Related papers: The BioDynaMo Project: a platform for computer sim…
It is essential to find new ways of enabling experts in different disciplines to collaborate more efficient in the development of ever more complex systems, under increasing market pressures. One possible solution for this challenge is to…
Dormancy is an essential strategy for microorganisms to cope with environmental stress. However, global ecosystem models typically ignore microbial dormancy, resulting in major model uncertainties. To facilitate the consideration of…
The concepts and methods of Systems Biology are being extended to neuropharmacology, to test and design drugs against neurological and psychiatric disorders. Computational modeling by integrating compartmental neural modeling technique and…
Quantum biology is an emerging field of research that concerns itself with the experimental and theoretical exploration of non-trivial quantum phenomena in biological systems. In this tutorial overview we aim to bring out fundamental…
The challenge of translating vast, multimodal biological data into predictive and mechanistic understanding of cellular function is a central theme in modern biology. Virtual cells, or digital cellular twins, have emerged as a critical…
Modeling and simulation of complex systems is key to explore systems dynamics. Many scientific approaches were developed to represent dynamic structure systems but most of these approaches are efficient for some kinds of systems and…
Modern biology and biomedicine are undergoing a big-data explosion needing advanced computational algorithms to extract mechanistic insights on the physiological state of living cells. We present the motivation for the Cell Physiome: a…
Biomolecular condensates constitute a newly recognized form of spatial organization in living cells. Although many condensates are believed to form as a result of phase separation, the physicochemical properties that determine the phase…
Event-driven molecular dynamics is a valuable tool in condensed and soft matter physics when particles can be modeled as hard objects or more generally if their interaction potential can be modeled in a stepwise fashion. Hard spheres model…
Molecular dynamics simulations have a prominent role in biophysics and drug discovery due to the atomistic information they provide on the structure, energetics and dynamics of biomolecules. Specialized software packages are required to…
While experimental advancements continue to expand the capabilities to control and probe non-equilibrium quantum matter at an unprecedented level, the numerical simulation of the dynamics of correlated quantum systems remains a pivotal…
With the rapid development of artificial intelligence (AI), it is foreseeable that the accuracy and efficiency of dynamic analysis for future power system will be greatly improved by the integration of dynamic simulators and AI. To explore…
Simulation of non-adiabatic dynamics of a quantum system coupled to dissipative environments poses significant challenges. New sophisticated methods are regularly being developed with an eye towards moving to larger systems and more…
In this paper we name some of the advantages of virtual laboratories; and propose that a Behaviours Virtual Laboratory should be useful for both biologists and AI researchers, offering a new perspective for understanding adaptive behaviour.…
A new approach to simulating warm and hot dense matter that combines density functional theory based calculations of the electronic structure to classical molecular dynamics simulations with pair interaction potentials is presented. The new…
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.…
Creating the best possible conditions is essential for proper cell growth. Incubators, a type of biotechnological instrument, are used to simulate this condition and maintain the cells within them. The processes involved in creating a…
A key element of the European Union's Human Brain Project (HBP) and other large-scale brain research projects is simulation of large-scale model networks of neurons. Here we argue why such simulations will likely be indispensable for…
The advent of hybrid computing platforms consisting of quantum processing units integrated with conventional high-performance computing brings new opportunities for algorithm design. By strategically offloading select portions of the…
Many aspects of the study of protein folding and dynamics have been affected by the recent advances in machine learning. Methods for the prediction of protein structures from their sequences are now heavily based on machine learning tools.…