Cluster-based reduced-order modelling of a mixing layer

We propose a novel cluster-based reduced-order modelling (CROM) strategy of unsteady flows. CROM combines the cluster analysis pioneered in Gunzburger's group (Burkardt et al. 2006) and and transition matrix models introduced in fluid dynamics in Eckhardt's group (Schneider et al. 2007). CROM constitutes a potential alternative to POD models and generalises the Ulam-Galerkin method classically used in dynamical systems to determine a finite-rank approximation of the Perron-Frobenius operator. The proposed strategy processes a time-resolved sequence of flow snapshots in two steps. First, the snapshot data are clustered into a small number of representative states, called centroids, in the state space. These centroids partition the state space in complementary non-overlapping regions (centroidal Voronoi cells). Departing from the standard algorithm, the probabilities of the clusters are determined, and the states are sorted by analysis of the transition matrix. Secondly, the transitions between the states are dynamically modelled using a Markov process. Physical mechanisms are then distilled by a refined analysis of the Markov process, e.g. using finite-time Lyapunov exponent and entropic methods. This CROM framework is applied to the Lorenz attractor (as illustrative example), to velocity fields of the spatially evolving incompressible mixing layer and the three-dimensional turbulent wake of a bluff body. For these examples, CROM is shown to identify non-trivial quasi-attractors and transition processes in an unsupervised manner. CROM has numerous potential applications for the systematic identification of physical mechanisms of complex dynamics, for comparison of flow evolution models, for the identification of precursors to desirable and undesirable events, and for flow control applications exploiting nonlinear actuation dynamics.Comment: 48 pages, 30 figures. Revised version with additional material. Accepted for publication in Journal of Fluid Mechanic

Simulation of fermionic lattice models in two dimensions with Projected Entangled-Pair States: Next-nearest neighbor Hamiltonians

In a recent contribution [Phys. Rev. B 81, 165104 (2010)] fermionic Projected Entangled-Pair States (PEPS) were used to approximate the ground state of free and interacting spinless fermion models, as well as the $t$-$J$ model. This paper revisits these three models in the presence of an additional next-nearest hopping amplitude in the Hamiltonian. First we explain how to account for next-nearest neighbor Hamiltonian terms in the context of fermionic PEPS algorithms based on simulating time evolution. Then we present benchmark calculations for the three models of fermions, and compare our results against analytical, mean-field, and variational Monte Carlo results, respectively. Consistent with previous computations restricted to nearest-neighbor Hamiltonians, we systematically obtain more accurate (or better converged) results for gapped phases than for gapless ones.Comment: 10 pages, 11 figures, minor change

Shell Model Monte Carlo Methods

We review quantum Monte Carlo methods for dealing with large shell model problems. These methods reduce the imaginary-time many-body evolution operator to a coherent superposition of one-body evolutions in fluctuating one-body fields; the resultant path integral is evaluated stochastically. We first discuss the motivation, formalism, and implementation of such Shell Model Monte Carlo (SMMC) methods. There then follows a sampler of results and insights obtained from a number of applications. These include the ground state and thermal properties of {\it pf}-shell nuclei, the thermal and rotational behavior of rare-earth and $\gamma$-soft nuclei, and the calculation of double beta-decay matrix elements. Finally, prospects for further progress in such calculations are discussed

Data-driven model reduction and transfer operator approximation

In this review paper, we will present different data-driven dimension reduction techniques for dynamical systems that are based on transfer operator theory as well as methods to approximate transfer operators and their eigenvalues, eigenfunctions, and eigenmodes. The goal is to point out similarities and differences between methods developed independently by the dynamical systems, fluid dynamics, and molecular dynamics communities such as time-lagged independent component analysis (TICA), dynamic mode decomposition (DMD), and their respective generalizations. As a result, extensions and best practices developed for one particular method can be carried over to other related methods

A finite state projection algorithm for the stationary solution of the chemical master equation

