Related papers: The BioDynaMo Project: a platform for computer sim…
This paper presents the principal challenges and opportunities associated with computational biomechanics research. The underlying cognitive control involved in the process of human motion is inherently complex, dynamic, multidimensional,…
Integrative biological simulations have a varied and controversial history in the biological sciences. From computational models of organelles, cells, and simple organisms, to physiological models of tissues, organ systems, and ecosystems,…
Along with recent progress in structural biology and genome biology, structural dynamics of molecular systems including nucleic acids has attracted attention in the context of gene regulation. Structure-function relationship is an important…
In the world of Information Technology, new computing paradigms, driven by requirements of different classes of problems and applications, emerge rapidly. These new computing paradigms pose many new research challenges. Researchers from…
Molecular dynamics simulations have the potential to provide atomic-level detail and insight to important questions in chemical physics that cannot be observed in typical experiments. However, simply generating a long trajectory is…
Exploration of the structure formation and dynamics of animate and inanimate matter on the nanometer scale is a highly interdisciplinary field of rapidly emerging research. It is relevant for various molecular and nanoscale systems of…
The recent attention towards research and development in cyber-physical energy systems has introduced the necessity of emerging multi-domain co-simulation tools. Different educational, research and industrial efforts have been set to tackle…
This paper, part of a Roadmap article, provides an account of the status and the current challenges in the area of nuclear quantum dynamics simulations, and presents advances in theory and computational techniques to address these…
Dynamical systems see widespread use in natural sciences like physics, biology, chemistry, as well as engineering disciplines such as circuit analysis, computational fluid dynamics, and control. For simple systems, the differential…
Co-simulation consists of the theory and techniques to enable global simulation of a coupled system via the composition of simulators. Despite the large number of applications and growing interest in the challenges, the field remains…
Our understanding of the physics of biological molecules, such as proteins and DNA, is limited because the approximations we usually apply to model inert materials are not in general applicable to soft, chemically inhomogeneous systems. The…
In living systems, we often see the emergence of the ingredients necessary for computation -- the capacity for information transmission, storage, and modification -- begging the question of how we may exploit or imitate such biological…
Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various…
Nanoinformatics is a novel, rapidly growing area of research that involves the application of computational techniques to several aspects of research in the field of nanotechnology, especially concerned its application to biotechnology.…
A major goal of modern computational biology is to simulate the collective behaviour of large cell populations starting from the intricate web of molecular interactions occurring at the microscopic level. In this paper we describe a…
Recently we proposed a new constant-pressure molecular dynamics method for finite systems. In this paper, we discuss the current understanding of this method and its technique details. We also review the recent theoretical advances of…
Quantum Computing promises accelerated simulation of certain classes of problems, in particular in plasma physics. Given the nascent interest in applying quantum computing techniques to study plasma systems, a compendium of the relevant…
The molecular simulations solve the equation of motion of molecular systems, making 3D shapes of molecules four-dimensional by adding the time coordinate. These methods have a great potential in drug discovery because they can realistically…
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…
This paper presents a molecular mechanics study using a molecular dynamics software (NAMD) coupled to virtual reality (VR) techniques for intuitive Bio-NanoRobotic prototyping. Using simulated Bio-Nano environments in VR, the operator can…