte Carlo for continuous time Markov chains, with applications in biochemical kinetics,” SIAM Multiscale Model. Simul. 10(1), 146–179 (2012)] tackles this problem. A base estimator is computed using many (cheap) sample paths at low accuracy. The bias inherent in this estimator is then reduced using a number of corrections. Each correction term is estimated using a collection of paired sample paths where one path of each pair is generated at a higher accuracy compared to the other (and so more expensive). By sharing random variables between these paired paths, the variance of each correction estimator can be reduced. This renders the multi-level method very efficient as only a relatively small number of paired paths are required to calculate each correction term. In the original multi-level method, each sample path is simulated using the tau-leap algorithm with a fixed value of τ. This approach can result in poor performance when the reaction activity of a system changes substantially over the timescale of interest. By introducing a novel adaptive time-stepping approach where τ is chosen according to the stochastic behaviour of each sample path, we extend the applicability of the multi-level method to such cases. We demonstrate the efficiency of our method using a number of examples.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Analysis of sparse recovery for Legendre expansions using envelope bound

We provide novel sufficient conditions for the uniform recovery of sparse Legendre expansions using ℓ 1 minimization, where the sampling points are drawn according to orthogonalization (uniform) measure. So far, conditions of the form m ≳ Θ 2 s x log factors have been relied on to determine the minimum number of samples m that guarantees successful reconstruction of s-sparse vectors when the measurement matrix is associated to an orthonormal system. However, in case of sparse Legendre expansions, the uniform bound Θ of Legendre systems is so high that these conditions are unable to provide meaningful guarantees. Here, in this paper, we present an analysis which employs the envelop bound of all Legendre polynomials instead, and prove a new recovery guarantee for s-sparse Legendre expansions, m ≳ Θs 2 x log factors, which is independent of Θ. Arguably, this is the first recovery condition established for orthonormal systems without assuming the uniform boundedness of the sampling matrix. The key ingredient of our analysis is an extension of chaining arguments, recently developed in Bourgain and Chkifa et al., to handle the envelope bound. Furthermore, our recovery condition is proved via restricted eigenvalue property, a less demanding replacement of restricted isometry property which is perfectly suited to the considered scenario. Along the way, we derive simple criteria to detect good sample sets. Our numerical tests show that sets of uniformly sampled points that meet these criteria will perform better recovery on average.

97 MATHEMATICS AND COMPUTING↗

The evaporation of black holes in supergravity

In supergravity, charged rotating black holes are generically driven towards becoming extremal and supersymmetric through the emission of Hawking radiation. Eventually, as the black hole approaches the BPS bound and is close to becoming supersymmetric, quantum gravity corrections become critical to describing the emission of Hawking radiation, making the QFT in curved spacetime approximation inaccurate. In this paper, we compute how such quantum gravity corrections affect the spectrum of Hawking radiation for black holes in $\mathcal{N}$ = 2 supergravity in flatspace. We show that due to such corrections, the spectrum of emitted Hawking radiation for both spin-0 and spin-1/2 particles deviates drastically at low temperatures from the naively expected black-body spectrum. Rather remarkably, the spectrum exhibits a discrete emission line from direct transitions from near-BPS to BPS states, providing the first controlled example where the discreteness of the black hole energies is visible in the emitted Hawking radiation. Similar quantum gravity effects drastically modify the absorption cross-section: BPS black holes are transparent to certain frequencies, while near-BPS black holes appear much larger than the semi-classical prediction.

