Related papers: Large-Scale Molecular Dynamics Simulations for Hig…
A central concern of molecular dynamics simulations are the potential energy surfaces that govern atomic interactions. These hypersurfaces define the potential energy of the system, and have generally been calculated using either predefined…
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…
The objective of this article is to report the parallel implementation of the 3D molecular dynamic simulation code for laser-cluster interactions. The benchmarking of the code has been done by comparing the simulation results with some of…
The paper deals with the developing of the methodological backgrounds for the modeling and simulation of complex dynamical objects. Such backgrounds allow us to perform coordinate transformation and formulate the algorithm of its usage for…
The molecular dynamics simulation code ls1 mardyn is presented. It is a highly scalable code, optimized for massively parallel execution on supercomputing architectures, and currently holds the world record for the largest molecular…
Stochastic, spatial reaction-diffusion simulations have been widely used in systems biology and computational neuroscience. However, the increasing scale and complexity of simulated models and morphologies have exceeded the capacity of any…
A combination of reaction-diffusion models with moving-boundary problems yields a system in which the diffusion (spreading and penetration) and reaction (transformation) evolve the system's state and geometry over time. These systems can be…
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…
We develop an algorithm suitable for parallel molecular dynamics simulations in $d$ spatial dimensions and describe its implementation in C++. All routines work in arbitrary $d$; the maximum simulated $d$ is limited only by available…
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…
Owing to the computational complexity of electronic structure algorithms running on classical digital computers, the range of molecular systems amenable to simulation remains tightly circumscribed even after many decades of work. Quantum…
Massively parallel computer architectures create new opportunities for the performance of long-timescale molecular dynamics (MD) simulations. Here, we introduce the path-accelerated molecular dynamics (PAMD) method that takes advantage of…
In recent years, simulation methods based on the scaling of atomic potential functions, such as quasi-coarse-grained dynamics and coarse-grained dynamics, have shown promising results for modeling crystalline systems at multiple scales.…
A parallelized quantum dynamics package using the Smolyak algorithm for general molecular simulation is introduced in this work. The program has no limitation of the Hamiltonian form and provides high flexibility on the simulation setup to…
Machine learning potentials have emerged as a means to enhance the accuracy of biomolecular simulations. However, their application is constrained by the significant computational cost arising from the vast number of parameters compared to…
A large number of powerful, high-quality, and open-source simulation packages exist to efficiently perform molecular dynamics simulations, and their prevalence has greatly accelerated discoveries across a wide range of scientific domains.…
As compute power increases with time, more involved and larger simulations become possible. However, it gets increasingly difficult to efficiently use the provided computational resources. Especially in particle-based simulations with a…
The advent of hybrid computing platforms consisting of quantum processing units integrated with conventional high-performance computing brings new opportunities for algorithm design. By strategically offloading select portions of the…
There are many problems in biochemistry that are difficult to study experimentally. Simulation methods are appealing due to direct availability of atomic coordinates as a function of time. However, direct molecular simulations are…
Molecular dynamics (MD) simulation is essential for various scientific domains but computationally expensive. Learning-based force fields have made significant progress in accelerating ab-initio MD simulation but are not fast enough for…