Related papers: Efficiency of linked cell algorithms
Recent results on supercomputers show that beyond 65K cores, the efficiency of molecular dynamics simulations of interfacial systems decreases significantly. In this paper, we introduce a dynamic cutoff method (DCM) for interfacial systems…
Molecular crystals play a central role in a wide range of scientific fields, including pharmaceuticals and organic semiconductor devices. However, they are challenging systems to model accurately with computational approaches because of a…
Discrete-state, continuous-time Markov models are becoming commonplace in the modelling of biochemical processes. The mathematical formulations that such models lead to are opaque, and, due to their complexity, are often considered…
We introduce polynomial couplings, a generalization of probabilistic couplings, to develop an algorithm for the computation of equivalence relations which can be interpreted as a lifting of probabilistic bisimulation to polynomial…
We analyze and compare the computational complexity of different simulation strategies for Monte Carlo in the setting of classically scaled population processes. This allows a range of widely used competing strategies to be judged…
Dose-finding trials are a key component of the drug development process and rely on a statistical design to help inform dosing decisions. Triallists wishing to choose a design require knowledge of operating characteristics of competing…
Distributed optimization algorithms are widely used in many industrial machine learning applications. However choosing the appropriate algorithm and cluster size is often difficult for users as the performance and convergence rate of…
A computer simulation has to be fast to be helpful, if it is employed to study the behavior of a multicomponent dynamic system. This paper discusses modeling concepts and algorithmic techniques useful for creating such fast simulations.…
Clustering is one of the major tasks in data mining. In the last few years, Clustering of spatial data has received a lot of research attention. Spatial databases are components of many advanced information systems like geographic…
Multilevel association rules explore the concept hierarchy at multiple levels which provides more specific information. Apriori algorithm explores the single level association rules. Many implementations are available of Apriori algorithm.…
We present an algorithmic framework for a variant of the quantum Monte Carlo operator-loop algorithm, where non-local cluster updates are constructed in a way that makes each individual loop smaller. The algorithm is designed to increase…
Particle-in-Cell Monte Carlo simulations on large-scale systems play a fundamental role in understanding the complexities of plasma dynamics in fusion devices. Efficient handling and analysis of vast datasets are essential for advancing…
A classification algorithm, called the Linear Centralization Classifier (LCC), is introduced. The algorithm seeks to find a transformation that best maps instances from the feature space to a space where they concentrate towards the center…
The lock-free, ordered, linked list is an important, standard example of a concurrent data structure. An obvious, practical drawback of textbook implementations is that failed compare-and-swap (CAS) operations lead to retraversal of the…
The introduction of accelerator devices such as graphics processing units (GPUs) has had profound impact on molecular dynamics simulations and has enabled order-of-magnitude performance advances using commodity hardware. To fully reap these…
The use of machine learning algorithms is an attractive way to produce very fast detector simulations for scattering reactions that can otherwise be computationally expensive. Here we develop a factorised approach where we deal with each…
This paper proposes a thought experiment to search for efficient bounded algorithms of NPC problems by machine enumeration. The key contributions are: -- On Universal Turing Machines, a program's time complexity should be characterized as:…
Today, very large amounts of data are produced and stored in all branches of society including science. Mining these data meaningfully has become a considerable challenge and is of the broadest possible interest. The size, both in numbers…
The computer revolution has been driven by a sustained increase of computational speed of approximately one order of magnitude (a factor of ten) every five years since about 1950. In natural sciences this has led to a continuous increase of…
We present a new scalable algorithm for short-range molecular dynamics simulations on distributed memory MIMD multicomputer based on a message-passing multi-cell approach. We have implemented the algorithm on the Connection Machine 5 (CM-5)…