AdS-CFT Correspondence↗

First-Principles Investigation of Ferromagnetic, Thermodynamic, Elastic, and Half-Metallic Behavior of ReCrTe and RuCrTe Half-Heusler Alloys

Calculations are realized within the full-potential linearized augmented plane wave (FP-LAPW) computational approach with the generalized gradient approximation (GGA) for the exchange-correlation potential. In this work, we present investigation of structural, electronic, ferromagnetic, elastic, and thermodynamic properties and half-metallic behavior of ReCrTe and RuCrTe compounds. Analysis of band structures and densities of states show the half-metallic ferromagnetic behavior of these compounds. The values of total magnetic moments µ{sub tot} are 1 µ{sub B} per unit cell for ReCrTe and 3 µ{sub B} per unit cell for RuCrTe. The contribution of Cr is the most important. The calculated values of a total magnetic moment nicely follow the rule µ{sub tot} = Z{sub t}− 18. The study of the impacts of strains on the magnetic moment reveals that the two compounds are stable ferromagnetic compounds. RuCrTe compound preserves the half-metallic behavior when the unit cell volume is changed in the range of [ − 4%, 4%], whereas, weak strain destroys the half metallic nature for ReCrTe compound. Using the quasi-harmonic Debye model, the effects of pressure P and temperature T on thermal expansion coefficient, Debye temperature, heat capacity and Grüneisen parameter for these two compounds are investigated for the first time. The study of the elastic constants shows that ReCrTe and RuCrTe are mechanically stable. RuCrTe is stiffer than ReCrTe compounds. The obtained values of Pugh’s ratio B/G and Cauchy pressure (C{sub 12} − C{sub 44}) reveal that ReCrTe and RuCrTe are brittle. The study of the electron charge density and Poisson’s ratio proves that the ionic character dominates the atomic bonding for the two compounds.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Investigation of Electronic, Magnetic, Thermodynamic, and Thermoelectric Properties of Half-Metallic XLiSn (X = Ce, Nd) Alloys

We have investigated the electronic, magnetic, thermodynamic, and thermoelectric properties of half-Heusler CeLiSn and NdLiSn using density functional theory. The materials crystallize in F 4-bar 3mstructure with ferromagnetic state at optimized lattice parameter of 6.73 Å for CeLiSn and 6.74 Å for NdLiSn. The modified Becke-Johnson potential (mBJ) and generalized gradient approximation (GGA) have been used for computation of band structure, where mBJ shows a perfect half-metallic nature of the bands in both the alloys. The calculated magnetic moment of 1.0 μ{sub B} for CeLiSn and 3.0 μ{sub B} for NdLiSn follow Slater-Pauling rule, with ferromagnetic interactions. The temperature variation of the Seebeck coefficient shows the p-type behavior with room temperature values of 27 μV/K (43 μV/K) for CeLiSn (NdLiSn). Pressure-dependent variation of specific heat, Debye temperature, and Gruneisen parameter were calculated to infer the nature of lattice vibration and stability at high pressures.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Localized Pisot Matrices and Joint Approximations of Algebraic Numbers

A development of the simplex-module algorithm for expansion of algebraic numbers in multidimensional continued fractions is proposed. To this end, localized Pisot matrices are constructed, whose eigenvalues with moduli less than one are contained in an interval of small length. Such Pisot matrices generate continued fractions whose convergents are arbitrarily close to the best approximations.

97 MATHEMATICS AND COMPUTING↗

High-Accuracy Mesh-Free Quadrature for Trimmed Parametric Surfaces and Volumes

This work presents a high-accuracy, mesh-free, generalized Stokes theorem-based numerical quadrature scheme for integrating functions over trimmed parametric surfaces and volumes. The algorithm relies on two fundamental steps: (1) We iteratively reduce the dimensionality of integration using the generalized Stokes theorem to line integrals over trimming curves, and (2) we employ numerical antidifferentiation in the generalized Stokes theorem using high-order quadrature rules. Additionally, the scheme achieves exponential convergence up to trimming curve approximation error and has applications to computation of geometric moments, immersogeometric analysis, conservative field transfer between high-order curvilinear meshes, and initialization of multi-material simulations. We compare the quadrature scheme to commonly-used quadrature schemes in the literature and show that our scheme is much more efficient in terms of number of quadrature points used. We provide an open-source implementation of the scheme in MATLAB as part of QuaHOG, a software package for Quadrature of High-Order Geometries.

