Related papers: The BioDynaMo Project: a platform for computer sim…
Scientific computing applications have benefited greatly from high performance computing infrastructure such as supercomputers. However, we are seeing a paradigm shift in the computational structure, design, and requirements of these…
Natural microbial communities contain hundreds to thousands of interacting species. For this reason, computational simulations are playing an increasingly important role in microbial ecology. In this manuscript, we present a new…
Recent research has extended methods from the fields of thermodynamics and statistical mechanics into other disciplines. Most notably, one recent work creates a unified theoretical framework to understand evolutionary biology, machine…
Nanoscale biosystems are widely used in numerous medical applications. The approaches for structure and function of the nanomachines that are available in the cell (natural nanomachines) are discussed. Molecular simulation studies have been…
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,…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
In this review we discuss the recent progress in the simulation of soft active matter systems and in particular the hydrodynamics of microswimmers using the method of multiparticle collision dynamics, which solves the hydrodynamic flows…
Biological systems are influenced by fluid mechanics at nearly all spatiotemporal scales. This broad relevance of fluid mechanics to biology has been increasingly appreciated by engineers and biologists alike, leading to continued expansion…
Agent-based modeling plays an essential role in gaining insights into biology, sociology, economics, and other fields. However, many existing agent-based simulation platforms are not suitable for large-scale studies due to the low…
We review recent advances in the design, synthesis, and modeling of active fluids. Active fluids have been at the center of many technological innovations and theoretical advances over the past two decades. Research on this new class of…
RNA function is intimately related to its structural dynamics. Molecular dynamics simulations are useful for exploring biomolecular flexibility but are severely limited by the accessible timescale. Enhanced sampling methods allow this…
After the emergence of quantum mechanics and realising its need for an accurate understanding of physical systems, numerical methods were being used to undergo quantum mechanical treatment. With increasing system correlations and size,…
The study of biological systems witnessed a pervasive cross-fertilization between experimental investigation and computational methods. This gave rise to the development of new methodologies, able to tackle the complexity of biological…
Although simulation represents a major advance in the understanding of problems in complex systems, the field currently does not has standards in place that would guide the reporting of the data underlying each model, the process for model…
With the rise of computers, simulation models have emerged beside the more traditional statistical and mathematical models as a third pillar for ecological analysis. Broadly speaking, a simulation model is an algorithm, typically…
Reaction systems are a computational model inspired by the bio-chemical reactions that happen inside biological cells. They have been and currently are studied for their many nice theoretical properties. They are also a useful modeling tool…
The ubiquitous presence of computer simulations in all kinds of research areas evidence their role as the new driving force for the advancement of science and engineering research. Nothing seems to escape the image of success that computer…
The number of tools for dynamics simulation has grown in the last years. It is necessary for the robotics community to have elements to ponder which of the available tools is the best for their research. As a complement to an objective and…
The emergence of multicellularity and developmental programs are among the major problems of evolutionary biology. Traditionally, research in this area has been based on the combination of data analysis and experimental work on one hand and…
Simulating the dynamics of non-equilibrium matter under extreme conditions lies beyond the capabilities of classical computation alone. Remarkable advances in quantum information science and technology are profoundly changing how we…