Related papers: Life in Silico - Simulation of Complex Systems by …
In this talk I discuss the general question of the portability of Molecular Dynamics codes for diffusive systems on parallel computers of the APE family. The intrinsic single precision arithmetics of the today available APE platforms does…
We present MISTIQS, a Multiplatform Software for Time-dependent Quantum Simulations. MISTIQS delivers end-to-end functionality for simulating the quantum many-body dynamics of systems governed by time-dependent Heisenberg Hamiltonians…
Metabolic pathways describe chains of enzymatic reactions. Their modelling is a key point to understand living systems. An enzymatic reaction is an interaction between one or several metabolites (substrates) and an enzyme (simple protein or…
Ecosystems are complex and dynamic systems. Over billions of years, they have developed advanced capabilities to provide stable functions, despite changes in their environment. In this paper, we argue that the laws of organization and…
The quasi-steady state assumption (QSSA) forms the basis for rigorous mathematical justification of the Michaelis-Menten formalism commonly used in modeling a broad range of intracellular phenomena. A critical supposition of QSSA-based…
Large language models (LLMs) have demonstrated strong capabilities in knowledge representation and reasoning based on textual data. However, their reliance on language material alone limits their ability to adapt, verify reasoning outcomes,…
Cellular automata are a class of computational models based on simple rules and algorithms that can simulate a wide range of complex phenomena. However, when using conventional computers, these 'simple' rules are only encapsulated at the…
Computer simulations of coarse-grained molecular models for amphiphilic systems can provide insight into the the structure of amphiphiles at interfaces. They can help to identify the factors that determine the phase behavior, and they can…
We present an approach for the semiclassical treatment of open quantum systems. An expansion into localized states allows restriction of a simulation to a fraction of the environment that is located within a predefined vicinity of the…
Molecular biology and biochemistry interpret microscopic processes in the living world in terms of molecular structures and their interactions, which are quantum mechanical by their very nature. Whereas the theoretical foundations of these…
One of the most compelling problems in science consists in understanding how living systems process information. After all, the way they process information defines their capacities to learning and adaptation. There is an increasing…
The modelling and analysis of biological systems has deep roots in Mathematics, specifically in the field of ordinary differential equations (ODEs). Alternative approaches based on formal calculi, often derived from process algebras or term…
Enzymes are nano-scale machines that have evolved to drive chemical reactions out of equilibrium in the right place at the right time. Given the complexity and specificity of enzymatic function, bottom-up design of enzymes presents a…
Quantum computing systems depend on the principles of quantum mechanics to perform multiple challenging tasks more efficiently than their classical counterparts. In classical software engineering, the software life cycle is used to document…
Accurate simulation of dynamical processes in molecules and reactions is among the most challenging problems in quantum chemistry. Quantum computers promise efficient chemical simulation, but the existing quantum algorithms require many…
In silico tools are important for generating novel hypotheses and exploring alternatives in de novo metabolic pathway design. However, while many computational frameworks have been proposed for retrobiosynthesis, few successful examples of…
The ribosome is a macromolecular complex which is responsible for protein synthesis in all living cells according to their transcribed genetic information. Using X-ray crystallography and, more recently, cryo-electron microscopy (cryo-EM),…
Dynamics of biological-ecological systems is strongly depending on spatial dimensions. Most of powerful simulators in ecology take into account for system spatiality thus embedding stochastic processes. Due to the difficulty of researching…
In the last two decades, the growing trend of software development industry has made different aspects of software engineering more interesting for the computer science research community. Software development life-cycle is one of these…
For complex molecules, nuclear degrees of freedom can act as an environment for the electronic `system' variables, allowing the theory and concepts of open quantum systems to be applied. However, when molecular system-environment…