Related papers: Large-Scale Molecular Dynamics Simulations for Hig…
We profile the impact of computation and inter-processor communication on the energy consumption and on the scaling of cortical simulations approaching the real-time regime on distributed computing platforms. Also, the speed and energy…
We study the computational complexity of the recently proposed nubot model of molecular-scale self-assembly. The model generalises asynchronous cellular automata to have non-local movement where large assemblies of molecules can be pushed…
The linked cell list algorithm is an essential part of molecular simulation software, both molecular dynamics and Monte Carlo. Though it scales linearly with the number of particles, there has been a constant interest in increasing its…
Modeling the dynamics of a quantum system connected to the environment is critical for advancing our understanding of complex quantum processes, as most quantum processes in nature are affected by an environment. Modeling a macroscopic…
We study a graph partitioning problem motivated by the simulation of the physical movement of multi-body systems on an atomistic level, where the forces are calculated from a quantum mechanical description of the electrons. Several advanced…
Simulating physical systems is a core component of scientific computing, encompassing a wide range of physical domains and applications. Recently, there has been a surge in data-driven methods to complement traditional numerical simulations…
High-performance graphical processing units (GPU) are used for the repeated parallelised propagation of non-linear partial differential equations on large spatio-temporal grids. The main challenge results as a combination of the requirement…
For decades, researchers have been applying computer simulation to address problems in biology. However, many of these "grand challenges" in computational biology, such as simulating how proteins fold, remained unsolved due to their great…
The Multilevel Monte Carlo (MLMC) method has proven to be an effective variance-reduction statistical method for Uncertainty Quantification (UQ) in Partial Differential Equation (PDE) models, combining model computations at different levels…
We demonstrate the feasibility of quantum computing for large-scale, realistic chemical systems through the development of a new interface using a quantum circuit simulator and CP2K, a highly efficient first-principles calculation software.…
The numerical simulation of multiphase flows involving dispersed components with large scale disparities, such as the collisions between millimeter-sized bubbles and micron-sized mineral particles in flotation, poses a significant…
Efficient implementations of the classical molecular dynamics (MD) method for Lennard-Jones particle systems are considered. Not only general algorithms but also techniques that are efficient for some specific CPU architectures are also…
While most work on the quantum simulation of chemistry has focused on computing energy surfaces, a similarly important application requiring subtly different algorithms is the computation of energy derivatives. Almost all molecular…
Quantum computers hold promise to enable efficient simulations of the properties of molecules and materials; however, at present they only permit ab initio calculations of a few atoms, due to a limited number of qubits. In order to harness…
Multidimensional nucleosynthesis studies with hundreds of nuclei linked through thousands of nuclear processes are still computationally prohibitive. To date, most nucleosynthesis studies rely either on hydrostatic/hydrodynamic simulations…
Particle-in-cell methods couple mesh-based methods for the solution of continuum mechanics problems, with the ability to advect and evolve particles. They have a long history and many applications in scientific computing. However, they have…
In the first part of a series of two papers, we present in considerable detail a collision-driven molecular dynamics algorithm for a system of nonspherical particles, within a parallelepiped simulation domain, under both periodic or…
Recent advances in quantum technologies and related experiments have created a need for highly accurate, versatile, and computationally efficient simulation techniques for the dynamics of open quantum systems. Long-lived correlation effects…
Magnetic molecules, modelled as finite-size spin systems, are test-beds for quantum phenomena and could constitute key elements in future spintronics devices, long-lasting nanoscale memories or noise-resilient quantum computing platforms.…
Quantum computing has the potential to revolutionize multiple fields by solving complex problems that can not be solved in reasonable time with current classical computers. Nevertheless, the development of quantum computers is still in its…