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We consider a sharp interface formulation for the multi-phase Mullins-Sekerka flow. The flow is characterized by a network of curves evolving such that the total surface energy of the curves is reduced, while the areas of the enclosed phases are conserved. Making use of a variational formulation, we introduce a fully discrete finite element method. Our discretization features a parametric approximation of the moving interfaces that is independent of the discretization used for the equations in the bulk. The scheme can be shown to be unconditionally stable and to satisfy an exact volume conservation property. Moreover, an inherent tangential velocity for the vertices on the discrete curves leads to asymptotically equidistributed vertices, meaning no remeshing is necessary in practice. Several numerical examples, including a convergence experiment for the three-phase Mullins-Sekerka flow, demonstrate the capabilities of the introduced method.

Many mechanisms behind the evolution of cooperation, such as reciprocity, indirect reciprocity, and altruistic punishment, require group knowledge of individual actions. But what keeps people cooperating when no one is looking? Conformist norm internalization, the tendency to abide by the behavior of the majority of the group, even when it is individually harmful, could be the answer. In this paper, we analyze a world where (1) there is group selection and punishment by indirect reciprocity but (2) many actions (half) go unobserved, and therefore unpunished. Can norm internalization fill this "observation gap" and lead to high levels of cooperation, even when agents may in principle cooperate only when likely to be caught and punished? Specifically, we seek to understand whether adding norm internalization to the strategy space in a public goods game can lead to higher levels of cooperation when both norm internalization and cooperation start out rare. We found the answer to be positive, but, interestingly, not because norm internalizers end up making up a substantial fraction of the population, nor because they cooperate much more than other agent types. Instead, norm internalizers, by polarizing, catalyzing, and stabilizing cooperation, can increase levels of cooperation of other agent types, while only making up a minority of the population themselves.

This work presents a systematic methodology for describing the transient dynamics of coarse-grained molecular systems inferred from all-atom simulated data. We suggest Langevin-type dynamics where the coarse-grained interaction potential depends explicitly on time to efficiently approximate the transient coarse-grained dynamics. We apply the path-space force matching approach at the transient dynamics regime to learn the proposed model parameters. In particular, we parameterize the coarse-grained potential both with respect to the pair distance of the CG particles and the time, and we obtain an evolution model that is explicitly time-dependent. Moreover, we follow a data-driven approach to estimate the friction kernel, given by appropriate correlation functions directly from the underlying all-atom molecular dynamics simulations. To explore and validate the proposed methodology we study a benchmark system of a moving particle in a box. We examine the suggested model's effectiveness in terms of the system's correlation time and find that the model can approximate well the transient time regime of the system, depending on the correlation time of the system. As a result, in the less correlated case, it can represent the dynamics for a longer time interval. We present an extensive study of our approach to a realistic high-dimensional water molecular system. Posing the water system initially out of thermal equilibrium we collect trajectories of all-atom data for the, empirically estimated, transient time regime. Then, we infer the suggested model and strengthen the model's validity by comparing it with simplified Markovian models.

We present a novel stabilized isogeometric formulation for the Stokes problem, where the geometry of interest is obtained via overlapping NURBS (non-uniform rational B-spline) patches, i.e., one patch on top of another in an arbitrary but predefined hierarchical order. All the visible regions constitute the computational domain, whereas independent patches are coupled through visible interfaces using Nitsche's formulation. Such a geometric representation inevitably involves trimming, which may yield trimmed elements of extremely small measures (referred to as bad elements) and thus lead to the instability issue. Motivated by the minimal stabilization method that rigorously guarantees stability for trimmed geometries [1], in this work we generalize it to the Stokes problem on overlapping patches. Central to our method is the distinct treatments for the pressure and velocity spaces: Stabilization for velocity is carried out for the flux terms on interfaces, whereas pressure is stabilized in all the bad elements. We provide a priori error estimates with a comprehensive theoretical study. Through a suite of numerical tests, we first show that optimal convergence rates are achieved, which consistently agrees with our theoretical findings. Second, we show that the accuracy of pressure is significantly improved by several orders using the proposed stabilization method, compared to the results without stabilization. Finally, we also demonstrate the flexibility and efficiency of the proposed method in capturing local features in the solution field.

We give a short survey of recent results on sparse-grid linear algorithms of approximate recovery and integration of functions possessing a unweighted or weighted Sobolev mixed smoothness based on their sampled values at a certain finite set. Some of them are extended to more general cases.

