Related papers: Coarse-graining and compounding as monads
We first define the coarse-graining of probability measures in terms of stochastic kernels. We define when a probability measure is part of another probability measure and say that two probability measures coexist if they are both parts of…
Coarse-graining is a standard method of extracting a simple Markov process from a more complicated one by identifying states. Here we extend coarse-graining to open Markov processes. An "open" Markov process is one where probability can…
Many biological systems can be described by finite Markov models. A general method for simplifying master equations is presented that is based on merging adjacent states. The approach preserves the steady-state probability distribution and…
In this paper, motivated by the theory of operads and PROPs we reveal the combinatorial nature of tensor calculus for strict tensor categories and show that there exists a monad which is described by the coarse-graining of graphs and…
Monads are a useful tool for structuring effectful features of computation such as state, non-determinism, and continuations. In the last decade, several generalisations of monads have been suggested which provide a more fine-grained model…
Structural and thermodynamic consistency of coarse-graining models across multiple length scales is essential for the predictive role of multi-scale modeling and molecular dynamic simulations that use mesoscale descriptions. Our approach is…
We review some recent coarse-graining and multi-scale methods, but also put forward some new ideas for addressing such issues. We find that, if one is guided by nonequilibrium statistical mechanics and thermodynamics, it is possible to…
Notions of computation can be modelled by monads. Algebraic effects offer a characterization of monads in terms of algebraic operations and equational axioms, where operations are basic programming features, such as reading or updating the…
Observing quantum effects such as superpositions and entanglement in macroscopic systems requires not only a system that is well protected against environmental decoherence, but also sufficient measurement precision. Motivated by recent…
We study a coarse-graining map arising from incomplete and imperfect addressing of particles in a multipartite quantum system. In its simplest form, corresponding to a two-qubit state, the resulting channel produces a convex mixture of the…
In the study of computational effects, it is important to consider the notion of computational effects with parameters. The need of such a notion arises when, for example, statically estimating the range of effects caused by a program, or…
For optimal processing and design of entangled polymeric materials it is important to establish a rigorous link between the detailed molecular composition of the polymer and the viscoelastic properties of the macroscopic melt. We review…
Data-based discovery of effective, coarse-grained (CG) models of high-dimensional dynamical systems presents a unique challenge in computational physics and particularly in the context of multiscale problems. The present paper offers a…
Multiscale molecular modeling is widely applied in scientific research of molecular properties over large time and length scales. Two specific challenges are commonly present in multiscale modeling, provided that information between the…
We implemented a coarse-graining procedure to construct mesoscopic models of complex molecules. The final aim is to obtain better results on properties depending on slow modes of the molecules. Therefore the number of particles considered…
The connection between coarse-graining of measurement and emergence of classicality has been investigated for some time, if not well understood. Recently in (PRL $\textbf{112}$, 010402, (2014)) it was pointed out that coarse-graining…
A coarse-grained simulation model eliminates microscopic degrees of freedom and represents a polymer by a simplified structure. A priori, two classes of coarse-grained models may be distinguished: those which are designed for a specific…
We present a categorical viewpoint of probability measures by showing that a probability measure can be viewed as a weakly averaging affine measurable functional taking values in the unit interval which preserves limits. The probability…
Coarse-graining has become an area of tremendous importance within many different research fields. For molecular simulation, coarse-graining bears the promise of finding simplified models such that long-time simulations of large-scale…
Simulations of condensed matter systems often focus on the dynamics of a few distinguished components but require integrating the dynamics of the full system. A prime example is a molecular dynamics simulation of a (macro)molecule in…