Related papers: Reliability Assessment for Large-Scale Molecular D…
Atomistic simulations using accurate energy functions can provide molecular-level insight into functional motions of molecules in the gas- and in the condensed phase. Together with recently developed and currently pursued efforts in…
Dynamical systems that evolve continuously over time are ubiquitous throughout science and engineering. Machine learning (ML) provides data-driven approaches to model and predict the dynamics of such systems. A core issue with this approach…
Molecular Dynamics (MD) is a powerful computational microscope for probing protein functions. However, the need for fine-grained integration and the long timescales of biomolecular events make MD computationally expensive. To address this,…
Only a small fraction of the data generated in state-of-the-art all-atom multi-microsecond molecular dynamics (MD) simulations is typically analyzed. With femtosecond integration steps, microsecond simulations generate billions of time…
Molecular dynamics is a powerful method for studying the behaviour of materials at high temperature. In practice, however, its effectiveness in representing real systems is limited by the accuracy of the forces, finite size effects,…
Classical Molecular Dynamics (MD) simulations are employed as a tool to investigate structural properties of ice crystals under several temperature and pressure conditions. All ice crystal phases are analyzed by means of a computational…
The evolution of molecular dynamics (MD) simulations has been intimately linked to that of computing hardware. For decades following the creation of MD, simulations have improved with computing power along the three principal dimensions of…
We propose a new model for the description of complex granular particles and their interaction in molecular dynamics simulations of granular material in two dimensions. The grains are composed of triangles which are connected by deformable…
We compare dynamical nonequilibrium molecular dynamics and continuum simulations of the dynamics of relaxation of a fluid system characterized by a non uniform density profile. Results match quite well as long as the lengthscale of density…
The implementation of Molecular Dynamics (MD) on FPGAs has received substantial attention. Previous work, however, has consisted of either proof-of-concept implementations of components, usually the range-limited force; full systems, but…
Molecular dynamics simulations have been performed on pure liquid water, aqueous solutions of sodium chloride, and polymer solutions exposed to a strong external electric field with the goal to gain molecular insight into the structural…
The dynamics of dissipative soft-sphere gases obeys Newton's equation of motion which are commonly solved numerically by (force-based) Molecular Dynamics schemes. With the assumption of instantaneous, pairwise collisions, the simulation can…
An important aspect of astrophysical MHD turbulence research is developing diagnostics to connect simulations with the observable universe. Turbulent systems are by definition structurally complex in all fluid variables (density, velocity,…
The Monte Carlo simulation of the dynamics of complex molecules produces trajectories with a large number of different configurations to sample configuration space. It is expected that these configurations can be classified into a small…
Molecular dynamics (MD) is a powerful tool for exploring the behavior of atomistic systems, but its reliance on sequential numerical integration limits simulation efficiency. We present a novel neural network architecture, MDtrajNet, and a…
Most computer simulations of molecular dynamics take place under equilibrium conditions--in a closed, isolated system, or perhaps one held at constant temperature or pressure. Sometimes, extra tensions, shears, or temperature gradients are…
Quantum mechanics based ab-initio molecular dynamics (MD) simulation schemes offer an accurate and direct means to monitor the time-evolution of materials. Nevertheless, the expensive and repetitive energy and force computations required in…
Material properties are fundamentally dictated by multiscale phenomena, which often reach mesoscale in size. The {\mu}m mesoscale is also the size which can be observed directly under an optical microscope, bridging the atomistic…
Mathematical methods provide useful framework for the analysis and design of complex systems. In newer contexts such as biology, however, there is a need to both adapt existing methods as well as to develop new ones. Using a combination of…
Post-transcriptional modifications are crucial for RNA function, with roles ranging from the stabilization of functional RNA structures to modulation of RNA--protein interactions. Additionally, artificially modified RNAs have been suggested…