Related papers: Coarse-graining and compounding as monads
Coarse-graining offers a means to extend the achievable time and length scales of molecular dynamics simulations beyond what is practically possible in the atomistic regime. Sampling molecular configurations of interest can be done…
In this paper we present a variational technique that handles coarse-graining and passing to a limit in a unified manner. The technique is based on a duality structure, which is present in many gradient flows and other variational…
We propose a new model for the description of complex granular particles and their interaction in molecular dynamics simulations of granular material in two dimensions. The grains are composed of triangles which are connected by deformable…
We develop a machine-learning method for coarse-graining condensed-phase molecular systems using anisotropic particles. The method extends currently available high-dimensional neural network potentials by addressing molecular anisotropy. We…
We study different fractional extensions of the Poisson process and generalized counting processes by introducing time-change represented by the inverse to the sums of stable and tempered stable subordinators. We state the governing…
It came to the attention of myself and the coauthors of (S., Rozowski, Silva, Rot, 2022) that a number of process calculi can be obtained by algebraically presenting the branching structure of the transition systems they specify. Labelled…
In recent years, simulation methods based on the scaling of atomic potential functions, such as quasi-coarse-grained dynamics and coarse-grained dynamics, have shown promising results for modeling crystalline systems at multiple scales.…
Folding and aggregation of proteins, the interaction between proteins and membranes, as well as the adsorption of organic soft matter to inorganic solid substrates belong to the most interesting challenges in understanding structure and…
In many contexts it is extremely costly to perform enough high quality experimental measurements to accurately parameterize a predictive quantitative model. However, it is often much easier to carry out large numbers of experiments that…
The framework of graded semantics uses graded monads to capture behavioural equivalences of varying granularity, for example as found on the linear-time/branching-time spectrum, over general system types. We describe a generic…
Constraints can be interpreted in a broad sense as any kind of explicit restriction over the parameters. While some constraints are defined directly on the parameter space, when they are instead defined by known behaviour on the model,…
We propose a new model for the description of complex granular particles and their interaction in molecular dynamics simulations of granular material in two dimensions. The grains are composed of triangles which are connected by deformable…
The notion of mutual unbiasedness for coarse-grained measurements of quantum continuous variable systems is considered. It is shown that while the procedure of "standard" coarse graining breaks the mutual unbiasedness between conjugate…
A point process on a space is a random bag of elements of that space. In this paper we explore programming with point processes in a monadic style. To this end we identify point processes on a space X with probability measures of bags of…
Many recursive functions can be defined elegantly as the unique homomorphisms, between two algebras, two coalgebras, or one each, that are induced by some universal property of a distinguished structure. Besides the well-known applications…
Some models of clustering processes are formulated and analytically solved employing generating functions methods. Those models include events which result from combined action of the coagulation and fragmentation processes. Fragmentation…
In the field of categorical probability, one uses concepts and techniques from category theory, such as monads and monoidal categories, to study the structures of probability and statistics. In this paper, we connect some ideas from…
Growing dimensionality of data calls for beyond-pairwise interactions quantification. Measures of multidimensional interactions quantification are hindered, among others, by two issues: 1. Interpretation difficulties, 2. the curse of…
We propose a degree-based coarse graining approach that not just accelerates the evaluation of dynamics on complex networks, but also satisfies the consistency conditions for both equilibrium statistical distributions and nonequilibrium…
A basic postulate of modern compositional approaches to generalised physical theories is the generalised Born rule, in which probabilities are postulated to be computable from the composition of states and effects. In this paper we consider…