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Molecular dynamics (MD) simulations play a crucial role in scientific research. Yet their computational cost often limits the timescales and system sizes that can be explored. Most data-driven efforts have been focused on reducing the…
We describe a framework for interactive molecular dynamics in a multiuser virtual reality environment, combining rigorous cloud-mounted physical atomistic simulation with commodity virtual reality hardware, which we have made accessible to…
Significant progress in computer hardware and software have enabled molecular dynamics (MD) simulations to model complex biological phenomena such as protein folding. However, enabling MD simulations to access biologically relevant…
Modelling has become a third distinct line of scientific enquiry, alongside experiments and theory. Molecular dynamics (MD) simulations serve to interpret, predict and guide experiments and to test and develop theories. A major limiting…
Modeling and simulation (M&S) has revolutionized the way modern engineered products are designed, tested and evaluated. Yet modeling and simulation is much less frequently applied in the study of natural biological and active matter…
Using a coarse molecular-dynamics (CMD) approach with an appropriate choice of coarse variable (order parameter), we map the underlying effective free-energy landscape for the melting of a crystalline solid. Implementation of this approach…
Molecular dynamics (MD) simulations provide considerable benefits for the investigation and experimentation of systems at atomic level. Their usage is widespread into several research fields, but their system size and timescale are also…
Understanding the complex combustion dynamics within scramjet engines is critical for advancing high-speed propulsion technologies. However, the large scale and high dimensionality of simulation-generated temporal flow field data present…
The accurate, reliable and efficient numerical approximation of multi-physics processes in heterogeneous porous media with varying media coefficients that include fluid flow and structure interactions is of fundamental importance in energy,…
Realistic physical systems are characterised by emergent interactions across multiple length and time scales, posing a significant challenge for predictive machine learning (ML) models. Most scientific ML models focus on a narrow range of…
As Moore's Law has slowed and Dennard Scaling has ended, architects are increasingly turning to heterogeneous parallelism and domain-specific hardware-software co-designs. These trends present new challenges for simulation-based performance…
The most important factor for quantitative results in molecular dynamics simulation are well developed force fields and models. In the present work, the development of new models and the usage of force fields from the literature in large…
Molecular dynamics (MD) simulations can model the interactions between macromolecules with high spatiotemporal resolution but at a high computational cost. By combining high-throughput MD with Markov state models (MSMs), it is now possible…
The computer revolution has been driven by a sustained increase of computational speed of approximately one order of magnitude (a factor of ten) every five years since about 1950. In natural sciences this has led to a continuous increase of…
An embodied system must not only model the patterns of the external world but also understand its own motion dynamics. A motion dynamic model is essential for efficient skill acquisition and effective planning. In this work, we introduce…
A new pairwise hybrid machine-learning/molecular mechanics (ML/MM) potential is introduced that is conceived for application to large, heterogeneous condensed-phase systems. The PhysNet ML method describes monomers and short-range dimer…
Fourier acceleration has been successfully applied to the simulation of lattice field theories for more than a decade. In this paper, we extend the method to the dynamics of discrete particles moving in continuum. Although our method is…
Classical molecular dynamics (MD) simulations are important tools in life and material sciences since they allow studying chemical and biological processes in detail. However, the inherent scalability problem of particle-particle…
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…
Supply chains (SCs), complex networks spanning from raw material acquisition to product delivery, with enterprises as interconnected nodes, play a pivotal role in organizational success. However, optimizing SCs remains challenging,…