The chemical master equation (CME) is frequently used in systems biology to quantify the effects of stochastic fluctuations that arise due to biomolecular species with low copy numbers. The CME is a system of ordinary differential equations that describes the evolution of probability density for each population vector in the state-space of the stochastic reaction dynamics. For many examples of interest, this state-space is infinite, making it difficult to obtain exact solutions of the CME. To deal with this problem, the Finite State Projection (FSP) algorithm was developed by Munsky and Khammash (Jour. Chem. Phys. 2006), to provide approximate solutions to the CME by truncating the state-space. The FSP works well for finite time-periods but it cannot be used for estimating the stationary solutions of CMEs, which are often of interest in systems biology. The aim of this paper is to develop a version of FSP which we refer to as the stationary FSP (sFSP) that allows one to obtain accurate approximations of the stationary solutions of a CME by solving a finite linear-algebraic system that yields the stationary distribution of a continuous-time Markov chain over the truncated state-space. We derive bounds for the approximation error incurred by sFSP and we establish that under certain stability conditions, these errors can be made arbitrarily small by appropriately expanding the truncated state-space. We provide several examples to illustrate our sFSP method and demonstrate its efficiency in estimating the stationary distributions. In particular, we show that using a quantised tensor train (QTT) implementation of our sFSP method, problems admitting more than 100 million states can be efficiently solved.Comment: 8 figure

The Dynamics of Group Codes: Dual Abelian Group Codes and Systems

Fundamental results concerning the dynamics of abelian group codes (behaviors) and their duals are developed. Duals of sequence spaces over locally compact abelian groups may be defined via Pontryagin duality; dual group codes are orthogonal subgroups of dual sequence spaces. The dual of a complete code or system is finite, and the dual of a Laurent code or system is (anti-)Laurent. If C and C^\perp are dual codes, then the state spaces of C act as the character groups of the state spaces of C^\perp. The controllability properties of C are the observability properties of C^\perp. In particular, C is (strongly) controllable if and only if C^\perp is (strongly) observable, and the controller memory of C is the observer memory of C^\perp. The controller granules of C act as the character groups of the observer granules of C^\perp. Examples of minimal observer-form encoder and syndrome-former constructions are given. Finally, every observer granule of C is an "end-around" controller granule of C.Comment: 30 pages, 11 figures. To appear in IEEE Trans. Inform. Theory, 200

A finite state projection algorithm for the stationary solution of the chemical master equation

The chemical master equation (CME) is frequently used in systems biology to quantify the effects of stochastic fluctuations that arise due to biomolecular species with low copy numbers. The CME is a system of ordinary differential equations that describes the evolution of probability density for each population vector in the state-space of the stochastic reaction dynamics. For many examples of interest, this state-space is infinite, making it difficult to obtain exact solutions of the CME. To deal with this problem, the Finite State Projection (FSP) algorithm was developed by Munsky and Khammash (Jour. Chem. Phys. 2006), to provide approximate solutions to the CME by truncating the state-space. The FSP works well for finite time-periods but it cannot be used for estimating the stationary solutions of CMEs, which are often of interest in systems biology. The aim of this paper is to develop a version of FSP which we refer to as the stationary FSP (sFSP) that allows one to obtain accurate approximations of the stationary solutions of a CME by solving a finite linear-algebraic system that yields the stationary distribution of a continuous-time Markov chain over the truncated state-space. We derive bounds for the approximation error incurred by sFSP and we establish that under certain stability conditions, these errors can be made arbitrarily small by appropriately expanding the truncated state-space. We provide several examples to illustrate our sFSP method and demonstrate its efficiency in estimating the stationary distributions. In particular, we show that using a quantised tensor train (QTT) implementation of our sFSP method, problems admitting more than 100 million states can be efficiently solved.Comment: 8 figure

Sensitivity Analysis for Mirror-Stratifiable Convex Functions

This paper provides a set of sensitivity analysis and activity identification results for a class of convex functions with a strong geometric structure, that we coined "mirror-stratifiable". These functions are such that there is a bijection between a primal and a dual stratification of the space into partitioning sets, called strata. This pairing is crucial to track the strata that are identifiable by solutions of parametrized optimization problems or by iterates of optimization algorithms. This class of functions encompasses all regularizers routinely used in signal and image processing, machine learning, and statistics. We show that this "mirror-stratifiable" structure enjoys a nice sensitivity theory, allowing us to study stability of solutions of optimization problems to small perturbations, as well as activity identification of first-order proximal splitting-type algorithms. Existing results in the literature typically assume that, under a non-degeneracy condition, the active set associated to a minimizer is stable to small perturbations and is identified in finite time by optimization schemes. In contrast, our results do not require any non-degeneracy assumption: in consequence, the optimal active set is not necessarily stable anymore, but we are able to track precisely the set of identifiable strata.We show that these results have crucial implications when solving challenging ill-posed inverse problems via regularization, a typical scenario where the non-degeneracy condition is not fulfilled. Our theoretical results, illustrated by numerical simulations, allow to characterize the instability behaviour of the regularized solutions, by locating the set of all low-dimensional strata that can be potentially identified by these solutions