Related papers: A numerical strategy for coarse-graining two-dimen…
Simulation schemes that allow to change molecular representation in a subvolume of the simulation box while preserving the equilibrium with the surrounding introduce conceptual problems of thermodynamic consistency. In this work we present…
We propose a numerical strategy to generate the anisotropic meshes and select the appropriate stabilized parameters simultaneously for two dimensional convection-dominated convection-diffusion equations by stabilized continuous linear…
Ideas and formalisms from far-from-equilibrium thermodynamics are ported to the context of stochastic computational processes, via following and extending Tadaki's algorithmic thermodynamics. A Principle of Maximum Algorithmic Caliber is…
The well-known Jewett-Krieger's Theorem states that each ergodic system has a strictly ergodic model. Strengthening the model by requiring that it is strictly ergodic under some group actions, and building the connection of the new model…
We study how to lift Markov bases and Gr\"obner bases along linear maps of lattices. We give a lifting algorithm that allows to compute such bases iteratively provided a certain associated semigroup is normal. Our main application is the…
We present a general and systematic theory of non-equilibrium dynamics of multi-component fluid membranes, in general, and membranes containing transmembrane proteins, in particular. Developed based on a minimal number of principles of…
We construct an ensemble distribution to describe steady immiscible two-phase flow of two incompressible fluids in a porous medium. The system is found to be ergodic. The distribution is used to compute macroscopic flow parameters. In…
We develop a new thermodynamic approach to stochastic graph-rewriting. The ingredients are a finite set of reversible graph-rewriting rules called generating rules, a finite set of connected graphs P called energy patterns and an energy…
The stochastic dynamics of biochemical networks are usually modelled with the chemical master equation (CME). The stationary distributions of CMEs are seldom solvable analytically, and numerical methods typically produce estimates with…
We employ the recently developed multi-time scale averaging method to study the large time behavior of slowly changing (in time) Hamiltonians. We treat some known cases in a new way, such as the Zener problem, and we give another proof of…
We consider the standard thermodynamic processes with constraints, but with additional uncertainty about the control parameters. Motivated by inductive reasoning, we assign prior distribution that provides a rational guess about likely…
We investigate one-dimensional families of diagonal forms, considering the evolution of the asymptotic formula and error term. We then discuss properties of the average asymptotic formula obtained. The subsequent second moment analysis…
This article concludes a three-part series developing a self-consistent theoretical framework of the electromechanics of lipid membranes at the continuum scale. Owing to their small thickness, lipid membranes are commonly modeled as…
We present an ab initio stochastic method for calculating thermal properties of a trapped, 1D Bose-gas covering the whole range from weak to strong interactions. Discretization of the problem results in a Bose-Hubbard-like Hamiltonian,…
We investigate the detailed properties of Observational entropy, introduced by \v{S}afr\'{a}nek et al. [Phys. Rev. A 99, 010101 (2019)] as a generalization of Boltzmann entropy to quantum mechanics. This quantity can involve multiple…
Tissue dynamics and collective cell motion are crucial biological processes. Their biological machinery is mostly known, and simulation models such as the "active vertex model" (AVM) exist and yield reasonable agreement with experimental…
We introduce and analyse ensembles of 2-regular random graphs with a tuneable distribution of short cycles. The phenomenology of these graphs depends critically on the scaling of the ensembles' control parameters relative to the number of…
Large-eddy simulation developments and validations are presented for an improved simulation of turbulent internal flows. Numerical methods are proposed according to two competing criteria: numerical qualities (precision and spectral…
The fluctuations of two-dimensional extended objects membranes is a rich and exciting field with many solid results and a wide range of open issues. We review the distinct universality classes of membranes, determined by the local order,…
We propose an efficient Markov Chain Monte Carlo method for sampling equilibrium distributions for stochastic lattice models, capable of handling correctly long and short-range particle interactions. The proposed method is a Metropolis-type…