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At least 127 records · Page 7

Detecting macroevolutionary genotype–phenotype associations using error-corrected rates of protein convergence

On macroevolutionary timescales, extensive mutations and phylogenetic uncertainty mask the signals of genotype–phenotype associations underlying convergent evolution. To overcome this problem, we extended the widely used framework of non-synonymous to synonymous substitution rate ratios and developed the novel metric ω C , which measures the error-corrected convergence rate of protein evolution. While ω C distinguishes natural selection from genetic noise and phylogenetic errors in simulation and real examples, its accuracy allows an exploratory genome-wide search of adaptive molecular convergence without phenotypic hypothesis or candidate genes. Using gene expression data, we explored over 20 million branch combinations in vertebrate genes and identified the joint convergence of expression patterns and protein sequences with amino acid substitutions in functionally important sites, providing hypotheses on undiscovered phenotypes. We further extended our method with a heuristic algorithm to detect highly repetitive convergence among computationally non-trivial higher-order phylogenetic combinations. Our approach allows bidirectional searches for genotype–phenotype associations, even in lineages that diverged for hundreds of millions of years.

59 BASIC BIOLOGICAL SCIENCES↗

Improving Time Step Convergence in an Atmosphere Model With Simplified Physics: The Impacts of Closure Assumption and Process Coupling

Convergence testing is a common practice in the development of dynamical cores of atmospheric models but is not as often exercised for the parameterization of sub-grid physics. An earlier study revealed that the stratiform cloud parameterizations in several predecessors of the Energy Exascale Earth System Model (E3SM) showed strong time-step sensitivity and slower-than-expected convergence when the model's time step was systematically refined. In this work, a simplified atmosphere model is configured that consists of the spectral-element dynamical core of the E3SM atmosphere model coupled with a large-scale condensation parameterization based on commonly used assumptions. This simplified model also resembles E3SM and its predecessors in the numerical implementation of process coupling and shows poor time-step convergence in short ensemble tests. We present a formal error analysis to reveal the expected time-step convergence rate and the conditions for obtaining such convergence. Numerical experiments are conducted to investigate the root causes of convergence problems. We show that revisions in the process coupling and closure assumption help to improve convergence in short simulations using the simplified model; the same revisions applied to a full atmosphere model lead to significant changes in the simulated long-term climate. This work demonstrates that causes of convergence issues in atmospheric simulations can be understood by combining analyses from physical and mathematical perspectives. Addressing convergence issues can help to obtain a discrete model that is more consistent with the intended representation of the physical phenomena.

54 ENVIRONMENTAL SCIENCES↗

Fibonacci fast convergence for neutrino oscillations in matter

Understanding neutrino oscillations in matter requires a non-trivial diagonalization of the Hamiltonian. As the exact solution is very complicated, many approximation schemes have been pursued. Here we show that one scheme, systematically applying rotations to change to a better basis, converges exponentially fast wherein the rate of convergence follows the Fibonacci sequence. We find that the convergence rate of this procedure depends very sensitively on the initial choices of the rotations as well as the mechanism of selecting the pivots. We then apply this scheme for neutrino oscillations in matter and discover that the optimal convergence rate is found using the following simple strategy: first apply the vacuum (2-3) rotation and then use the largest off-diagonal element as the pivot for each of the following rotations. The Fibonacci convergence rate presented here may be extendable to systems beyond neutrino oscillations.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Vortex breakdown simulation

In this paper, steady, axisymmetric inviscid, and viscous (laminar) swirling flows representing vortex breakdown phenomena are simulated using a stream function-vorticity-circulation formulation and two numerical methods. The first is based on an inverse iteration, where a norm of the solution is prescribed and the swirling parameter is calculated as a part of the output. The second is based on direct Newton iterations, where the linearized equations, for all the unknowns, are solved simultaneously by an efficient banded Gaussian elimination procedure. Several numerical solutions for inviscid and viscous flows are demonstrated, followed by a discussion of the results. Some improvements on previous work have been achieved: first order upwind differences are replaced by second order schemes, line relaxation procedure (with linear convergence rate) is replaced by Newton's iterations (which converge quadratically), and Reynolds numbers are extended from 200 up to 1000.

