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Wu, Sheng

Publications and source records attributed to Wu, Sheng.

6 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist

We present StochSS: Stochastic Simulation as a Service, an integrated development environment for modeling and simulation of both deterministic and discrete stochastic biochemical systems in up to three dimensions. An easy to use graphical user interface enables researchers to quickly develop and simulate a biological model on a desktop or laptop, which can then be expanded to incorporate increasing levels of complexity. StochSS features state-of-the-art simulation engines. As the demand for computational power increases, StochSS can seamlessly scale computing resources in the cloud. In addition, StochSS can be deployed as a multi-user software environment where collaborators share computational resources and exchange models via a public model repository. We also demonstrate the capabilities and ease of use of StochSS with an example of model development and simulation at increasing levels of complexity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

The time dependent propensity function for acceleration of spatial stochastic simulation of reaction–diffusion systems

The inhomogeneous stochastic simulation algorithm (ISSA) is a fundamental method for spatial stochastic simulation. However, when diffusion events occur more frequently than reaction events, simulating the diffusion events by ISSA is quite costly. To reduce this cost, we propose to use the time dependent propensity function in each step. In this way we can avoid simulating individual diffusion events, and use the time interval between two adjacent reaction events as the simulation stepsize. We demonstrate that the new algorithm can achieve orders of magnitude efficiency gains over widely-used exact algorithms, scales well with increasing grid resolution, and maintains a high level of accuracy.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

Tunable single-mode slot waveguide quantum cascade lasers

We report experimental demonstration of tunable, monolithic, single-mode quantum cascade lasers (QCLs) at ∼10 μm with a two-section etched slot structure. A single-mode tuning range of 77 cm{sup −1} (785 nm), corresponding to ∼7.8% of the relative tuning range, was realized with a ∼20 dB side mode suppression ratio within the whole tuning range. Compared with integrated distributed feedback QCLs, our devices have the advantages of easy fabrication and a broader tuning range. Further theoretical analyses and numerical simulations show that it is possible to achieve a broad continuous tuning range by optimizing the slot structures. The proposed slot-waveguide design could provide an alternative but simple approach to the existing tuning schemes for realizing broadly continuous tunable single-mode QCLs.

42 ENGINEERING↗
DOE OSTI2013

Novel Multidimensional Tracers for Geothermal Inter-Well Diagnostics

This is the Final Report of the three-year project “Novel Multidimensional Tracers for Geothermal Inter-Well Diagnostics” (DE-EE00003032, April 1, 2010 – March 30, 2013), in which we present our major accomplishments with detailed descriptions of our experimental and theoretical efforts. Upon the successful conduction of this project, we have followed our proposed breakdown work structure completing most of the technical tasks. Finally, we have developed and demonstrated the matrix of smart geothermal tracers and the corresponding interpretation tools together with the novel pre-concentration technique – the Hollow Fiber Liquid-Liquid Micro-Extraction (HFLLME), which present superior performance in terms of the ultralow detection limits (up to 10-12g/mL with signal-to-noise ratio of 2); high workable temperature up to 300°C; and the significant enhancement in the characterization of subsurface environment. We have developed in- depth mechanistic understandings on the complicated chemistry involved in the tracer- matrix interaction as well as developed the unique yet effective experimental protocols (screening methodologies, analytical tools, pre-concentration and derivatization techniques) for achieving a highly efficient yet economically feasible and environmentally friendly geothermal tracer system. The most important findings have been reported to DOE in this Final Report and our 12 Quarterly Reports.

15 GEOTHERMAL ENERGY↗
DOE OSTI2013

Time dependent solution for acceleration of tau-leaping

The tau-leaping method is often effective for speeding up discrete stochastic simulation of chemically reacting systems. However, when fast reactions are involved, the speed-up for this method can be quite limited. One way to address this is to apply a stochastic quasi-steady state assumption. However we must be careful when using this assumption. If the fast subsystem cannot reach a steady distribution fast enough, the quasi-steady-state assumption will propagate error into the simulation. To avoid these errors, we propose to use the time dependent solution rather than the quasi-steady-state. Generally speaking, the time dependent solution is not easy to derive for an arbitrary network. However, for some common motifs we do have time dependent solutions. We derive the time dependent solutions for these motifs, and then show how they can be used with tau-leaping to achieve substantial speed-ups, including for a realistic model of blood coagulation. Although the method is complicated, we have automated it.

97 MATHEMATICS AND COMPUTING↗