97 MATHEMATICS AND COMPUTING↗

Dynamics of charge at water-to-semiconductor interface: Case study of wet [0 0 1] anatase TiO 2 nanowire

Here, the behavior of water molecules on the surfaces of the TiO 2 nanowire grown in [0 0 1] direction has been investigated by combining theoretical calculations and experiments. Calculated UV–visible absorption spectra reproduce the main features of the experimental spectra. Computations predict that a photoexcitation followed by a sequence of relaxation events results in photoluminescence across the gap. TiO 2 nanowires in vacuum and aqueous environment exhibit different dynamics of photo-excited charge carriers. In water, computed relaxation of electrons (holes) is approximately 2 (4) times faster compared with vacuum environment. Faster relaxation of holes vs. electrons and specific spatial localization of holes result to formation of long lived charge transfer excitation with positive charge at the surface of the nanowire. Comparison of relaxation process in TiO 2 /water interfaces focusing on different surfaces and nanostructures has potential in identifying structural characteristics of TiO 2 materials important for efficient photo-electrochemical water splitting.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A projection-based analytical Jacobian framework for chemical kinetics applications

A major challenge in simulating complex combustion systems with detailed chemical kinetic models is the cost of integrating the chemical source terms, often done using stiff ODE solvers that require frequent Jacobian evaluations. Using analytically derived Jacobian matrices instead of divided-difference-based numerical Jacobian approximations can significantly reduce the associated computational cost. However, ambiguities arise in the formulation of analytical Jacobians because the chemical state of the system, or state vector, can be expressed in multiple ways, involving variables that are typically not independent from one another. Here, in this work, the consequences of those ambiguities on practical calculations are characterized in detail, and a generalized, projection-based framework is proposed as a mitigation strategy. Performances are assessed in a series of test cases involving a variety of configurations and numerical solution approaches. Results show that with proper treatment, commonly used analytical Jacobian formulations can be considered as equivalent for practical purposes, thereby alleviating concerns that the state vector chosen to express the governing equations and corresponding analytical Jacobian may significantly impact the accuracy of the simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Optimization-based control using input convex neural networks

Input convex neural networks (ICNNs) are a family of deep learning models where the outputs are constructed to be convex functions of the inputs. By parameterizing system models using ICNNs, optimization-based control problems can be solved as convex optimization problems, leading to improved performance and robustness. This work proposes a novel framework where the control objective function and constraints are modelled using ICNNs. A case study of optimization-based control with output constraints is conducted on a process with input multiplicity and nonminimum phase behavior. The simulation results demonstrate improved economic yield compared with normal neural networks. Additionally, the input convexity formulation is compared with simple regularization techniques, and unique benefits such as improved data efficiency and robustness of the proposed formulation are shown. Finally, by explicitly incorporating prior knowledge about convexity, this framework provides a good balance between the universal approximation power of deep learning and computational feasibility required by control.

42 ENGINEERING↗

Assessing exchange-correlation functionals for elasticity and thermodynamics of α - ZrW 2 O 8 : A density functional perturbation theory study

Elastic and thermodynamic properties of negative thermal expansion (NTE) αα-ZrW2O8 have been calculated using PBEsol and PBE exchange-correlation functionals within the framework of density functional perturbation theory (DFPT). Measured elastic constants are reproduced within ~2% with PBEsol and 6% with PBE. The thermal evolution of the Grüneisen parameter computed within the quasi-harmonic approximation exhibits negative values below the Debye temperature, consistent with observation. The standard molar heat capacity is predicted to be C $O\atop{P}$=192.2 and 193.8 J mol -1 K -1 with PBEsol and PBE, respectively. These results suggest superior accuracy of DFPT/PBEsol for studying the lattice dynamics, elasticity and thermodynamics of NTE materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