Hafez, M.↗

An efficient method for solving the steady Euler equations

An efficient numerical procedure for solving a set of nonlinear partial differential equations is given, specifically for the steady Euler equations. Solutions of the equations were obtained by Newton's linearization procedure, commonly used to solve the roots of nonlinear algebraic equations. In application of the same procedure for solving a set of differential equations we give a theorem showing that a quadratic convergence rate can be achieved. While the domain of quadratic convergence depends on the problems studied and is unknown a priori, we show that firstand second-order derivatives of flux vectors determine whether the condition for quadratic convergence is satisfied. The first derivatives enter as an implicit operator for yielding new iterates and the second derivatives indicates smoothness of the flows considered. Consequently flows involving shocks are expected to require larger number of iterations. First-order upwind discretization in conjunction with the Steger-Warming flux-vector splitting is employed on the implicit operator and a diagonal dominant matrix results. However the explicit operator is represented by first- and seond-order upwind differencings, using both Steger-Warming's and van Leer's splittings. We discuss treatment of boundary conditions and solution procedures for solving the resulting block matrix system. With a set of test problems for one- and two-dimensional flows, we show detailed study as to the efficiency, accuracy, and convergence of the present method.

Liou, M. S.↗

A Chebyshev spectral collocation method using a staggered grid for the stability of cylindrical flows

A staggered spectral collocation method for the stability of cylindrical flows is developed. In this method the pressure is evaluated at different nodal points than the three velocity components. These modified nodal points do not include the two boundary nodes; therefore the need for the two artificial pressure boundary conditions employed by Khorrami et al. is eliminated. It is shown that the method produces very accurate results and has a better convergence rate than the spectral tau formulation. However, through extensive convergence tests it was found that elimination of the artificial pressure boundary conditions does not result in any significant change in the convergence behavior of spectral collocation methods.

Khorrami, Mehdi R.↗

Stability Quantification for Consensus-Based Power Flow Control between Transmission and Distribution Power Systems

With increasing integration of distributed energy resources (DERs), distribution systems (DS) with DERs are expected to provide proactive grid services. The result is that power references, or known as dispatch signals, required for DS can become faster changing than in legacy power system. Consensus-based integral controls have been proposed for the purpose of coordinating power generations of DERs in DS to match the power references. These existing controls assume the integral control signal to be sufficiently slow or constant, and ignore the potential dynamics of the integral controller when tracking more varying power references. Therefore, in this paper we present an improvement for such controls by deriving the stability condition utilizing generalized Nyquist criterion. The stability condition is quantified by a set of integral gains that guarantee stability in closed-loop system without assuming a constant integral signal. A rule-of-thumb criterion is also derived to instruct the design of the consensus topology that can provide faster convergence rate for the closed-loop system. Here, the stability and convergence improvements developed in this paper are demonstrated and verified through numerical examples.

42 ENGINEERING↗

On the Convergence of Overlapping Schwarz Decomposition for Nonlinear Optimal Control

Here, we study the convergence properties of an overlapping Schwarz decomposition algorithm for solving nonlinear optimal control problems (OCPs). The algorithm decomposes the time domain into a set of overlapping subdomains, and solves all subproblems defined over subdomains in parallel. The convergence is attained by updating primal-dual information at the boundaries of overlapping subdomains. We show that the algorithm exhibits local linear convergence, and that the convergence rate improves exponentially with the overlap size. We also establish global convergence results for a general quadratic programming, which enables the application of the Schwarz scheme inside second-order optimization algorithms (e.g., sequential quadratic programming). The theoretical foundation of our convergence analysis is a sensitivity result of nonlinear OCPs, which we call "exponential decay of sensitivity" (EDS). Intuitively, EDS states that the impact of perturbations at domain boundaries (i.e., initial and terminal time) on the solution decays exponentially as one moves into the domain. Here, we expand a previous analysis available in the literature by showing that EDS holds for both primal and dual solutions of nonlinear OCPs, under uniform second-order sufficient condition, controllability condition, and boundedness condition. We conduct experiments with a quadrotor motion planning problem and a partial differential equations (PDE) control problem to validate our theory, and show that the approach is significantly more efficient than alternating direction method of multipliers and as efficient as the centralized interior-point solver.

42 ENGINEERING↗

Eigenmode analysis of unsteady one-dimensional Euler equations

The initial boundary value problem describing the evolution of unsteady linearized perturbations of a steady, uniform subsonic flow is analyzed. The eigenmodes and eigenfrequencies of the system are derived and several examples are presented to illustrate the effect of different boundary conditions on the exponential decay rate of the eigenmodes. The resultant implications for the stability and convergence rates of finite difference computations are discussed.

