Related papers: Life in Silico - Simulation of Complex Systems by …
Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists…
MiMiC is a framework for performing multiscale simulations in which loosely coupled external programs describe individual subsystems at different resolutions and levels of theory. To make it highly efficient and flexible, we adopt an…
There has been on-going philosophical debate on whether artificial life models, also known as digital organisms, are truly alive. The main difficulty appears to be finding an encompassing and definite definition of life. By examining…
Many texts, especially in chemistry and biology, describe complex processes. We focus on texts that describe a chemical reaction process and questions that ask about the process's outcome under different environmental conditions. To answer…
Living organisms are not just random collections of organic molecules. There is continuous information processing going on in the apparent bouncing around of molecules of life. Optimisation criteria in this information processing can be…
To appear in Theory and Practice of Logic Programming (TPLP). Dynamic systems play a central role in fields such as planning, verification, and databases. Fragmented throughout these fields, we find a multitude of languages to formally…
Simulations, although powerful in accurately replicating real-world systems, often remain inaccessible to non-technical users due to their complexity. Conversely, large language models (LLMs) provide intuitive, language-based interactions…
Cellular automata are arrays of finite state machines that can exist in a finite number of states. These machines update their states simultaneously based on specific local rules that govern their interactions. This framework provides a…
One of the defining features of living systems is their adaptability to changing environmental conditions. This requires organisms to extract temporal and spatial features of their environment, and use that information to compute the…
The cognitive sciences aim to understand intelligence by formalizing underlying operations as computational models. Traditionally, this follows a cycle of discovery where researchers develop paradigms, collect data, and test predefined…
We describe a visual programming language for defining behaviors manifested by reified actors in a 2D virtual world that can be compiled into programs comprised of sequences of combinators that are themselves reified as actors. This makes…
An approach for incorporating embedded simulation and analysis capabilities in complex simulation codes through template-based generic programming is presented. This approach relies on templating and operator overloading within the C++…
Quantum simulation is central to understanding and designing quantum systems across physics and chemistry. Yet it has barriers to access from both computational complexity and computational perspectives, due to the exponential growth of…
Composition is a powerful principle for systems biology, focused on the interfaces, interconnections, and orchestration of distributed processes to enable integrative multiscale simulations. Whereas traditional models focus on the structure…
Scientific applications produce a huge amount of data, which imposes serious management and analysis challenges. In particular, limitations in current database management systems prevent their adoption in simulation applications, in which…
The term "In Silico Trial" indicates the use of computer modelling and simulation to evaluate the safety and efficacy of a medical product, whether a drug, a medical device, a diagnostic product or an advanced therapy medicinal product.…
We introduce \textsc{qcmath}, a user-friendly quantum chemistry software tailored for electronic structure calculations, implemented using the Wolfram Mathematica language and available at \url{https://github.com/LCPQ/qcmath}. This…
Computation is commonly defined as the execution of abstract algorithms over symbolic representations, with physical systems treated as substrates that realise predefined operations. While effective for engineered machines, this separation…
The network of biochemical reactions inside living organisms is characterized by an overwhelming complexity which stems from the sheer number of reactions and from the complicated topology of biochemical cycles. However the high speed of…
Simulating the unitary dynamics of a quantum system is a fundamental problem of quantum mechanics, in which quantum computers are believed to have significant advantage over their classical counterparts. One prominent such instance is the…