An approximate Riemann solver for real gas parabolized Navier-Stokes equations

Under specific assumptions, parabolized Navier-Stokes equations are a suitable mean to study channel flows. A special case is that of high pressure flow of real gases in cooling channels where large crosswise gradients of thermophysical properties occur. To solve the parabolized Navier-Stokes equations by a space marching approach, the hyperbolicity of the system of governing equations is obtained, even for very low Mach number flow, by recasting equations such that the streamwise pressure gradient is considered as a source term. For this system of equations an approximate Roe's Riemann solver is developed as the core of a Godunov type finite volume algorithm. The properties of the approximated Riemann solver, which is a modification of Roe's Riemann solver for the parabolized Navier-Stokes equations, are presented and discussed with emphasis given to its original features introduced to handle fluids governed by a generic real gas EoS. Sample solutions are obtained for low Mach number high compressible flows of transcritical methane, heated in straight long channels, to prove the solver ability to describe flows dominated by complex thermodynamic phenomena.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Hybrid massively parallel fast sweeping method for static Hamilton–Jacobi equations

The fast sweeping method is a popular algorithm for solving a variety of static Hamilton–Jacobi equations. Fast sweeping algorithms for parallel computing have been developed, but are severely limited. In this work, we present a multilevel, hybrid parallel algorithm that combines the desirable traits of two distinct parallel methods. The fine and coarse grained components of the algorithm take advantage of heterogeneous computer architecture common in high performance computing facilities. We present the algorithm and demonstrate its effectiveness on a set of example problems including optimal control, dynamic games, and seismic wave propagation. We give results for convergence, parallel scaling, and show state-of-the-art speedup values for the fast sweeping method.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

A fast marching algorithm for the factored eikonal equation

The eikonal equation is instrumental in many applications in several fields ranging from computer vision to geoscience. This equation can be efficiently solved using the iterative Fast Sweeping (FS) methods and the direct Fast Marching (FM) methods. However, when used for a point source, the original eikonal equation is known to yield inaccurate numerical solutions, because of a singularity at the source. In this case, the factored eikonal equation is often preferred, and is known to yield a more accurate numerical solution. One application that requires the solution of the eikonal equation for point sources is travel time tomography. This inverse problem may be formulated using the eikonal equation as a forward problem. While this problem has been solved using FS in the past, the more recent choice for applying it involves FM methods because of the efficiency in which sensitivities can be obtained using them. However, while several FS methods are available for solving the factored equation, the FM method is available only for the original eikonal equation. In this paper we develop a Fast Marching algorithm for the factored eikonal equation, using both first and second order finite-difference schemes. Our algorithm follows the same lines as the original FM algorithm and requires the same computational effort. In addition, we show how to obtain sensitivities using this FM method and apply travel time tomography, formulated as an inverse factored eikonal equation. Numerical results in two and three dimensions show that our algorithm solves the factored eikonal equation efficiently, and demonstrate the achieved accuracy for computing the travel time. We also demonstrate a recovery of a 2D and 3D heterogeneous medium by travel time tomography using the eikonal equation for forward modeling and inversion by Gauss–Newton.

97 MATHEMATICS AND COMPUTING↗

Non -degenerate marginal-likelihood calibration with application to quantum characterization

Here, we propose a marginal likelihood strategy within the Kennedy-O’Hagan (KOH) Bayesian framework, where a Gaussian process (GP) models the discrepancy between a physical system and its simulator. Our approach introduces a novel marginalized likelihood by integrating out the degenerate eigenspace of the covariance matrix, rather than approximating the original likelihood. Unlike approximation methods that compromise accuracy for computational efficiency, our method defines an exact likelihood—distinct from the original but preserving all relevant information. This formulation achieves computational efficiency and stability, even for large datasets where the covariance matrix nears degeneracy. Applied to the characterization of a superconducting quantum device at Lawrence Livermore National Laboratory, the approach enhances the predictive accuracy of the Lindblad master equations for modeling Ramsey measurement data by effectively quantifying uncertainties consistent with the quantum data.

