Related papers: Life in Silico - Simulation of Complex Systems by …
Traditionally, numerical algorithms are seen as isolated pieces of code confined to an {\em in silico} existence. However, this perspective is not appropriate for many modern computational approaches in control, learning, or optimization,…
Human intelligence emerged through the process of natural selection and evolution on Earth. We investigate what it would take to re-create this process in silico. While past work has often focused on low-level processes (such as simulating…
Biology has taken strong steps towards becoming a computer science aiming at reprogramming nature after the realisation that nature herself has reprogrammed organisms by harnessing the power of natural selection and the digital prescriptive…
Simulations of biophysical systems inevitably include steps that correspond to time integrations of ordinary differential equations. These equations are often related to enzyme action in the synthesis and destruction of molecular species,…
A cellular automaton is a deterministic and exactly computable dynamical system which mimics certain fundamental aspects of physical dynamics such as spatial locality and finite entropy. CA systems can be constructed which have additional…
Scientific computation is a discipline that combines numerical analysis, physical understanding, algorithm development, and structured programming. Several yottacycles per year on the world's largest computers are spent simulating problems…
We introduce a natural language interface for building stochastic pi calculus models of biological systems. In this language, complex constructs describing biochemical events are built from basic primitives of association, dissociation and…
Many real-world dynamic systems, both natural and artificial, are understood to be performing computations. For artificial dynamic systems, explicitly designed to perform computation - such as digital computers - by construction, we can…
Quantum computers could potentially simulate the dynamics of systems such as polyatomic molecules on a much larger scale than classical computers. We investigate a general quantum computational algorithm that simulates the time evolution of…
Biology stores information and computes at the molecular scale, yet the ways in which it does so are often distinct from human-engineered computers. Mapping biological computation onto architectures familiar to computer science remains an…
The study of system complexity primarily has two objectives: to explore underlying patterns and to develop theoretical explanations. Pattern exploration seeks to clarify the mechanisms behind the emergence of system complexity, while…
This study examines the simulation of quantum algorithms on a classical computer. The program code implemented on a classical computer will be a straight connection between the mathematical formulation of quantum mechanics and computational…
Computer simulations have become a very powerful tool for scientific research. In order to facilitate research in computational biology, the BioDynaMo project aims at a general platform for biological computer simulations, which should be…
An object-oriented combinator chemistry was used to construct an artificial organism with a system architecture possessing characteristics necessary for organisms to evolve into more complex forms. This architecture supports modularity by…
Models of complicated systems can be represented in different ways - in scientific papers, they are represented using natural language text as well as equations. But to be of real use, they must also be implemented as software, thus making…
Nature has found one method of organizing living matter, but maybe other options exist -- not yet discovered -- on how to create life. To study the life "as it could be" is the objective of an interdisciplinary field called Artificial Life…
The difficulty of simulating quantum systems, well-known to quantum chemists, prompted the idea of quantum computation. One can avoid the steep scaling associated with the exact simulation of increasingly large quantum systems on…
Enhanced sampling algorithms have emerged as powerful methods to extend the utility of molecular dynamics simulations and allow the sampling of larger portions of the configuration space of complex systems in a given amount of simulation…
System and synthetic biology are rapidly evolving systems, but both lack tools such as those used in engineering environments to shift the their focus from the design of parts (details) to the design of systems (behaviors); to aggravate,…
We advocate here the use of computational logic for systems biology, as a \emph{unified and safe} framework well suited for both modeling the dynamic behaviour of biological systems, expressing properties of them, and verifying these…