Automata networks, and in particular Boolean networks, are used to model diverse networks of interacting entities. The interaction graph of an automata network is its most important parameter, as it represents the overall architecture of the network. A continuous amount of work has been devoted to infer dynamical properties of the automata network based on its interaction graph only. Robert's theorem is the seminal result in this area; it states that automata networks with an acyclic interaction graph converge to a unique fixed point. The feedback bound can be viewed as an extension of Robert's theorem; it gives an upper bound on the number of fixed points of an automata network based on the size of a minimum feedback vertex set of its interaction graph. Boolean networks can be viewed as self-mappings on the power set lattice of the set of entities. In this paper, we consider self-mappings on a general complete lattice. We make two conceptual contributions. Firstly, we can view a digraph as a residuated mapping on the power set lattice; as such, we define a graph on a complete lattice as a residuated mapping on that lattice. We extend and generalise some results on digraphs to our setting. Secondly, we introduce a generalised notion of dependency whereby any mapping $\phi$ can depend on any other mapping $\alpha$. In fact, we are able to give four kinds of dependency in this case. We can then vastly expand Robert's theorem to self-mappings on general complete lattices; we similarly generalise the feedback bound. We then obtain stronger results in the case where the lattice is a complete Boolean algebra. We finally show how our results can be applied to prove the convergence of automata networks.

Ordinary state-based peridynamic (OSB-PD) models have an unparalleled capability to simulate crack propagation phenomena in solids with arbitrary Poisson's ratio. However, their non-locality also leads to prohibitively high computational cost. In this paper, a fast solution scheme for OSB-PD models based on matrix operation is introduced, with which, the graphics processing units (GPUs) are used to accelerate the computation. For the purpose of comparison and verification, a commonly used solution scheme based on loop operation is also presented. An in-house software is developed in MATLAB. Firstly, the vibration of a cantilever beam is solved for validating the loop- and matrix-based schemes by comparing the numerical solutions to those produced by a FEM software. Subsequently, two typical dynamic crack propagation problems are simulated to illustrate the effectiveness of the proposed schemes in solving dynamic fracture problems. Finally, the simulation of the Brokenshire torsion experiment is carried out by using the matrix-based scheme, and the similarity in the shapes of the experimental and numerical broken specimens further demonstrates the ability of the proposed approach to deal with 3D non-planar fracture problems. In addition, the speed-up of the matrix-based scheme with respect to the loop-based scheme and the performance of the GPU acceleration are investigated. The results emphasize the high computational efficiency of the matrix-based implementation scheme.

We study solute-laden flow through permeable geological formations with a focus on advection-dominated transport and volume reactions. As the fluid flows through the permeable medium, it reacts with the medium, thereby changing the morphology and properties of the medium; this in turn, affects the flow conditions and chemistry. These phenomena occur at various lengths and time scales, and makes the problem extremely complex. Multiscale modeling addresses this complexity by dividing the problem into those at individual scales, and systematically passing information from one scale to another. However, accurate implementation of these multiscale methods are still prohibitively expensive. We present a methodology to overcome this challenge that is computationally efficient and quantitatively accurate. We introduce a surrogate for the solution operator of the lower scale problem in the form of a recurrent neural operator, train it using one-time off-line data generated by repeated solutions of the lower scale problem, and then use this surrogate in application-scale calculations. The result is the accuracy of concurrent multiscale methods, at a cost comparable to those of classical models. We study various examples, and show the efficacy of this method in understanding the evolution of the morphology, properties and flow conditions over time in geological formations.

We investigate the dynamics of chemical reaction networks (CRNs) with the goal of deriving an upper bound on their reaction rates. This task is challenging due to the nonlinear nature and discrete structure inherent in CRNs. To address this, we employ an information geometric approach, using the natural gradient, to develop a nonlinear system that yields an upper bound for CRN dynamics. We validate our approach through numerical simulations, demonstrating faster convergence in a specific class of CRNs. This class is characterized by the number of chemicals, the maximum value of stoichiometric coefficients of the chemical reactions, and the number of reactions. We also compare our method to a conventional approach, showing that the latter cannot provide an upper bound on reaction rates of CRNs. While our study focuses on CRNs, the ubiquity of hypergraphs in fields from natural sciences to engineering suggests that our method may find broader applications, including in information science.

Ordinary differential equations (ODEs) are widely used to model complex dynamics that arises in biology, chemistry, engineering, finance, physics, etc. Calibration of a complicated ODE system using noisy data is generally very difficult. In this work, we propose a two-stage nonparametric approach to address this problem. We first extract the de-noised data and their higher order derivatives using boundary kernel method, and then feed them into a sparsely connected deep neural network with ReLU activation function. Our method is able to recover the ODE system without being subject to the curse of dimensionality and complicated ODE structure. When the ODE possesses a general modular structure, with each modular component involving only a few input variables, and the network architecture is properly chosen, our method is proven to be consistent. Theoretical properties are corroborated by an extensive simulation study that demonstrates the validity and effectiveness of the proposed method. Finally, we use our method to simultaneously characterize the growth rate of Covid-19 infection cases from 50 states of the USA.