Related papers: Life in Silico - Simulation of Complex Systems by …
The goal of this paper is to advance an extensible theory of living systems using an approach to biomathematics and biocomputation that suitably addresses self-organized, self-referential and anticipatory systems with multi-temporal…
Enzyme-catalysed reactions involve two distinct timescales. There is a short timescale on which enzymes bind to substrate molecules to produce bound complexes, and a comparatively long timescale on which the complex is transformed into a…
The aim of this paper is to propose an alternative behavioural definition of computation (and of a computer) based simply on whether a system is capable of reacting to the environment-the input-as reflected in a measure of programmability.…
Since the turn of the millennium, computational modelling of biological systems has evolved remarkably and sees matured use spanning basic and clinical research. While the topic of the peri-millennial debate about the virtues and…
Recently, symbolic computation and computer algebra systems have been successfully applied in systems biology, especially in chemical reaction network theory. One advantage of symbolic computation is its potential for qualitative answers to…
We introduce Simulation Streams, a programming paradigm designed to efficiently control and leverage Large Language Models (LLMs) for complex, dynamic simulations and agentic workflows. Our primary goal is to create a minimally interfering…
The standard engineering approach to modelling of complex systems is highly compositional. In order to be able to understand (or to control) the behavior of a complex dynamical systems, it is often desirable, if not necessary, to view this…
Bio-digital systems that merge microbial life with technology promise new modes of computation, combining biological adaptability with digital precision. Yet realizing this potential symbiotically -- where biological and digital agents…
Entropic dynamics, a program that aims at deriving the laws of physics from standard probabilistic and entropic rules for processing information, is developed further. We calculate the probability for an arbitrary path followed by a system…
Quantum computing, an innovative computing system carrying prominent processing rate, is meant to be the solutions to problems in many fields. Among these realms, the most intuitive application is to help chemical researchers correctly…
The introduction of computational models in cardiovascular sciences has been progressively bringing new and unique tools for the investigation of the physiopathology. Together with the dramatic improvement of imaging and measuring devices…
Quantum computing employs controllable interactions to perform sequences of logical gates and entire algorithms on quantum registers. This paradigm has been widely explored, e.g., for simulating dynamics of manybody systems by decomposing…
We present a composable design scheme for the development of hybrid quantum/classical algorithms and workflows for applications of quantum simulation. Our object-oriented approach is based on constructing an expressive set of common data…
Computation, if treated as a set of physical processes that act on information represented by states of matter, encompasses biological systems, digital systems, and other constructs, and may be a fundamental measure of living systems. The…
An early-stage version of simulation package is developed for electronic structure calculation and dynamics of atom process in large-scale systems, particularly, nm-scale or 10nm-scale systems. We adopted the Extensible Markup Language…
As known, any numerical simulation is composed of two parts: (1) the initial part of writing the relevant code and (2) the running of this code on the computer screen. The second part of running the program is extensively discussed…
In a world made of atoms, the computer simulation of molecular systems, such as proteins in water, plays an enormous role in science. Software packages that perform these computations have been developed for decades. In molecular…
The multifarious internal workings of organisms are difficult to reconcile with a single feature defining a state of being alive. Indeed, definitions of life rely on emergent properties (growth, capacity to evolve, agency) only symptomatic…
Quantum computers are expected to be considerably more efficient than classical computers for the execution of some specific tasks. The difficulty in the practical implementation of thoose computers is to build a microscopic quantum system…
We introduce tqix.pis, a library of tqix, for quantum dynamics simulation of spin ensembles. The library emulates a dynamic process by a quantum circuit, including initializing a quantum state, executing quantum operators, and measuring the…