Related papers: Implementing Dimer Metadynamics using GROMACS
We present the implementation and performance of a class of directionally unsplit Riemann-solver-based hydrodynamic schemes on Graphic Processing Units (GPU). These schemes, including the MUSCL-Hancock method, a variant of the MUSCL-Hancock…
A novel multiscale numerical method is developed to accelerate direct simulation Monte Carlo (DSMC) simulations for polyatomic gases with internal energy. This approach applies the general synthetic iterative scheme to stochastic…
We investigate the collective dynamics of self-propelled droplets, confined in a one dimensional micro-fluidic channel. On one hand, neighboring droplets align and form large trains of droplets moving in the same direction. On the other…
Elongate animals and robots use undulatory body waves to locomote through diverse environments. Geometric mechanics provides a framework to model and optimize such systems in highly damped environments, connecting a prescribed shape change…
Adaptive mesh refinement (AMR) is often used when solving time-dependent partial differential equations using numerical methods. It enables time-varying regions of much higher resolution, which can be used to track discontinuities in the…
Quantum effects due to the spatial delocalization of light atoms are treated in molecular simulation via the path integral technique. Among several methods, Path Integral (PI) Molecular Dynamics (MD) is nowadays a powerful tool to…
An efficient parallelization approach to simulate optical properties of ensembles of quantum emitters in realistic electromagnetic environments is considered. It relies on balancing computing load of utilized processors and is built into…
GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest…
Metadynamics, a member of the `flat histogram' class of advanced sampling algorithms, has been widely used in molecular simulations to drive the exploration of states separated by high free energy barriers and promote comprehensive sampling…
We present a theoretical approach to scale the artificially fast dynamics of simulated coarse-grained polymer liquids down to its realistic value. As coarse-graining affects entropy and dissipation, two factors enter the rescaling:…
We propose Flow Mismatching, an unsupervised anomaly detection method that deliberately avoids reconstruction-based paradigms. Instead, we treat flow matching as geometric dynamics and leverage a key insight: anomalies occur at places where…
We have investigated thermodynamic and dynamic properties as well as the dielectric constant of water-metha\-nol model mixtures in the entire range of composition by using constant pressure molecular dynamics simulations at ambient…
We have developed a technique to accelerate the acquisition of effectively uncorrelated configurations for off-lattice models of dense polymer melts which makes use of both parallel tempering and large scale Monte Carlo moves. The method is…
The synchronized molecular dynamics simulation via macroscopic heat and momentum transfer is proposed for the non-isothermal flow behaviors of complex fluids. In this method, the molecular dynamics simulations are assigned to small fluid…
Dissipative particle dynamics is a widely used mesoscale technique for the simulation of hydrodynamics (as well as immersed particles) utilizing coarse-grained molecular dynamics. While the method is capable of describing any fluid, the…
Dissipation can be represented in Hamiltonian mechanics in an extended phase space as a symplectic process. The method uses an auxiliary variable which represents the excitation of unresolved dynamics and a Hamiltonian for the interaction…
We draw an analogy between droplet formation in dilute particle and polymer systems. Our arguments are based on finite-size scaling results from studies of a two-dimensional lattice gas to three-dimensional bead-spring polymers. To set the…
The present paper describes a parallel unstructured-mesh Plasma simulation code based on Finite Volume method. The code dynamically refines and coarses mesh for accurate resolution of the different features regarding the electron density.…
We propose a dynamic coarse-graining (CG) scheme for mapping heterogeneous polymer fluids onto extremely CG models in a dynamically consistent manner. The idea is to use as target function for the mapping a wave-vector dependent mobility…
Industry 4.0's highly networked Machine Tool Controllers (MTCs) are prime targets for replay attacks that use outdated sensor data to manipulate actuators. Dynamic watermarking can reveal such tampering, but current schemes assume…