相关论文: Parallel Tempering: Theory, Applications, and New …
Experiment directed simulation is a technique to minimally bias molecular dynamics simulations to match experimentally observed results. The method improves accuracy but does not address the sampling problem of molecular dynamics…
This article describes algorithms for the hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-range forces. The parallelization method combines domain decomposition with a thread-based parallelization…
Using previous experimental data of diffusion in metallic alloys, we obtain real values for an interpolation parameter introduced in a mean-field theory for diffusion with interaction. Values of order 1 were found as expected, finding…
In this paper I describe some results on the use of virtual processors technology for parallelize some SPMD computational programs. The tested technology is the INTEL Hyper Threading on real processors, and the programs are MATLAB scripts…
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…
The dynamics of non-equilibrium Ising model with parallel updates is investigated using a generalized mean field approximation that incorporates multiple two-site correlations at any two time steps, which can be obtained recursively. The…
Parallel tempering (PT), also known as replica exchange, is the go-to workhorse for simulations of multi-modal distributions. The key to the success of PT is to adopt efficient swap schemes. The popular deterministic even-odd (DEO) scheme…
The availability of large amounts of time series data, paired with the performance of deep-learning algorithms on a broad class of problems, has recently led to significant interest in the use of sequence-to-sequence models for time series…
Control parallelism and data parallelism is mostly reasoned and optimized as separate functions. Because of this, workloads that are irregular, fine-grain and dynamic such as dynamic graph processing become very hard to scale. An…
Regular expression matching is essential for many applications, such as finding patterns in text, exploring substrings in large DNA sequences, or lexical analysis. However, sequential regular expression matching may be time-prohibitive for…
The wide application of estimation techniques in system analysis enable us to best determine and understand the history of system states. This paper attempts to delineate the theory behind linear and non-linear estimation with a suitable…
We prove that parallel processing with homogeneous processors is logically equivalent to fast serial processing. The reverse proposition can also be used to identify obscure opportunities for applying parallelism. To our knowledge, this…
A brief review is presented of the scaling of complex fluids, polymers and polyelectrolytes in solution and in confined geometry, in thermodynamical, structural and rheology properties using equilibrium and nonequilibrium dissipative…
We study the first order phase transition of the fixed-connectivity triangulated surface model using the Parallel Tempering Monte Carlo (PTMC) technique on relatively large lattices. From the PTMC results, we find that the transition is…
Quantum Mechanics/Molecular Mechanics (QM/MM) simulations are a popular approach to study various features of large systems. A common application of QM/MM calculations is in the investigation of reaction mechanisms in condensed-phase and…
Differentiable physics provides a new approach for modeling and understanding the physical systems by pairing the new technology of differentiable programming with classical numerical methods for physical simulation. We survey the rapidly…
Serial, or sequential, fusion of multiple biometric matchers has been not thoroughly investigated so far. However, this approach exhibits some advantages with respect to the widely adopted parallel approaches. In this paper, we propose a…
We are living in the big data age: An ever increasing amount of data is being produced through data acquisition and computer simulations. While large scale analysis and simulations have received significant attention for cloud and…
Molecular Dynamics simulations are becoming a powerful tool for examining and predicting atomic and molecular processes in various environment. The present review shows how, in the fields of plasma physics, chemistry and interactions with…
Metastability is a common obstacle to performing long molecular dynamics simulations. Many numerical methods have been proposed to overcome it. One method is parallel replica dynamics, which relies on the rapid convergence of the underlying…