Related papers: On Designing Multicore-aware Simulators for Biolog…
In this tutorial paper, we will firstly review some basic simulation concepts and then introduce the parallel and distributed simulation techniques in view of some new challenges of today and tomorrow. More in particular, in the last years…
Modern high performance computing (HPC) systems exhibit a rapid growth in size, both "horizontally" in the number of nodes, as well as "vertically" in the number of cores per node. As such, they offer additional levels of hardware…
MiMiC is a framework for performing multiscale simulations in which loosely coupled external programs describe individual subsystems at different resolutions and levels of theory. To make it highly efficient and flexible, we adopt an…
Building oscillator based computing systems with emerging nano-device technologies has become a promising solution for unconventional computing tasks like computer vision and pattern recognition. However, simulation and analysis of these…
Increasing complexity of modern multi-processor system on chip (MPSoC) and the decreasing feature size have introduced new challenges. System designers have to consider now aspects which were not part of the design process in past times.…
Simulating physical systems is a core component of scientific computing, encompassing a wide range of physical domains and applications. Recently, there has been a surge in data-driven methods to complement traditional numerical simulations…
In this paper is proposed a technique to integrate and simulate a dynamic memory in a multiprocessor framework based on C/C++/SystemC. Using host machine's memory management capabilities, dynamic data processing is supported without…
High-performance, multi-core processors are the key to accelerating workloads in several application domains. To continue to scale performance at the limit of Moore's Law and Dennard scaling, software and hardware designers have turned to…
Stochastic, spatial reaction-diffusion simulations have been widely used in systems biology and computational neuroscience. However, the increasing scale and complexity of simulated models and morphologies have exceeded the capacity of any…
We propose a new multi-scale molecular dynamics simulation method which can achieve high accuracy and high sampling efficiency simultaneously without aforehand knowledge of the coarse grained (CG) potential and test it for a biomolecular…
Computational systems and methods are often being used in biological research, including the understanding of cancer and the development of treatments. Simulations of tumor growth and its response to different drugs are of particular…
Parallel computing is a standard approach to achieving high-performance computing (HPC). Three commonly used methods to implement parallel computing include: 1) applying multithreading technology on single-core or multi-core CPUs; 2)…
Design of next generation computer systems should be supported by simulation infrastructure that must achieve a few contradictory goals such as fast execution time, high accuracy, and enough flexibility to allow comparison between large…
The increase in complexity of autonomous systems is accompanied by a need of data-driven development and validation strategies. Advances in computer graphics and cloud clusters have opened the way to massive parallel high fidelity…
Co-simulation consists of the theory and techniques to enable global simulation of a coupled system via the composition of simulators. Despite the large number of applications and growing interest in the challenges, the field remains…
Today, many scientific and engineering areas require high performance computing to perform computationally intensive experiments. For example, many advances in transport phenomena, thermodynamics, material properties, computational…
Recent advances in both theory and methods have created opportunities to simulate biomolecular processes more efficiently using adaptive ensemble simulations. Ensemble-based simulations are used widely to compute a number of individual…
Cycle-accurate software simulation of multicores with complex microarchitectures is often excruciatingly slow. People use simplified core models to gain simulation speed. However, a persistent question is to what extent the results derived…
The latest trends in high-performance computing systems show an increasing demand on the use of a large scale multicore systems in a efficient way, so that high compute-intensive applications can be executed reasonably well. However, the…
The complex regulatory dynamics of a biological network can be succinctly captured using discrete logic models. Given even sparse time-course data from the system of interest, previous work has shown that global optimization schemes are…