Related papers: Parallel implementation of three-dimensional molec…
Graph clustering has many important applications in computing, but due to growing sizes of graphs, even traditionally fast clustering methods such as spectral partitioning can be computationally expensive for real-world graphs of interest.…
This paper addresses the problem of parallelizing computations to study non-linear dynamics in large networks of non-locally coupled oscillators using heterogeneous computing resources. The proposed approach can be applied to a variety of…
We present a comprehensive approach to the modeling, performance analysis, and design of clustered molecular nanonetworks in which nano-machines of different clusters release an appropriate number of molecules to transmit their sensed…
Vertex models represent confluent tissue by polygonal or polyhedral tilings of space, with the individual cell interacting via force laws that depend on both the geometry of the cells and the topology of the tessellation. This dependence on…
Discovering causal relationships from observational data is a crucial problem and it has applications in many research areas. The PC algorithm is the state-of-the-art constraint based method for causal discovery. However, runtime of the PC…
Sequential computation is well understood but does not scale well with current technology. Within the next decade, systems will contain large numbers of processors with potentially thousands of processors per chip. Despite this, many…
Molecular dynamics (MD) simulations are a crucial computational tool for researchers to understand and engineer molecular structure and function in areas such as drug discovery, protein engineering, and material design. Despite their…
An adpative integration technique for time advancement of particle motion in the context of coupled computational fluid dynamics (CFD) - discrete element method (DEM) simulations is presented in this work. CFD-DEM models provide an accurate…
This study aims at finding a method for constructing molecular dynamics like models using the formalism of cellular automata for fast simulation of fluid dynamic systems (including compressible phenomena). In as much as the results…
Molecular dynamics (MD) simulations allow investigating the structural dynamics of biomolecular systems with unrivaled time and space resolution. However, in order to compensate for the inaccuracies of the utilized empirical force fields,…
Research in cell biology is steadily contributing new knowledge about many different aspects of physiological processes like polymerization, both with respect to the involved molecular structures as well as their related function.…
The Particle-In-Cell (PIC) method for plasma simulation tracks particle phase space information using particle and grid data structures. High computational costs in 2D and 3D device-scale PIC simulations necessitate parallelization, with…
Stochastic models of reaction-diffusion systems are important for the study of biochemical reaction networks where species are present in low copy numbers or if reactions are highly diffusion limited. In living cells many such systems…
In this article we present a parallel algorithm for simulation of the heat conduction process inside the so-called pulse cryogenic cell. This simulation is important for designing the device for portion injection of working gases into…
Scalable and efficient numerical simulations continue to gain importance, as computation is firmly established as the third pillar of discovery, alongside theory and experiment. Meanwhile, the performance of computing hardware grows through…
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…
We have developed the first laser damage simulation algorithm capable of determining crater and surface modification morphology from microscopic physics. Rapid progress in the field of high intensity ultrafast lasers has enabled its utility…
A novel algorithm and implementation of real-time identification and tracking of blob-filaments in fusion reactor data is presented. Similar spatio-temporal features are important in many other applications, for example, ignition kernels in…
Long ranged electrostatic interactions are time consuming to calculate in molecular dynamics and Monte-Carlo simulations. We introduce an algorithmic framework for simulating charged particles which modifies the dynamics so as to allow…
Distributed Computation has been a recent trend in engineering research. Parallel Computation is widely used in different areas of Data Mining, Image Processing, Simulating Models, Aerodynamics and so forth. One of the major usage of…