Isogeometric collocation method for the fractional Laplacian in the 2D bounded domain
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Engineering↗
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Generative AI models for learning flow maps of stochastic dynamical systems in bounded domains
Simulating stochastic differential equations (SDEs) in bounded domains, presents significant computational challenges due to particle exit phenomena, which requires accurate modeling of interior stochastic dynamics and boundary interactions. Despite the success of machine learning-based methods in learning SDEs, existing learning methods are not applicable to SDEs in bounded domains because they cannot accurately capture the particle exit dynamics. We present a unified hybrid data-driven approach that combines a conditional diffusion model with an exit prediction neural network to capture both interior stochastic dynamics and boundary exit phenomena. Our ML model consists of two major components: a neural network that learns exit probabilities using binary cross-entropy loss with rigorous convergence guarantees, and a training-free diffusion model that generates state transitions for non-exiting particles using closed-form score functions. The two components are integrated through a probabilistic sampling algorithm that determines particle exit at each time step and generates appropriate state transitions. Here, the performance of the proposed approach is demonstrated via three test cases: a one-dimensional simplified problem for theoretical verification, a two-dimensional advection-diffusion problem in a bounded domain, and a three-dimensional problem of interest to magnetically confined fusion plasmas.
Bounded domains↗
Design procedure for satisfying time domain bounds for nonminimum-phase systems
Design techniques are presented applicable to nonminimum-phase systems. They are designed to handle plants with one right-half-plane zero which may vary, and any other variation of the plant parameters within known limits. The specifications that must be designed are given as a set of step response bounds in the time domain. A completed design will yield responses that stay within the time domain bounds at all times and utilize the entire region of allowed variation.
Ostheimer, W. D.↗
Inverse point source location with the Helmholtz equation on a bounded domain
The problem of recovering acoustic sources, more specifically monopoles, from point-wise measurements of the corresponding acoustic pressure at a limited number of frequencies is addressed. To this purpose, a family of sparse optimization problems in measure space in combination with the Helmholtz equation on a bounded domain is considered in this study. A weighted norm with unbounded weight near the observation points is incorporated into the formulation. Optimality conditions and conditions for recovery in the small noise case are discussed, which motivates concrete choices of the weight. The numerical realization is based on an accelerated conditional gradient method in measure space and a finite element discretization.
97 MATHEMATICS AND COMPUTING↗
Synchronous and asynchronous optimized Schwarz methods for one-way subdivision of bounded domains
Convergence of both synchronous and asynchronous optimized Schwarz algorithms for the shifted Laplacian operator on a bounded rectangular domain, in a one-way subdivision of the computational domain, with overlap, is shown. Convergence results are obtained under very mild conditions on the size of the subdomains and on the amount of overlap. A couple of results are also given, relating the convergence rate of the asynchronous method to changes in the size of the domain. Numerical experiments illustrate the theoretical results.
97 MATHEMATICS AND COMPUTING↗
Crystal structure of the CDK11 kinase domain bound to the small-molecule inhibitor OTS964
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Kelso, Susan↗
Robust Design Optimization via Failure Domain Bounding
This paper extends and applies the strategies recently developed by the authors for handling constraints under uncertainty to robust design optimization. For the scope of this paper, robust optimization is a methodology aimed at problems for which some parameters are uncertain and are only known to belong to some uncertainty set. This set can be described by either a deterministic or a probabilistic model. In the methodology developed herein, optimization-based strategies are used to bound the constraint violation region using hyper-spheres and hyper-rectangles. By comparing the resulting bounding sets with any given uncertainty model, it can be determined whether the constraints are satisfied for all members of the uncertainty model (i.e., constraints are feasible) or not (i.e., constraints are infeasible). If constraints are infeasible and a probabilistic uncertainty model is available, upper bounds to the probability of constraint violation can be efficiently calculated. The tools developed enable approximating not only the set of designs that make the constraints feasible but also, when required, the set of designs for which the probability of constraint violation is below a prescribed admissible value. When constraint feasibility is possible, several design criteria can be used to shape the uncertainty model of performance metrics of interest. Worst-case, least-second-moment, and reliability-based design criteria are considered herein. Since the problem formulation is generic and the tools derived only require standard optimization algorithms for their implementation, these strategies are easily applicable to a broad range of engineering problems.
