A novel approach to hydrodynamics for long-range generalized exclusion

We consider a class of generalized long-range exclusion processes evolving either on Z or on a finite lattice with an open boundary. The jump rates are given in terms of a general kernel depending on both the departure and destination sites, and it is such that the particle displacement has an infinite expectation, but some tail bounds are satisfied. We study the superballisitic scaling limit of the particle density and prove that its space-time evolution is concentrated on the set of weak solutions to a non-local transport equation. Since the stationary states of the dynamics are unknown, we develop a new approach to such a limit relying only on the algebraic structure of the Markovian generator

An inflated dynamic Laplacian to track the emergence and disappearance of semi-material coherent sets

Lagrangian methods continue to stand at the forefront of the analysis of time-dependent dynamical systems. Most Lagrangian methods have criteria that must be fulfilled by trajectories as they are followed throughout a given finite flow duration. This key strength of Lagrangian methods can also be a limitation in more complex evolving environments. It places a high importance on selecting a time window that produces useful results, and these results may vary significantly with changes in the flow duration. We show how to overcome this drawback in the tracking of coherent flow features. Finite-time coherent sets (FTCS) are material objects that strongly resist mixing in complicated nonlinear flows. Like other materially coherent objects, by definition they must retain their coherence properties throughout the specified flow duration. Recent work [Froyland and Koltai, CPAM, 2023] introduced the notion of semi-material FTCS, whereby a balance is struck between the material nature and the coherence properties of FTCS. This balance provides the flexibility for FTCS to come and go, merge and separate, or undergo other changes as the governing unsteady flow experiences dramatic shifts. The purpose of this work is to illustrate the utility of the inflated dynamic Laplacian introduced in [Froyland and Koltai, CPAM, 2023] in a range of dynamical systems that are challenging to analyse by standard Lagrangian means, and to provide an efficient meshfree numerical approach for the discretisation of the inflated dynamic Laplacian

A simple refined DNA minimizer operator enables 2-fold faster computation

Motivation The minimizer concept is a data structure for sequence sketching. The standard canonical minimizer selects a subset of k-mers from the given DNA sequence by comparing the forward and reverse k-mers in a window simultaneously according to a predefined selection scheme. It is widely employed by sequence analysis such as read mapping and assembly. k-mer density, k-mer repetitiveness (e.g. k-mer bias), and computational efficiency are three critical measurements for minimizer selection schemes. However, there exist trade-offs between kinds of minimizer variants. Generic, effective, and efficient are always the requirements for high-performance minimizer algorithms. Results We propose a simple minimizer operator as a refinement of the standard canonical minimizer. It takes only a few operations to compute. However, it can improve the k-mer repetitiveness, especially for the lexicographic order. It applies to other selection schemes of total orders (e.g. random orders). Moreover, it is computationally efficient and the density is close to that of the standard minimizer. The refined minimizer may benefit high-performance applications like binning and read mapping. Availability and implementation The source code of the benchmark in this work is available at the github repository https://github.com/xp3i4/mini_benchmar

Uncertainty quantification for random domains using periodic random variables

Partial differential equations (PDEs) with uncertain or random inputs have been considered in many studies of uncertainty quantification. In forward uncertainty quantification, one is interested in analyzing the stochastic response of the PDE subject to input uncertainty, which usually involves solving high-dimensional integrals of the PDE output over a sequence of stochastic variables. In practical computations, one typically needs to discretize the problem in several ways: approximating an infinite-dimensional input random field with a finite-dimensional random field, spatial discretization of the PDE using, e.g., finite elements, and approximating high-dimensional integrals using cubatures such as quasi-Monte Carlo methods. In this paper, we focus on the error resulting from dimension truncation of an input random field. We show how Taylor series can be used to derive theoretical dimension truncation rates for a wide class of problems and we provide a simple checklist of conditions that a parametric mathematical model needs to satisfy in order for our dimension truncation error bound to hold. Some of the novel features of our approach include that our results are applicable to non-affine parametric operator equations, dimensionally-truncated conforming finite element discretized solutions of parametric PDEs, and even compositions of PDE solutions with smooth nonlinear quantities of interest. As a specific application of our method, we derive an improved dimension truncation error bound for elliptic PDEs with lognormally parameterized diffusion coefficients. Numerical examples support our theoretical findings

