Related papers: Life in Silico - Simulation of Complex Systems by …
Membrane systems are a biologically-inspired computational model based on the structure of biological cells and the way chemicals interact and traverse their membranes. Although their dynamics are described by rules, encoding membrane…
By introducing a common representational system for metadata that describe the employed simulation workflows, diverse sources of data and platforms in computational molecular engineering, such as workflow management systems, can become…
Cognitive BASIC is a minimal, BASIC-style prompting language and in-model interpreter that structures large language model (LLM) reasoning into explicit, stepwise execution traces. Inspired by the simplicity of retro BASIC, we repurpose…
Simulation models often have parameters as input and return outputs to understand the behavior of complex systems. Calibration is the process of estimating the values of the parameters in a simulation model in light of observed data from…
Declarative modeling uses symbolic expressions to represent models. With such expressions one can formalize high-level mathematical computations on models that would be difficult or impossible to perform directly on a lower-level simulation…
This paper is a brief update on developments in the BioDynaMo project, a new platform for computer simulations for biological research. We will discuss the new capabilities of the simulator, important new concepts simulation methodology as…
Catalytic nanoparticles restructure dynamically under reaction conditions, so their working morphology and activity are governed by temperature, pressure, and gas composition. However, converting experimentally specified environments into…
A modeling formalism is proposed for the description and study of living and life-like systems. It provides an abstract conceptual model framework for real life and evolution of biological organisms. It is proposed, that this model…
The emergence of a complex, large-scale organisation of cosmic matter into the Cosmic Web is a beautiful exemplification of how complexity can be produced by simple initial conditions and simple physical laws. In the epoch of Big Data in…
The simulation of complex stochastic network dynamics arising, for instance, from models of coupled biomolecular processes remains computationally challenging. Often, the necessity to scan a models' dynamics over a large parameter space…
We implement in a reactive programming framework a simulation of three aspects of quantum mechanics: self-interference, state superposition, and entanglement. The simulation basically consists in a cellular automaton embedded in a…
Splicing systems are generative mechanisms introduced by Tom Head in 1987 to model the biological process of DNA recombination. The computational engine of a splicing system is the "splicing operation", a cut-and-paste binary string…
This paper establishes a general framework for describing hybrid dynamical systems which is particularly suitable for numerical simulation. In this context, the data structures used to describe the sets and functions which comprise the…
Integrative biological simulations have a varied and controversial history in the biological sciences. From computational models of organelles, cells, and simple organisms, to physiological models of tissues, organ systems, and ecosystems,…
The basic idea of lifelike computing systems is the transfer of concepts in living systems to technical use that goes even beyond existing concepts of self-adaptation and self-organisation (SASO). As a result, these systems become even more…
Computer simulations have become an important tool across the biomedical sciences and beyond. For many important problems several different models or hypotheses exist and choosing which one best describes reality or observed data is not…
Control systems are usually modeled by differential equations describing how physical phenomena can be influenced by certain control parameters or inputs. Although these models are very powerful when dealing with physical phenomena, they…
This paper is a first step to chase the ambitious objective of developing a mathmatical theory of living systems. The contents refer modeling large systems of interacting living entities with the aim of describing their collective behaviors…
Molecular dynamics simulations use statistical mechanics at the atomistic scale to enable both the elucidation of fundamental mechanisms and the engineering of matter for desired tasks. The behavior of molecular systems at the microscale is…
Decades of hardware, methodological, and algorithmic development have propelled molecular dynamics (MD) simulations to the forefront of materials-modeling techniques, bridging the gap between electronic-structure theory and continuum…