相关论文: ppsim: A software package for efficiently simulati…
Improving the efficiency of current neural networks and modeling them in biological neural systems have become popular research directions in recent years. Pulse-coupled neural network (PCNN) is a well applicated model for imitating the…
Synthetic biology is a rapidly emerging research area, with expected wide-ranging impact in biology, nanofabrication, and medicine. A key technical challenge lies in embedding computation in molecular contexts where electronic…
We introduce an alternative formulation of the exact stochastic simulation algorithm (SSA) for sampling trajectories of the chemical master equation for a well-stirred system of coupled chemical reactions. Our formulation is based on…
The inner operations of the human brain as a biological processing system remain largely a mystery. Inspired by the function of the human brain and based on the analysis of simple neural network systems in other species, such as Drosophila,…
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…
Cosmic-ray acceleration processes in astrophysical plasmas are often investigated with fully-kinetic or hybrid kinetic numerical simulations, which enable us to describe a detailed microphysics of particle energization mechanisms. Tracing…
Quantum computers hold great promise for arriving at exact simulations of nuclear dynamical processes (e.g., scattering and reactions) that are paramount to the study of nuclear matter at the limit of stability and to explaining the…
Peptide Optimization is a highly complex problem and it takes very long time of computation. This optimization process uses many software applications in a cluster running GNU/Linux Operating System that perform special tasks. The…
Compute the coarsest simulation preorder included in an initial preorder is used to reduce the resources needed to analyze a given transition system. This technique is applied on many models like Kripke structures, labeled graphs, labeled…
The simulation of high-energy physics collision events is a key element for data analysis at present and future particle accelerators. The comparison of simulation predictions to data allows looking for rare deviations that can be due to…
Health economic models simulate the costs and effects of health technologies for use in health technology assessment (HTA) to inform efficient use of scarce resources. Models have historically been developed using spreadsheet software…
Low-cost, high-throughput DNA and RNA sequencing (HTS) data is the backbone of the life sciences. Genome sequencing is now becoming a part of Predictive, Preventive, Personalized, and Participatory (termed 'P4') medicine. All genomic data…
We show that protein sequences can be thought of as sentences in natural language processing and can be parsed using the existing Quantum Natural Language framework into parameterized quantum circuits of reasonable qubits, which can be…
Across many disciplines, chemical reaction networks (CRNs) are an established population model defined as a system of coupled nonlinear ordinary differential equations. In many applications, for example, in systems biology and epidemiology,…
The recent development of multi-agent simulations brings about a need for population synthesis. It is a task of reconstructing the entire population from a sampling survey of limited size (1% or so), supplying the initial conditions from…
Proteins perform their functions usually by interacting with other proteins. Predicting which proteins interact is a fundamental problem. Experimental methods are slow, expensive, and have a high rate of error. Many computational methods…
Microkinetics allows detailed modelling of chemical transformations occurring in many industrially relevant reactions. Traditional way of solving the microkinetics model for Fischer-Tropsch synthesis (FTS) becomes inefficient when it comes…
Let $G$ be a graph on $n$ nodes. In the stochastic population protocol model, a collection of $n$ indistinguishable, resource-limited nodes collectively solve tasks via pairwise interactions. In each interaction, two randomly chosen…
We present an unsupervised data processing workflow that is specifically designed to obtain a fast conformational clustering of long molecular dynamics simulation trajectories. In this approach we combine two dimensionality reduction…
We introduce PULSEDYN, a particle dynamics program in $C++$, to solve many-body nonlinear systems in one dimension. PULSEDYN is designed to make computing accessible to non-specialists in the field of nonlinear dynamics of many-body systems…