general physics↗

Neutrino oscillation probabilities through the looking glass

In this paper we review different expansions for neutrino oscillation probabilities in matter in the context of long-baseline neutrino experiments. We examine the accuracy and computational efficiency of different exact and approximate expressions. We find that many of the expressions used in the literature are not precise enough for the next generation of long-baseline experiments, but several of them are while maintaining comparable simplicity. Furthermore the results of this paper can be used as guidance to both phenomenologists and experimentalists when implementing the various oscillation expressions into their analysis tools.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Uncertainty estimation of bifurcated solutions in the Rayleigh–Bénard problem for advanced nuclear reactors applications

Multiphysics models of nuclear reactors frequently comprise nonlinear systems of equations. The nonlinear nature of these models could lead to solution bifurcations, where a small change in a certain parameter, e.g., the thermophysical properties of the coolant, can lead to a sudden change in the system’s behavior. At the point in parameter space where this happens, called a critical point, the Jacobian matrix of the model’s nonlinear operator becomes singular potentially permitting multiple solutions to coexist. In this paper, we perform uncertainty estimation (UE) in a parameter range that includes bifurcated solutions within the context of Rayleigh–Bénard problem. We perform this analysis assuming uncertain temperature difference, and tilt angle for the iterative solution algorithm with a unit Prandtl number (Pr = 1). Also, we perform this analysis under uncertain thermophysical properties for both FLiBe molten salt and liquid sodium as working fluid. We deploy two approaches to compute statistical moments for the resulting distributions of selected flow-field variables. The first approach is the blind computation of the mean and the standard deviation without any consideration of solution bifurcation, while the second approach utilizes k-means clustering to cluster each branch’s solutions together and compute separate statistical moments for each branch. The statistical distributions are obtained by perturbing the selected parameters about nominal values that correspond to a solution on one of the valid branches, and that solution is used as initial guess for the iterative solution algorithm. We found that perturbation of any parameter when its nominal value is close to its critical point always leads to branch jumping, i.e., the iterations converge to a solution on a branch different from the branch of the initial guess. This produces a statistical ensemble comprised of fundamentally different solutions leading to wrong mean values and uncertainty estimates, whereas clustering provides an efficient way to deal with this type of computation. This work is important for developing Gen IV nuclear systems because many of these systems rely on natural convection for cooling especially in accident conditions.

97 - MATHEMATICS AND COMPUTING↗

Entanglement Effect and Angular Momentum Conservation in a Nonseparable Tunneling Treatment

The important, and often dominant, role of tunneling in low temperature kinetics has resulted in numerous theoretical explorations into the methodology for predicting it. Nevertheless, there are still key aspects of the derivations that are lacking, particularly for nonseparable systems in the low temperature regime, and further explorations of the physical factors affecting the tunneling rate are warranted. In this work we obtain a closed-form rate expression for the tunneling rate constant that is a direct analog of the rigid-rotor-harmonic-oscillator expression. This expression introduces a novel "entanglement factor" that modulates the reaction rate. Furthermore, we are able to extend this expression, which is valid for nonseparable systems at low temperatures, to properly account for the conservation of angular momentum. In contrast, previous calculations have considered only vibrational transverse modes and so effectively employ a decoupled rotational partition function for the orientational modes. We also suggest a simple theoretical model to describe the tunneling effects in the vicinity of the crossover temperature (the temperature where tunneling becomes the dominating mechanism). This model allows one to naturally classify, interpret, and predict experimental data. Among other things, it quantitatively explains in simple terms the so-called "quantum bobsled" effect, also known as the negative centrifugal effect, which is related to curvature of the reaction path. Taken together, the expressions obtained here allow one to predict the thermal and E-resolved rate constants over broad ranges of temperatures and energies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