Bridging discrete and continuous state spaces: Exploring the Ehrenfest process in time-continuous diffusion models

Generative modeling via stochastic processes has led to remarkable empirical results as well as to recent advances in their theoretical understanding. In principle, both space and time of the processes can be discrete or continuous. In this work, we study time-continuous Markov jump processes on discrete state spaces and investigate their correspondence to state-continuous diffusion processes given by SDEs. In particular, we revisit the Ehrenfest process, which converges to an Ornstein-Uhlenbeck process in the infinite state space limit. Likewise, we can show that the time-reversal of the Ehrenfest process converges to the time-reversed Ornstein-Uhlenbeck process. This observation bridges discrete and continuous state spaces and allows to carry over methods from one to the respective other setting. Additionally, we suggest an algorithm for training the time-reversal of Markov jump processes which relies on conditional expectations and can thus be directly related to denoising score matching. We demonstrate our methods in multiple convincing numerical experiments

Reaction coordinate flows for model reduction of molecular kinetics

In this work, we introduce a flow based machine learning approach called reaction coordinate (RC) flow for the discovery of low-dimensional kinetic models of molecular systems. The RC flow utilizes a normalizing flow to design the coordinate transformation and a Brownian dynamics model to approximate the kinetics of RC, where all model parameters can be estimated in a data-driven manner. In contrast to existing model reduction methods for molecular kinetics, RC flow offers a trainable and tractable model of reduced kinetics in continuous time and space due to the invertibility of the normalizing flow. Furthermore, the Brownian dynamics-based reduced kinetic model investigated in this work yields a readily discernible representation of metastable states within the phase space of the molecular system. Numerical experiments demonstrate how effectively the proposed method discovers interpretable and accurate low-dimensional representations of given full-state kinetics from simulations

Asymptotic stability of the equilibrium for the free boundary problem of a compressible atmospheric primitive model with physical vacuum

This paper concerns the large time asymptotic behavior of solutions to the free boundary problem of the compressible primitive equations in atmospheric dynamics with physical vacuum. Up to second order of the perturbations of an equilibrium, we have introduced a model of the compressible primitive equations with a specific viscosity and shown that the physical vacuum free boundary problem for this model system has a global-in-time solution converging to an equilibrium exponentially, provided that the initial data is a small perturbation of the equilibrium. More precisely, we introduce a new coordinate system by choosing the enthalpy (the square of sound speed) as the vertical coordinate, and thanks to the hydrostatic balance, the degenerate density at the free boundary admits a representation with separation of variables in the new coordinates. Such a property allows us to establish horizontal derivative estimates without involving the singular vertical derivative of the density profile, which plays a key role in our analysis

Application of dimension truncation error analysis to high-dimensional function approximation To appear in: 2022. Springer Verlag, 2024.

Parametric mathematical models such as parameterizations of partial differential equations with random coefficients have received a lot of attention within the field of uncertainty quantification. The model uncertainties are often represented via a series expansion in terms of the parametric variables. In practice, this series expansion needs to be truncated to a finite number of terms, introducing a dimension truncation error to the numerical simulation of a parametric mathematical model. There have been several studies of the dimension truncation error corresponding to different models of the input random field in recent years, but many of these analyses have been carried out within the context of numerical integration. In this paper, we study the L2 dimension truncation error of the parametric model problem. Estimates of this kind arise in the assessment of the dimension truncation error for function approximation in high dimensions. In addition, we show that the dimension truncation error rate is invariant with respect to certain transformations of the parametric variables. Numerical results are presented which showcase the sharpness of the theoretical results