Related papers: Structural Cellular Hash Chemistry
Discovering the underlying relationships among variables from temporal observations has been a longstanding challenge in numerous scientific disciplines, including biology, finance, and climate science. The dynamics of such systems are…
This article shows how to specify and construct a discrete, stochastic, continuous-time model specifically for ecological systems. The model is more broad than typical chemical kinetics models in two ways. First, using time-dependent hazard…
We have extended our chemical and cosmological galaxy evolution model to calculate the abundance evolution for altogether 16 different elements in spiral galaxies in a chemically consistent way which is a considerable step towards a more…
This paper describes a novel approach to neighbour-finding in Smoothed Particle Hydrodynamics (SPH) simulations with large dynamic range in smoothing length. This approach is based on hierarchical cell decompositions, sorted interactions,…
The rapid advancement of artificial intelligence (AI) has demonstrated substantial potential in chemical engineering, yet existing AI systems remain limited in interdisciplinary collaboration and exploration of uncharted problems. To…
Since its introduction in 1952, Turing's (pre-)pattern theory ("the chemical basis of morphogenesis") has been widely applied to a number of areas in developmental biology. The related pattern formation models normally comprise a system of…
Biological living systems in general exhibit complex and diverse dynamics. The latter, in particular, is essential, since diversification increases the odds of survival of an organism while reducing the risk of extinction of the population.…
We develop a model to implement metal enrichment in a cosmological context based on the hydrodynamical AP3MSPH code described by Tissera, Lambas and Abadi (1997).The star formation model is based on the Schmidt law and has been modified in…
Disordered proteins and nucleic acids play key roles in cellular function and disease. Here we review recent advances in the computational exploration of the conformational dynamics of flexible biomolecules. We focus on hierarchical chain…
Metaheuristic algorithms such as Particle Swarm Optimization (PSO) and Evolutionary Algorithms (EA) excel at exploring solution spaces but lack mechanisms to accumulate and reuse procedural knowledge from successful search trajectories.…
Simulation of stochastic spatially-extended systems is a challenging problem. The fundamental quantities in these models are individual entities such as molecules, cells, or animals, which move and react in a random manner. In big systems,…
The Calculus of Wrapped Compartments (CWC) is a recently proposed modelling language for the representation and simulation of biological systems behaviour. Although CWC has no explicit structure modelling a spatial geometry, its compartment…
We propose SHARC, a novel framework that synthesizes arbitrary, genus-agnostic shapes by means of a collection of Spherical Harmonic (SH) representations of distance fields. These distance fields are anchored at optimally placed reference…
We take up the challenge of designing realistic computational models of large interacting cell populations. The goal is essentially to bring Gillespie's celebrated stochastic methodology to the level of an interacting population of cells.…
Self-evolution methods enhance code generation through iterative "generate-verify-refine" cycles, yet existing approaches suffer from low exploration efficiency, failing to discover solutions with superior complexity within limited budgets.…
Stochastic fluctuations of molecule numbers are ubiquitous in biological systems. Important examples include gene expression and enzymatic processes in living cells. Such systems are typically modelled as chemical reaction networks whose…
A series of modified cognitive-only particle swarm optimization (PSO) algorithms effectively mitigate premature convergence by constructing distinct vectors for different particles. However, the underutilization of these constructed vectors…
Understanding how chemical perturbations propagate through biological systems is essential for robust molecular property prediction. While most existing methods focus on chemical structures alone, recent advances highlight the crucial role…
The structural and dynamic properties of the dark matter halos, though an important ingredient in understanding large-scale structure formation, require more conservative particle resolution than those required by halo mass alone in a…
Issues in co-evolutionary population dynamics have long been studied via computationally intensive simulations of minimally simple agent-based models, known as Evolutionary Spatial Cyclic Games (ESCGs), involving multiple interacting…