Related papers: Scalable and fast heterogeneous molecular simulati…
We present an algorithm for the stochastic simulation of gene expression and heterogeneous population dynamics. The algorithm combines an exact method to simulate molecular-level fluctuations in single cells and a constant-number Monte…
Unraveling the dynamical motions of biomolecules is essential for bridging their structure and function, yet it remains a major computational challenge. Molecular dynamics (MD) simulation provides a detailed depiction of biomolecular…
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…
Heterogeneous many-cores are now an integral part of modern computing systems ranging from embedding systems to supercomputers. While heterogeneous many-core design offers the potential for energy-efficient high-performance, such potential…
In this paper, a parallel domain decomposition method is proposed for solving the fully-mixed Stokes-dual-permeability fluid flow model with Beavers-Joseph (BJ) interface conditions. Three Robin-type boundary conditions and a modified weak…
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…
We introduce Adjoint Sampling, a highly scalable and efficient algorithm for learning diffusion processes that sample from unnormalized densities, or energy functions. It is the first on-policy approach that allows significantly more…
Hydrodynamical simulations are the most accurate way to model structure formation in the universe, but they often involve a large number of astrophysical parameters modeling subgrid physics, in addition to cosmological parameters. This…
We propose an algorithm for the computational homogenization of locally periodic hyperelastic structures undergoing large deformations due to external quasi-static loading. The algorithm performs clustering of macroscopic deformations into…
Two of the most challenging tasks in molecular simulation consist in capturing the properties of systems with long-range interactions (e.g. electrolyte solutions) as well as systems containing large molecules such as hydrogels. For the…
The next generation of force fields for molecular dynamics will be developed using a wealth of data. Training systematically with experimental data remains a challenge, however, especially for machine learning potentials. Differentiable…
Nowadays, multiscale modelling is recognized as the most suitable way to study biological processes. Indeed, almost every phenomenon in nature exhibits a multiscale behaviour, i.e., it is the outcome of interactions that occur at different…
A novel parallelization paradigm has been developed for multi-GPU architectures. Classical multi-GPU parallelization for SPH rely on domain decomposition. In our approach each particle can be assigned to a GPU independently of its position…
We present a hybrid continuum-atomistic scheme which combines molecular dynamics (MD) simulations with on-the-fly machine learning techniques for the accurate and efficient prediction of multiscale fluidic systems. By using a Gaussian…
Stochastic simulation methods can be applied successfully to model exact spatio-temporally resolved reaction-diffusion systems. However, in many cases, these methods can quickly become extremely computationally intensive with increasing…
This study develops a scalable co-optimization strategy for the joint bidding of cascaded hydropower, wind, and solar energy units, treated as a unified entity in the day-ahead market. Although hydropower flexibility can manage the…
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…
Conjugated organic molecules play a central role in a wide range of optoelectronic devices, including organic light-emitting diodes, organic field-effect transistors, and organic solar cells. A major bottleneck in the computational design…
Machine learning has made important headway in helping to improve the treatment of quantum many-body systems. A domain of particular relevance are correlated inhomogeneous systems. What has been missing so far is a general, scalable…
Theoretical concepts in condensed matter physics are typically verified and also developed by exploiting computer simulations mostly in simple models. Predictions based on these usually isotropic models are often at odds with measurement…