Related papers: Multiscale Biomolecular Simulations in the Exascal…
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…
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…
Exascale computing holds great opportunities for molecular dynamics (MD) simulations. However, to take full advantage of the new possibilities, we must learn how to focus computational power on the discovery of complex molecular mechanisms,…
Molecular dynamics (MD) simulations are used in biochemistry, physics, and other fields to study the motions, thermodynamic properties, and the interactions between molecules. Computational limitations and the complexity of these problems,…
Molecular dynamics (MD) simulations have transformed our understanding of the nanoscale, driving breakthroughs in materials science, computational chemistry, and several other fields, including biophysics and drug design. Even on exascale…
Simulations of biomolecules have enormous potential to inform our understanding of biology but require extremely demanding calculations. For over twenty years, the Folding@home distributed computing project has pioneered a massively…
Molecular dynamics (MD) has become a powerful tool for studying biophysical systems, due to increasing computational power and availability of software. Although MD has made many contributions to better understanding these complex…
Computational prediction of enzyme mechanism and protein function requires accurate physics-based models and suitable sampling. We discuss recent advances in large-scale quantum mechanical (QM) modeling of biochemical systems that have…
With the rapid advancement of computational techniques, Molecular Dynamics (MD) simulations have emerged as powerful tools in biomedical research, enabling in-depth investigations of biological systems at the atomic level. Among the diverse…
Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists…
Quantum Mechanics/Molecular Mechanics (QM/MM) simulations are a popular approach to study various features of large systems. A common application of QM/MM calculations is in the investigation of reaction mechanisms in condensed-phase and…
High performance computing numerical simulations are today one of the more effective instruments to implement and study new theoretical models, and they are mandatory during the preparatory phase and operational phase of any scientific…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
Quantum simulation is a leading candidate for demonstrating practical quantum advantage over classical computation, as it is believed to provide exponentially more compute power than any classical system. It offers new means of studying the…
Quantum computers have the potential to simulate chemical systems beyond the capability of classical computers. Recent developments in hybrid quantum-classical approaches enable the determinations of the ground or low energy states of…
Simulating spontaneous structural rearrangements in macromolecules with classical Molecular Dynamics (MD) is an outstanding challenge. Conventional supercomputers can access time intervals up to tens of $\mu$s, while many key events occur…
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…
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…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
We expect that multiscale simulations will be one of the main high performance computing workloads in the exascale era. We propose multiscale computing patterns as a generic vehicle to realise load balanced, fault tolerant and energy aware…