Crespo, Luis G.↗
To Err is Normable: The Computation of Frequency-Domain Error Bounds from Time-Domain Data
This paper exploits the relationships among the time-domain and frequency-domain system norms to derive information useful for modeling and control design, given only the system step response data. A discussion of system and signal norms is included. The proposed procedures involve only simple numerical operations, such as the discrete approximation of derivatives and integrals, and the calculation of matrix singular values. The resulting frequency-domain and Hankel-operator norm approximations may be used to evaluate the accuracy of a given model, and to determine model corrections to decrease the modeling errors.
Hartley, Tom T.↗
Interaction dynamics of multiple autonomous mobile robots in bounded spatial domains
A general navigation strategy for multiple autonomous robots in a bounded domain is developed analytically. Each robot is modeled as a spherical particle (i.e., an effective spatial domain about the center of mass); its interactions with other robots or with obstacles and domain boundaries are described in terms of the classical many-body problem; and a collision-avoidance strategy is derived and combined with homing, robot-robot, and robot-obstacle collision-avoidance strategies. Results from homing simulations involving (1) a single robot in a circular domain, (2) two robots in a circular domain, and (3) one robot in a domain with an obstacle are presented in graphs and briefly characterized.
Wang, P. K. C.↗
A Particle-in-Cell Method for Plasmas with a Generalized Momentum Formulation, Part I: Model Formulation
Here, this paper formulates a new particle-in-cell method for the Vlasov–Maxwell system. Under the Lorenz gauge condition, Maxwell’s equations for the electromagnetic fields can be written as a collection of scalar and vector wave equations. The use of potentials for the fields motivates the adoption of a Hamiltonian formulation for particles that employs the generalized (conjugate) momentum. A notable advantage offered by the Hamiltonian formulation is the elimination of time derivatives in the Lorenz gauge formulation that are required by the standard Newton–Lorentz treatment of the particles. This allows the fields to retain the full time-accuracy guaranteed by the field solver. The resulting updates for particles require only knowledge of the fields and their spatial derivatives. An analytical method for constructing these spatial derivatives is presented that exploits the underlying integral solution used in the field solver for the wave equations. Moreover, these derivatives are demonstrated to converge at the same rate as the fields in both time and space. The Method of Lines Transpose field solver we consider in this work is globally first-order accurate in time and high-order accurate in space (e.g., fourth- and fifth-order) and belongs to a larger class of methods which are unconditionally stable, can address geometry, and leverage $\mathcal {O}(N)$ fast summation methods for efficiency. We demonstrate the method on several well-established benchmark problems on bounded domains, including a plasma sheath as well as a relativistic particle beam. The efficacy of the proposed formulation is established by comparing with a second-order accurate finite-difference time-domain method that employs a leapfrog time advance for particles and a charge conserving map suitable for bounded domains. The new method shows mesh-independent numerical heating properties even in cases where the plasma Debye length is smaller than the grid spacing. This is an important feature of the new method for problems defined on bounded domains, because it permits the use of coarser grids in space in the representation of the fields. Such a capability has significant implications for the simulation of plasmas in bounded domains with complex geometry, where the ratio between the largest and smallest cells can vary significantly. The use of high-order spatial approximations in the new method also means that fewer grid points are required in order to achieve a fixed accuracy. Our results also suggest that the new method can be used with fewer simulation particles per cell compared to the benchmark explicit method, which permits further computational savings.
97 MATHEMATICS AND COMPUTING↗
Robust time and frequency domain estimation methods in adaptive control
A robust identification method was developed for use in an adaptive control system. The type of estimator is called the robust estimator, since it is robust to the effects of both unmodeled dynamics and an unmeasurable disturbance. The development of the robust estimator was motivated by a need to provide guarantees in the identification part of an adaptive controller. To enable the design of a robust control system, a nominal model as well as a frequency-domain bounding function on the modeling uncertainty associated with this nominal model must be provided. Two estimation methods are presented for finding parameter estimates, and, hence, a nominal model. One of these methods is based on the well developed field of time-domain parameter estimation. In a second method of finding parameter estimates, a type of weighted least-squares fitting to a frequency-domain estimated model is used. The frequency-domain estimator is shown to perform better, in general, than the time-domain parameter estimator. In addition, a methodology for finding a frequency-domain bounding function on the disturbance is used to compute a frequency-domain bounding function on the additive modeling error due to the effects of the disturbance and the use of finite-length data. The performance of the robust estimator in both open-loop and closed-loop situations is examined through the use of simulations.
