Related papers: A numerical strategy for coarse-graining two-dimen…
We introduce a closure model for coarse-grained kinetic theories of polar active fluids. Based on a quasi-equilibrium approximation of the particle distribution function, the model closely captures important analytical properties of the…
We review a coarse-graining strategy (multiblob approach) for polymer solutions in which groups of monomers are mapped onto a single atom (a blob) and effective blob-blob interactions are obtained by requiring the coarse-grained model to…
The Numerical Assembly Technique is extended to investigate arbitrary planar frame structures with the focus on the computation of natural frequencies. This allows us to obtain highly accurate results without resorting to spatial…
Stochastic Thermodynamics uses Markovian jump processes to model random transitions between observable mesoscopic states. Physical currents are obtained from anti-symmetric jump observables defined on the edges of the graph representing the…
A common tool in the practice of Markov Chain Monte Carlo is to use approximating transition kernels to speed up computation when the desired kernel is slow to evaluate or intractable. A limited set of quantitative tools exist to assess the…
The recently introduced concept of generalized thermodynamics is explored here in the context of 1d, 2d and 3d data analysis, performed on samples drawn from a 3d X-ray soil sample image. Different threshold levels are used to binarize the…
We establish, through coarse-grained computation, a connection between traditional, continuum numerical algorithms (initial value problems as well as fixed point algorithms) and atomistic simulations of the Larson model of micelle…
Descriptions of molecular systems usually refer to two distinct theoretical frameworks. On the one hand the quantum pure state, i.e. the wavefunction, of an isolated system which is determined to calculate molecular properties and to…
Markov state models (MSMs)---or discrete-time master equation models---are a powerful way of modeling the structure and function of molecular systems like proteins. Unfortunately, MSMs with sufficiently many states to make a quantitative…
The recently proposed strategy for studying the equilibrium thermodynamics of the glass phase using a molecular liquid is reviewed and tested in details on the solvable case of the $p$-spin model. We derive the general phase diagram, and…
A piecewise-deterministic Markov process, specified by random jumps and switching semi-flows, as well as the associated Markov chain given by its post-jump locations, are investigated in this paper. The existence of an exponentially…
In this manuscript, an original numerical procedure for the nonlinear peridynamics on arbitrarily--shaped two-dimensional (2D) closed manifolds is proposed. When dealing with non parameterized 2D manifolds at the discrete scale, the problem…
The second-order, small-scale dependence structure of a stochastic process defined in the space-time domain is key to prediction (or kriging). While great efforts have been dedicated to developing models for cases in which the spatial…
A generalized understanding of protein dynamics is an unsolved scientific problem, the solution of which is critical to the interpretation of the structure-function relationships that govern essential biological processes. Here, we approach…
Gauge-invariant polynomial functions of matrix and tensor variables capture combinatorial structures of gauge-string duality, which can be usefully organised using finite-dimensional associative algebras. I review recent work on eigenvalue…
For a 2-dimensional freely jointed chain with 3 particles and a related model, the average and variance of the kinetic energies of each particle in thermal equilibrium are exactly obtained. The same is done for a related model. The excess…
We present a rigorous thermodynamic treatment of irreversible binary aggregation. We construct the Smoluchowski ensemble as the set of discrete finite distributions generated from the same initial state of all monomers upon fixed number…
Progress in describing thermodynamic phase transitions in quantum systems is obtained by noticing that the Gibbs operator $e^{-\beta H}$ for a two-dimensional (2D) lattice system with a Hamiltonian $H$ can be represented by a…
We derive an upper bound for the expected gain of informed traders in the Glosten-Milgrom model with finite horizon, fully analogous to a generalized second law of thermodynamics. This result extends that obtained by Touzo et al. a couple…
We survey an area of recent development, relating dynamics to theoretical computer science. We discuss the theoretical limits of simulation and computation of interesting quantities in dynamical systems. We will focus on central objects of…