Related papers: Structural Cellular Hash Chemistry
The modelling and analysis of biological systems has deep roots in Mathematics, specifically in the field of ordinary differential equations (ODEs). Alternative approaches based on formal calculi, often derived from process algebras or term…
System dynamics (SD) is an effective approach for helping reveal the temporal behavior of complex systems. Although there have been recent developments in expanding SD to include systems' spatial dependencies, most applications have been…
Stochastic agent-based models can account for millions of cells with spatiotemporal movement that can be a function of different factors. However, these simulations can be computationally expensive. In this work, we develop a novel…
We present a new, open source, free semi-analytic model (SAM) of galaxy formation, Shark, designed to be highly flexible and modular, allowing easy exploration of different physical processes and ways of modelling them. We introduce the…
Biological cells can exchange messages through soluble molecules or membrane-bound receptors. In particular in the latter case, the interaction is usually located in specific regions of the interacting cells and may depend on or induce…
Costly cooperation and costly signaling are both difficult to reconcile with simple fitness maximization, yet both are common in biological and social systems. We study a model in which agents emit costly signals and condition their actions…
The M{\O}D computational framework implements rule-based generative chemistries as explicit transformations of graphs representing chemical structural formulae. Here, we expand M{\O}D by a stochastic simulation module that simulates the…
Localized representation of the Kohn-Sham subspace plays an important role in quantum chemistry and materials science. The recently developed selected columns of the density matrix (SCDM) method [J. Chem. Theory Comput. 11, 1463, 2015] is a…
Earth system models (ESMs) are fundamental for understanding Earth's complex climate system. However, the computational demands and storage requirements of ESM simulations limit their utility. For the newly published CESM2-LENS2 data, which…
The design and engineering of molecular communication (MC) components capable of processing chemical concentration signals is the key to unleashing the potential of MC for interdisciplinary applications. By controlling the signaling pathway…
This study explores the emergence of life through a simulation model approach. The model "Multi-set chemical lattice model" is a model that allows virtual molecules of multiple types to be placed in each lattice cell on a two-dimensional…
We present a novel methodology to improve predictions of galaxy formation histories by incorporating semi-stochastic corrections to account for short-timescale variability. Our paper addresses limitations in existing models that capture…
Coarse-grained (CG) conformational surface hopping (SH) adapts the concept of multisurface dynamics, initially developed to describe electronic transitions in chemical reactions, to accurately describe classical molecular dynamics at a…
The dynamics of cellular aggregates is driven by the interplay of mechanochemical processes and cellular activity. Although deterministic models may capture mechanical features, local chemical fluctuations trigger random cell responses,…
Traditional regression models assume stationary relationships between predictors and responses, failing to capture the spatial heterogeneity present in many environmental, epidemiological, and ecological processes. To address this…
We study the stochastic evolution of four species in cyclic competition in a well mixed environment. In systems composed of a finite number $N$ of particles these simple interaction rules result in a rich variety of extinction scenarios,…
Simulations are performed to investigate the nonlinear dynamics of a (2+1)-dimensional chemotaxis model of Keller-Segel (KS) type with a logistic growth term. Because of its ability to display auto-aggregation, the KS model has been widely…
Biochemical processes typically involve many chemical species, some in abundance and some in low molecule numbers. Here we first identify the rate constant limits under which the concentrations of a given set of species will tend to…
This paper presents the first substantial study of the chemistry of the envelopes around a sample of 18 low-mass pre- and protostellar objects for which physical properties have previously been derived from radiative transfer modeling of…
StocHy is a software tool for the quantitative analysis of discrete-time stochastic hybrid systems (SHS). StocHy accepts a high-level description of stochastic models and constructs an equivalent SHS model. The tool allows to (i) simulate…