Giles, M.↗

On a numerical sufficiency test for monotonic convergence of finite element models

Finite element analyses characterized by monotonic convergence include the discipline for meaningful measurements of convergence rate and consequently economical extrapolation. Few proposers of element models guarantee monotonic convergence for their elements. Thus, a need exists for an automatic test to classify available element models. This paper describes such a test - a test can be performed using a digital computer to guarantee that a particular element model imbues monotonicity. It describes the test and its basis. It examines seven element models for a rectangular membrane to illustrate the value of the tests. Besides confirming results already known, the application yields new data. It 'proves' monotonicity for two improved models, defines the range of element proportions for which another element can be guaranteed to exhibit monotonicity, and suggests that another element is deficient. In the special case of absolutely convergent membrane displacement models, proof of monotonicity is a necessary and sufficient condition to insure that upper bound estimates of strain energy are developed. Accordingly, the test furnishes a proof of bound solutions independently of requirements on displacement continuity the element basis may or may not satisfy.

Melosh, R. J.↗

Development of a boundary-layer-type solver based on simultaneous iteration technique for axisymmetric separated flows

A boundary-layer-type solver is developed for the numerical solution of axisymmetric separated flows. A new fully implicit coupling scheme for the viscous and inviscid regions is demonstrated. This fully implicit coupling technique is similar to the work of Carter, Veldman, and an extension of an earlier work of Halim and Hafez. A comparison is made for the convergence rate using this new fully implicit coupling technique and the semiimplicit coupling of Halim and Hafez. Numerical results using the fully implicit coupling are obtained for laminar incompressible separated flows, including a boattail and a series of trough geometries. Also, the near-wake flow problem is considered using the present formulation. A clear conclusion of this investigation is that the present scheme using the fully implicit coupling method converges at a faster rate than the semiimplicit coupling and the partially parabolized Navier-Stokes (PPNS) procedures.

Halim, A. A. M.↗

Lossy checkpoint compression in full waveform inversion: a case study with ZFPv0.5.5 and the overthrust model

This paper proposes a new method that combines checkpointing methods with error-controlled lossy compression for large-scale high-performance full-waveform inversion (FWI), an inverse problem commonly used in geophysical exploration. This combination can significantly reduce data movement, allowing a reduction in run time as well as peak memory. In the exascale computing era, frequent data transfer (e.g., memory bandwidth, PCIe bandwidth for GPUs, or network) is the performance bottleneck rather than the peak FLOPS of the processing unit. Like many other adjoint-based optimization problems, FWI is costly in terms of the number of floating-point operations, large memory footprint during backpropagation, and data transfer overheads. Past work for adjoint methods has developed checkpointing methods that reduce the peak memory requirements during backpropagation at the cost of additional floating-point computations. Combining this traditional checkpointing with error-controlled lossy compression, we explore the three-way tradeoff between memory, precision, and time to solution. We investigate how approximation errors introduced by lossy compression of the forward solution impact the objective function gradient and final inverted solution. Empirical results from these numerical experiments indicate that high lossy-compression rates (compression factors ranging up to 100) have a relatively minor impact on convergence rates and the quality of the final solution.

58 GEOSCIENCES↗

Reducing measurement costs by recycling the Hessian in adaptive variational quantum algorithms

Abstract Adaptive protocols enable the construction of more efficient state preparation circuits in variational quantum algorithms (VQAs) by utilizing data obtained from the quantum processor during the execution of the algorithm. This idea originated with Adaptive Derivative-Assembled Problem-Tailored variational quantum eigensolver (ADAPT-VQE), an algorithm that iteratively grows the state preparation circuit operator by operator, with each new operator accompanied by a new variational parameter, and where all parameters acquired thus far are optimized in each iteration. In ADAPT-VQE and other adaptive VQAs that followed it, it has been shown that initializing parameters to their optimal values from the previous iteration speeds up convergence and avoids shallow local traps in the parameter landscape. However, no other data from the optimization performed at one iteration is carried over to the next. In this work, we propose an improved quasi-Newton optimization protocol specifically tailored to adaptive VQAs. The distinctive feature in our proposal is that approximate second derivatives of the cost function are recycled across iterations in addition to optimal parameter values. We implement a quasi-Newton optimizer where an approximation to the inverse Hessian matrix is continuously built and grown across the iterations of an adaptive VQA. The resulting algorithm has the flavor of a continuous optimization where the dimension of the search space is augmented when the gradient norm falls below a given threshold. We show that this inter-optimization exchange of second-order information leads the approximate Hessian in the state of the optimizer to be consistently closer to the exact Hessian. As a result, our method achieves a superlinear convergence rate even in situations where the typical implementation of a quasi-Newton optimizer converges only linearly. Our protocol decreases the measurement costs in implementing adaptive VQAs on quantum hardware as well as the runtime of their classical simulation.