Lamaire, Richard Orville↗
Crescendo beyond the horizon: More gravitational waves from domain walls bounded by inflated cosmic strings
Gravitational-wave (GW) signals offer a unique window into the dynamics of the early universe. GWs may be generated by the topological defects produced in the early universe, which contain information on the symmetry of UV physics. We consider the case in which a two-step phase transition produces a network of domain walls bounded by cosmic strings. Specifically, we focus on the case in which there is a hierarchy in the symmetry-breaking scales, and a period of inflation pushes the cosmic string generated in the first phase transition outside the horizon before the second phase transition. We show that the GW signal from the evolution and collapse of this string-wall network has a unique spectrum, and the resulting signal strength can be sizeable. In particular, depending on the model parameters, the resulting signal can show up in a broad range of frequencies and can be discovered by a multitude of future probes, including the pulsar timing arrays and space- and ground-based GW observatories. As an example that naturally gives rise to this scenario, we present a model with the first phase transition followed by a brief period of thermal inflation driven by the field responsible for the second stage of symmetry breaking. Here, the model can be embedded into a supersymmetric setup, which provides a natural realization of this scenario. In this case, the successful detection of the peak of the GW spectrum probes the soft supersymmetry breaking scale and the wall tension.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Robust Metric-Aligned Quad-Dominant Meshing Using L(sub p) Centroidal Voronoi Tessellation
We introduce a meshing algorithm that can be used to both generate and adapt meshes for bounded domains in an anisotropic manner. This is particularly beneficial when anisotropic flow features like shock waves or contact discontinuities are present in the computational domain. The algorithm presented in this paper is based upon meshing under the imposed Riemannian metric tensor, which controls the orientation and size of the mesh elements. In this way there is no need for user intervention to recognize these features. We demonstrate that the method indeed aligns the elements with the underlying metric and produces right-angled simplices that can be recombined into quadrilateral elements. The aim is to eventually incorporate this meshing strategy in the monolithic high-order spectral element solver that is currently being developed at NASA Ames. This paper has two main contributions: First, we demonstrate that we can generate quad-dominant metric-aligned meshes for bounded domains using a generalized form of L(sub p)-Centroidal Voronoi Tessellation (L(sub p)-CVT). Unlike previous works, we do not rely on a background mesh and discretize the bounded domain in a hierarchical way by first discretizing the boundaries and then the volume using the underlying metric. Second, we present an alternative for clipping the Voronoi cells on the boundary, which is common practice in CVT-based meshing algorithms, by reconstructing the Voronoi cells using the defined metric field. In this way we avoid the geometrical complexity of the clipping procedure and we show that we evaluate the energy and its gradient correctly. We show that the reconstruction of the computational domain is consistent with the Lloyds’ algorithm that is used to compute the L(sub p)-CVT.
Centroidal↗
A Particle-in-Cell Method for Plasmas with a Generalized Momentum Formulation, Part II: Enforcing the Lorenz Gauge Condition
In a previous paper Christlieb et al. (A particle-in-cell method for plasmas with a generalized momentum formulation, part I: Model formulation, 2024), we developed a new particle-in-cell (PIC) method for the relativistic Vlasov–Maxwell system in which the electromagnetic fields and the equations of motion for the particles were cast in terms of scalar and vector potentials through a Hamiltonian formulation. This new method evolved the potentials under the Lorenz gauge using integral equation methods. New methods to construct spatial derivatives of the potentials that converge at the same rates as the fields were also presented. The new particle method was compared against standard explicit discretizations, including the well-known FDTD-PIC method, for a range of applications involving sheaths and particle beams. Here, this paper extends this new class of methods by focusing on the enforcement the Lorenz gauge condition in both exact and approximate forms using co-located meshes. A time-consistency property of the proposed field solver for the vector potential form of Maxwell’s equations is established, which is shown to preserve the equivalence between the semi-discrete Lorenz gauge condition and the analogous semi-discrete continuity equation. Using this property, we present three methods to enforce a semi-discrete gauge condition. The first method introduces an update for the continuity equation that is consistent with the discretization of the Lorenz gauge condition. Both the finite difference and spectral implementations satisfy this discrete gauge condition to machine precision. The second approach we propose enforces a semi-discrete continuity equation using the boundary integral solution to the field equations. The potential benefit of this approach is that it eliminates spatial derivatives that appear on the particle data, namely the current density, which is often calculated by linear combinations of low-order spline basis functions. This method is ideally suited to boundary integral equation methods that invert multi-dimensional operators without dimensional splitting techniques and will be the subject of future work. The third approach introduces a gauge correcting method that makes direct use of the gauge condition to modify the scalar potential and uses local maps for both the charge and current densities. This results in a gauge error, as the maps do not enforce the continuity equation. The vector potential coming from the current density is taken to be exact, and using the Lorenz gauge, we compute a correction to the scalar potential that makes the two potentials satisfy the gauge condition. This method also enforces the gauge condition to machine precision. We demonstrate two of the proposed methods in the context of periodic domains. Problems defined on bounded domains, including those with complex geometric features remain an ongoing effort. However, this work shows that it is possible to design computationally efficient methods that can effectively enforce the Lorenz gauge condition in a non-staggered PIC formulation.
