Related papers: The Software Anatomy of a Flexible Accelerator Sim…
RNA function is intimately related to its structural dynamics. Molecular dynamics simulations are useful for exploring biomolecular flexibility but are severely limited by the accessible timescale. Enhanced sampling methods allow this…
Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations…
A series of simulations aimed at elucidating the self-assembly dynamics of spherical virus capsids is described. This little-understood phenomenon is a fascinating example of the complex processes that occur in the simplest of organisms.…
The aim of this paper is to propose a new numerical model to simulate 2D vesicles interacting with a newtonian fluid. The inextensible membrane is modeled by a chain of circular rigid particles which are maintained in cohesion by using two…
Particle-in-cell methods couple mesh-based methods for the solution of continuum mechanics problems, with the ability to advect and evolve particles. They have a long history and many applications in scientific computing. However, they have…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
Real-life control tasks involve matters of various substances---rigid or soft bodies, liquid, gas---each with distinct physical behaviors. This poses challenges to traditional rigid-body physics engines. Particle-based simulators have been…
The high-performance computing (HPC) community has recently seen a substantial diversification of hardware platforms and their associated programming models. From traditional multicore processors to highly specialized accelerators, vendors…
Particle acceleration in collisionless plasma systems is a central question in astroplasma and astroparticle physics. The structure of the acceleration regions, electron-ion energy equilibration, preacceleration of particles at shocks to…
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…
The success of high energy physics programs relies heavily on accurate detector simulations and beam interaction modeling. The increasingly complex detector geometries and beam dynamics require sophisticated techniques in order to meet the…
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.…
Soft slender structures are ubiquitous in natural and artificial systems and can be observed at scales that range from the nanometric to the kilometric, from polymers to space tethers. We present a practical numerical approach to simulate…
Although software and firmware co-simulation is gaining popularity, it is still not widely used in the FPGA designs. This work presents easy and structured approach for software and firmware co-simulation for bus centric designs. The…
Computer simulations of coarse-grained molecular models for amphiphilic systems can provide insight into the the structure of amphiphiles at interfaces. They can help to identify the factors that determine the phase behavior, and they can…
Accelerated algorithms for simulating the morphological evolution of strained heteroeptiaxy based on a ball and spring lattice model in three dimensions are explained. We derive exact Green's function formalisms for boundary values in the…
Particle accelerators are among the largest, most complex devices. To meet the challenges of increasing energy, intensity, accuracy, compactness, complexity and efficiency, increasingly sophisticated computational tools are required for…
Rigid body dynamics simulators are important tools for the design, analysis and optimization of mechanical systems in a variety of technical and scientific applications. This study examines four different simulation environments (Adams,…
PyMembrane is a software package for simulating liquid and elastic membranes using a discretisation of the continuum description based on unstructured triangulated two-dimensional meshes embedded in three-dimensional space. The package is…
The edge computing paradigm has emerged to handle cloud computing issues such as scalability, security and low response time among others. This new computing trend heavily relies on ubiquitous embedded systems on the edge. Performance and…