Related papers: Life in Silico - Simulation of Complex Systems by …
Reaction systems are discrete dynamical systems inspired by bio-chemical processes, whose dynamical behaviour is expressed by set-theoretic operations on finite sets. Reaction systems thus provide a description of bio-chemical phenomena…
The use of computer simulations to study the properties of aqueous systems is, today more than ever, an active area of research. In this context, during the last decade there has been a tremendous growth in the use of data-driven approaches…
The genetic blueprint for the essential functions of life is encoded in DNA, which is translated into proteins -- the engines driving most of our metabolic processes. Recent advancements in genome sequencing have unveiled a vast diversity…
The modelling and analysis of biological systems has deep roots in Mathematics, specifically in the field of Ordinary Differential Equations. Alternative approaches based on formal calculi, often derived from process algebras or term…
Computer-aided design for synthetic biology promises to accelerate the rational and robust engineering of biological systems; it requires both detailed and quantitative mathematical and experimental models of the processes to (re)design,…
The in silico simulations are widely used in contemporary systems biology including the analysis of nerve pulse propagation. As known from numerous experiments, the propagation of an action potential is accompanied by mechanical and thermal…
We present an approach of using AI to model and simulate biology and life. Why is it important? Because at the core of medicine, pharmacy, public health, longevity, agriculture and food security, environmental protection, and clean energy,…
A universal framework is proposed, where all laws are regularities of relations between things or agents. Parts of the world at one or all times are modeled as networks called SYSTEMS with a minimum of axiomatic properties. A notion of…
Owing to the computational complexity of electronic structure algorithms running on classical digital computers, the range of molecular systems amenable to simulation remains tightly circumscribed even after many decades of work. Quantum…
This paper is an opinion paper that looks at the future of computing in the age of Generative \& Agentic AI. Current software systems are static and inflexible, leading to significant challenges in translating human goals into computational…
The aim of this review is to highlight the possibility to apply the mathematical formalism and methodology of quantum theory to model behaviour of complex biosystems, from genomes and proteins to animals, humans, ecological and social…
Unlike computation or the numerical analysis of differential equations, simulation does not have a well established conceptual and mathematical foundation. Simulation is an arguable unique union of modeling and computation. However,…
A unified mathematical language for medicine and science will be presented. Using this language, models for DNA replication, protein synthesis, chemical reactions, neurons and a cardiac cycle of a heart have been built. Models for Turing…
Probabilistic inference provides a language for describing how organisms may learn from and adapt to their environment. The computations needed to implement probabilistic inference often require specific representations, akin to having the…
A central strategy of synthetic biology is to understand the basic processes of living creatures through engineering organisms using the same building blocks. Biological machines described in terms of parts can be studied by computer…
We extend the concept that life is an informational phenomenon, at every level of organisation, from molecules to the global ecological system. According to this thesis: (a) living is information processing, in which memory is maintained by…
Computational screening of naturally occurring proteins has the potential to identify efficient catalysts among the hundreds of millions of sequences that remain uncharacterized. Current experimental methods remain time, cost and labor…
Automation is becoming ubiquitous in all laboratory activities, leading towards precisely defined and codified laboratory protocols. However, the integration between laboratory protocols and mathematical models is still lacking. Models…
Systems Biology has emerged in the last years as a new holistic approach based on the global understanding of cells instead of only being focused on their individual parts (genes or proteins), to better understand the complexity of human…
Both experimental and computational biology is becoming increasingly automated. Laboratory experiments are now performed automatically on high-throughput machinery, while computational models are synthesized or inferred automatically from…