Related papers: The BioDynaMo Project
Biology is at the precipice of a new era where AI accelerates and amplifies the ability to study how cells operate, organize, and work as systems, revealing why disease happens and how to correct it. Organizations globally are prioritizing…
The growth of the software industry has gone hand in hand with the development of tools and cultural practices for ensuring the reliability of complex pieces of software. These tools and practices are now acknowledged to be essential to the…
In research labs, there is often a need to customise software at every step in a given bioinformatics workflow, but traditionally it has been difficult to obtain both a high degree of customisability and good performance.…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
Artificial life is a research field studying what processes and properties define life, based on a multidisciplinary approach spanning the physical, natural and computational sciences. Artificial life aims to foster a comprehensive study of…
The advent of experimental science facilities-instruments and observatories, such as the Large Hadron Collider, the Laser Interferometer Gravitational Wave Observatory, and the upcoming Large Synoptic Survey Telescope-has brought about…
The past decade has witnessed a dramatic increase in the size and scope of biological and behavioral experiments. These experiments are providing an unprecedented level of detail and depth of data. However, this increase in data presents…
Neural MMO is a computationally accessible research platform that combines large agent populations, long time horizons, open-ended tasks, and modular game systems. Existing environments feature subsets of these properties, but Neural MMO is…
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…
High-performance scientific simulations, important for comprehension of complex systems, encounter computational challenges especially when exploring extensive parameter spaces. There has been an increasing interest in developing deep…
The speed and the versatility of today's computers open up new opportunities to simulate complex biological systems. Here we review a computational approach recently proposed by us to model large tumor cell populations and spheroids, and we…
The complexity of biological systems and processes, spanning molecular to macroscopic scales, necessitates the use of multiscale simulations to get a comprehensive understanding. Quantum mechanics/molecular mechanics (QM/MM) molecular…
Simulations - utilizing computers to solve complicated science and engineering problems - are a key ingredient of modern science. The U.S. Department of Energy (DOE) is a world leader in the development of high-performance computing (HPC),…
Molecular-dynamics algorithms for systems of particles interacting through discrete or "hard" potentials are fundamentally different to the methods for continuous or "soft" potential systems. Although many software packages have been…
Excellent computer simulations are done for a purpose. The most valid purposes are to explore uncharted territory, to resolve a well-posed scientific or technical question, or to make a design choice. Stand-alone modeling can serve the…
This paper presents the design, development, and application of a novel space simulation environment for rapidly prototyping and testing flight software for distributed space systems. The environment combines the flexibility, determinism,…
Multiscale simulations are essential in the biomedical domain to accurately model human physiology. We present a modular approach for designing, constructing and executing multiscale simulations on a wide range of resources, from desktops…
Brain computer interfaces (BCI) provide a direct communication link between the brain and a computer or other external devices. They offer an extended degree of freedom either by strengthening or by substituting human peripheral working…
Understanding the behaviour of biological systems requires a complex setting of in vitro and in vivo experiments, which attracts high costs in terms of time and resources. The use of mathematical models allows researchers to perform…
Dynamics play a critical role in computation. The principled evolution of states over time enables both biological and artificial networks to represent and integrate information to make decisions. In the past few decades, significant…