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Genome assembly is a prominent problem studied in bioinformatics, which computes the source string using a set of its overlapping substrings. Classically, genome assembly uses assembly graphs built using this set of substrings to compute the source string efficiently, having a tradeoff between scalability and avoiding information loss. The scalable de Bruijn graphs come at the price of losing crucial overlap information. The complete overlap information is stored in overlap graphs using quadratic space. Hierarchical overlap graphs [IPL20] (HOG) overcome these limitations, avoiding information loss despite using linear space. After a series of suboptimal improvements, Khan and Park et al. simultaneously presented two optimal algorithms [CPM2021], where only the former was seemingly practical. We empirically analyze all the practical algorithms for computing HOG, where the optimal algorithm [CPM2021] outperforms the previous algorithms as expected, though at the expense of extra memory. However, it uses non-intuitive approach and non-trivial data structures. We present arguably the most intuitive algorithm, using only elementary arrays, which is also optimal. Our algorithm empirically proves even better for both time and memory over all the algorithms, highlighting its significance in both theory and practice. We further explore the applications of hierarchical overlap graphs to solve various forms of suffix-prefix queries on a set of strings. Loukides et al. [CPM2023] recently presented state-of-the-art algorithms for these queries. However, these algorithms require complex black-box data structures and are seemingly impractical. Our algorithms, despite failing to match the state-of-the-art algorithms theoretically, answer different queries ranging from 0.01-100 milliseconds for a data set having around a billion characters.

By computing a feedback control via the linear quadratic regulator (LQR) approach and simulating a non-linear non-autonomous closed-loop system using this feedback, we combine two numerically challenging tasks. For the first task, the computation of the feedback control, we use the non-autonomous generalized differential Riccati equation (DRE), whose solution determines the time-varying feedback gain matrix. Regarding the second task, we want to be able to simulate non-linear closed-loop systems for which it is known that the regulator is only valid for sufficiently small perturbations. Thus, one easily runs into numerical issues in the integrators when the closed-loop control varies greatly. For these systems, e.g., the A-stable implicit Euler methods fails.\newline On the one hand, we implement non-autonomous versions of splitting schemes and BDF methods for the solution of our non-autonomous DREs. These are well-established DRE solvers in the autonomous case. On the other hand, to tackle the numerical issues in the simulation of the non-linear closed-loop system, we apply a fractional-step-theta scheme with time-adaptivity tuned specifically to this kind of challenge. That is, we additionally base the time-adaptivity on the activity of the control. We compare this approach to the more classical error-based time-adaptivity.\newline We describe techniques to make these two tasks computable in a reasonable amount of time and are able to simulate closed-loop systems with strongly varying controls, while avoiding numerical issues. Our time-adaptivity approach requires fewer time steps than the error-based alternative and is more reliable.

The scale function holds significant importance within the fluctuation theory of Levy processes, particularly in addressing exit problems. However, its definition is established through the Laplace transform, thereby lacking explicit representations in general. This paper introduces a novel series representation for this scale function, employing Laguerre polynomials to construct a uniformly convergent approximate sequence. Additionally, we derive statistical inference based on specific discrete observations, presenting estimators of scale functions that are asymptotically normal.

This manuscript develops edge-averaged virtual element (EAVE) methodologies to address convection-diffusion problems effectively in the convection-dominated regime. It introduces a variant of EAVE that ensures monotonicity (producing an $M$-matrix) on Voronoi polygonal meshes, provided their duals are Delaunay triangulations with acute angles. Furthermore, the study outlines a comprehensive framework for EAVE methodologies, introducing another variant that integrates with the stiffness matrix derived from the lowest-order virtual element method for the Poisson equation. Numerical experiments confirm the theoretical advantages of the monotonicity property and demonstrate an optimal convergence rate across various mesh configurations.

We present a fully-integrated lattice Boltzmann (LB) method for fluid--structure interaction (FSI) simulations that efficiently models deformable solids in complex suspensions and active systems. Our Eulerian method (LBRMT) couples finite-strain solids to the LB fluid on the same fixed computational grid with the reference map technique (RMT). An integral part of the LBRMT is a new LB boundary condition for moving deformable interfaces across different densities. With this fully Eulerian solid--fluid coupling, the LBRMT is well-suited for parallelization and simulating multi-body contact without remeshing or extra meshes. We validate its accuracy via a benchmark of a deformable solid in a lid-driven cavity, then showcase its versatility through examples of soft solids rotating and settling. With simulations of complex suspensions mixing, we highlight potentials of the LBRMT for studying collective behavior in soft matter and biofluid dynamics.

Motivated by a recent work on a preconditioned MINRES for flipped linear systems in imaging, in this note we extend the scope of that research for including more precise boundary conditions such as reflective and anti-reflective ones. We prove spectral results for the matrix-sequences associated to the original problem, which justify the use of the MINRES in the current setting. The theoretical spectral analysis is supported by a wide variety of numerical experiments, concerning the visualization of the spectra of the original matrices in various ways. We also report numerical tests regarding the convergence speed and regularization features of the associated GMRES and MINRES methods. Conclusions and open problems end the present study.

Complex interval arithmetic is a powerful tool for the analysis of computational errors. The naturally arising rectangular, polar, and circular (together called primitive) interval types are not closed under simple arithmetic operations, and their use yields overly relaxed bounds. The later introduced polygonal type, on the other hand, allows for arbitrarily precise representation of the above operations for a higher computational cost. We propose the polyarcular interval type as an effective extension of the previous types. The polyarcular interval can represent all primitive intervals and most of their arithmetic combinations precisely and has an approximation capability competing with that of the polygonal interval. In particular, in antenna tolerance analysis it can achieve perfect accuracy for lower computational cost then the polygonal type, which we show in a relevant case study. In this paper, we present a rigorous analysis of the arithmetic properties of all five interval types, involving a new algebro-geometric method of boundary analysis.

In a regression model with multiple response variables and multiple explanatory variables, if the difference of the mean vectors of the response variables for different values of explanatory variables is always in the direction of the first principal eigenvector of the covariance matrix of the response variables, then it is called a multivariate allometric regression model. This paper studies the estimation of the first principal eigenvector in the multivariate allometric regression model. A class of estimators that includes conventional estimators is proposed based on weighted sum-of-squares matrices of regression sum-of-squares matrix and residual sum-of-squares matrix. We establish an upper bound of the mean squared error of the estimators contained in this class, and the weight value minimizing the upper bound is derived. Sufficient conditions for the consistency of the estimators are discussed in weak identifiability regimes under which the difference of the largest and second largest eigenvalues of the covariance matrix decays asymptotically and in ``large $p$, large $n$" regimes, where $p$ is the number of response variables and $n$ is the sample size. Several numerical results are also presented.

A discretization method with non-matching grids is proposed for the coupled Stokes-Darcy problem that uses a mortar variable at the interface to couple the marker and cell (MAC) method in the Stokes domain with the Raviart-Thomas mixed finite element pair in the Darcy domain. Due to this choice, the method conserves linear momentum and mass locally in the Stokes domain and exhibits local mass conservation in the Darcy domain. The MAC scheme is reformulated as a mixed finite element method on a staggered grid, which allows for the proposed scheme to be analyzed as a mortar mixed finite element method. We show that the discrete system is well-posed and derive a priori error estimates that indicate first order convergence in all variables. The system can be reduced to an interface problem concerning only the mortar variables, leading to a non-overlapping domain decomposition method. Numerical examples are presented to illustrate the theoretical results and the applicability of the method.