Ramôa, Mafalda (ORCID:0000000302187801)↗

A parallel algorithm for the eigenvalues and eigenvectors for a general complex matrix

A new parallel Jacobi-like algorithm is developed for computing the eigenvalues of a general complex matrix. Most parallel methods for this parallel typically display only linear convergence. Sequential norm-reducing algorithms also exit and they display quadratic convergence in most cases. The new algorithm is a parallel form of the norm-reducing algorithm due to Eberlein. It is proven that the asymptotic convergence rate of this algorithm is quadratic. Numerical experiments are presented which demonstrate the quadratic convergence of the algorithm and certain situations where the convergence is slow are also identified. The algorithm promises to be very competitive on a variety of parallel architectures.

Shroff, Gautam↗

Convergence of Defect-Correction and Multigrid Iterations for Inviscid Flows

Convergence of multigrid and defect-correction iterations is comprehensively studied within different incompressible and compressible inviscid regimes on high-density grids. Good smoothing properties of the defect-correction relaxation have been shown using both a modified Fourier analysis and a more general idealized-coarse-grid analysis. Single-grid defect correction alone has some slowly converging iterations on grids of medium density. The convergence is especially slow for near-sonic flows and for very low compressible Mach numbers. Additionally, the fast asymptotic convergence seen on medium density grids deteriorates on high-density grids. Certain downstream-boundary modes are very slowly damped on high-density grids. Multigrid scheme accelerates convergence of the slow defect-correction iterations to the extent determined by the coarse-grid correction. The two-level asymptotic convergence rates are stable and significantly below one in most of the regions but slow convergence is noted for near-sonic and very low-Mach compressible flows. Multigrid solver has been applied to the NACA 0012 airfoil and to different flow regimes, such as near-tangency and stagnation. Certain convergence difficulties have been encountered within stagnation regions. Nonetheless, for the airfoil flow, with a sharp trailing-edge, residuals were fast converging for a subcritical flow on a sequence of grids. For supercritical flow, residuals converged slower on some intermediate grids than on the finest grid or the two coarsest grids.

Diskin, Boris↗

Aspects and applications of patched grid calculations

Patched grid calculations within the framework of an implicit, flux vector split upwind/relaxation algorithm for the Euler equations are presented. Aspects of computing on patched grids are discussed including the effect of a metric-discontinuous interface on the convergence rate of the algorithm, and the effect of curvature along an interface. Applications to a converging-diverging nozzle including effects of choking and bypass slots in two dimensions are presented.

Walters, Robert W.↗

Towards sharp error analysis of extended Lagrangian molecular dynamics

The extended Lagrangian molecular dynamics (XLMD) method provides a useful framework for reducing the computational cost of a class of molecular dynamics simulations with constrained latent variables. The XLMD method relaxes the constraints by introducing a fictitious mass ε for the latent variables and solving a set of singularly perturbed ordinary differential equations. While favorable numerical performance of XLMD has been demonstrated in several different contexts in the past decade, mathematical analysis of the method remains scarce. Here, we propose the first error analysis of the XLMD method in the context of a classical polarizable force field model. While the dynamics with respect to the atomic degrees of freedom are general and nonlinear, the key mathematical simplification of the polarizable force field model is that the constraints on the latent variables are given by a linear system of equations. We prove that when the initial value of the latent variables is compatible in a sense that we define, XLMD converges as the fictitious mass ε is made small with $\mathscr{O}$(ε) error for the atomic degrees of freedom and with $\mathscr{O}$($\sqrt{ε}$) error for the latent variables, when the dimension of the latent variable d' is 1. Furthermore, when the initial value of the latent variables is improved to be optimally compatible in a certain sense, we prove that the convergence rate can be improved to $\mathscr{O}$(ε) for the latent variables as well. Numerical results verify that both estimates are sharp not only for d'=1, but also for arbitrary d'. In the setting of general d', we do obtain convergence, but with the non-sharp rate of $\mathscr{O}$($\sqrt{ε}$) for both the atomic and latent variables.

74 ATOMIC AND MOLECULAR PHYSICS↗

Vectorizable multigrid algorithms for transonic-flow calculations

The analysis and the incorporation into a multigrid scheme of several vectorizable algorithms are discussed. von Neumann analyses of vertical-line, horizontal-line, and alternating-direction ZEBRA algorithms were performed; and the results were used to predict their multigrid damping rates. The algorithms were then successfully implemented in a transonic conservative full-potential computer program. The convergence acceleration effect of multiple grids is shown, and the convergence rates of the vectorizable algorithms are compared with those of standard successive-line overrelaxation (SLOR) algorithms.

Melson, N. D.↗