Stochastic simulations are able to capture the fine grain behaviour and randomness of outcome of biological networks not captured by deterministic techniques. As such they are becoming an increasingly important tool in the biological community. However, current efforts in the stochastic simulation of biological networks are hampered by two main problems: firstly the lack of complete knowledge o...

Introduction: The key characteristics of positron emission tomography (PET) are its quantitative capability and its sensitivity, which allow the in vivo imaging of biochemical interactions with small amounts of tracer concentrations. Therefore, accurate quantification is important. However, it can be sensitive to several physical factors. The aim of this investigation is the assessment of the e...

Large-eddy simulations described here have included the effect of canopy drag through the depth of a plant canopy. Specifically, we have considered the simulation of flow through a forest. Drag forces enter the simulation with the inclusion of form and viscous drag forces in the momentum equation. In addition, we have carried a variable to represent the kinetic energy (KE) associated with the t...

If the collisional time scale for Coulomb collisions is comparable to the characteristic time scales for a plasma, then simulation of Coulomb collisions may be important for computation of kinetic plasma dynamics. This can be a computational bottleneck because of the large number of simulated particles and collisions (or phase-space resolution requirements in continuum algorithms), as well as t...

In recent years, lots of research has been done on effective usage of natural gas; the first step in these processes is conversion of natural gas to Syngas. Natural gas reforming process by refomer furnace is commonly used for syngas and hydrogen production. In this paper, a windows based software, RIPI-RefSim, is introduced. By using proper heat, mass, kinetic and thermodynamic models as w...

Equilibrium formally can be represented as an ensemble of uncoupled systems undergoing unbiased dynamics in which detailed balance is maintained. Many nonequilibrium processes can be described by suitable subsets of the equilibrium ensemble. Here, we employ the "weighted ensemble" (WE) simulation protocol [Huber and Kim, Biophys. J.1996, 70, 97-110] to generate equilibrium trajectory ensembles ...

Photosystem I (PSI), a photoactive protein complex that participates in the light reactions of natural photosynthesis, can exhibit photocatalytic capabilities when incorporated to electrochemical systems. Here we present a simulation for the photoelectrochemical behavior of an electrode modified with a monolayer of Photosystem I complexes during photochronoamperometric experiments in which the ...

Modeling, simulation, and integrated guidance-control of a kinetic warhead utilizing moving-mass actuators are discussed. Moving masses can be used in any speed range both in the atmosphere as well as outside it, as long as there is a force, either aerodynamic or propulsive, acting on the vehicle. The moving-mass actuation technique offers significant advantages over conventional aerodynamic co...