97 MATHEMATICS AND COMPUTING↗
ALS mutations disrupt self-association between the ubiquilin STI1 hydrophobic groove and internal placeholder sequences
Ubiquilins are molecular chaperones that play multifaceted roles in proteostasis, with point mutations in UBQLN2 leading to altered phase-separation properties and amyotrophic lateral sclerosis (ALS). Our mechanistic understanding of this essential process has been hindered by a lack of structural information on the STI1 domain, which is essential for ubiquilin chaperone activity and phase separation. Here, we present the first crystal structure of a ubiquilin-family STI1 domain bound to a transmembrane domain (TMD), and show that ALS mutations disrupt the STI1-TMD interaction. We further demonstrate that ubiquilins contain multiple conserved internal sequences that bind to the STI1 domain, including the PXX-repeat region that is a hotspot for ALS mutations. We propose that these placeholder sequences prevent solvent exposure of the STI1 hydrophobic groove and contribute to the multivalency that drives ubiquilin phase-separation. Together, this work provides a new paradigm for understanding how STI1 domains modulate ubiquilin chaperone activity and phase separation, and offers insights into the molecular basis of ALS pathogenesis.
Onwunma, Joan [Univ. of Toledo, OH (United States)↗
Computer program for single input-output, single-loop feedback systems
Additional work is reported on a completely automatic computer program for the design of single input/output, single loop feedback systems with parameter uncertainly, to satisfy time domain bounds on the system response to step commands and disturbances. The inputs to the program are basically the specified time-domain response bounds, the form of the constrained plant transfer function and the ranges of the uncertain parameters of the plant. The program output consists of the transfer functions of the two free compensation networks, in the form of the coefficients of the numerator and denominator polynomials, and the data on the prescribed bounds and the extremes actually obtained for the system response to commands and disturbances.
Source record↗
Solution of the stochastic control problem in unbounded domains.
Bellman's dynamic programming equation for the optimal index and control law for stochastic control problems is a parabolic or elliptic partial differential equation frequently defined in an unbounded domain. Existing methods of solution require bounded domain approximations, the application of singular perturbation techniques or Monte Carlo simulation procedures. In this paper, using the fact that Poisson impulse noise tends to a Gaussian process under certain limiting conditions, a method which achieves an arbitrarily good approximate solution to the stochastic control problem is given. The method uses the two iterative techniques of successive approximation and quasi-linearization and is inherently more efficient than existing methods of solution.
Robinson, P.↗
Structure-function studies of Vibrio cholerae quorum-sensing receptor CqsR signal recognition
Ethanolamine signaling through the transmembrane quorum-sensing receptor CqsR influencesVibrio choleraeniche recognition and host colonization. In this study, we present a comprehensive structure-function analysis of CqsR. Specifically, we have determined X-ray crystal structures of the CqsR periplasmic domain bound to the signaling agonist ethanolamine and its analogs, serinol and L-alaninol, as well as the ligand-free (apo) form of CqsR. The periplasmic ligand-binding domain of CqsR is a Cache domain, the most prevalent extracellular sensory module in prokaryotes. Our findings provide a rare structural comparison of ligand-bound and unbound states of a Cache domain receptor. Coupled with thermodynamic binding assays and genetic analyses, these structures elucidate the molecular basis of CqsR ligand specificity. This study not only advances the understanding of Cache domain function but also informs the identification of ligands for orphan Cache receptors and the rational design of signaling agonists and antagonists. Lastly, we discuss ligand-induced conformational changes in the CqsR Cache domains and explore the potential for the existence of additional regulatory ligands.
Microbiology↗