Filtered density function for large eddy simulation of turbulent reacting flows

A methodology termed the “filtered density function” (FDF) is developed and implemented for large eddy simulation (LES) of chemically reacting turbulent flows. In this methodology, the effects of the unresolved scalar fluctuations are taken into account by considering the probability density function (PDF) of subgrid scale (SGS) scalar quantities. A transport equation is derived for the FDF in which the effect of chemical reactions appears in a closed form. The influences of scalar mixing and convection within the subgrid are modeled. The FDF transport equation is solved numerically via a Lagrangian Monte Carlo scheme in which the solutions of the equivalent stochastic differential equations (SDEs) are obtained. These solutions preserve the Itô-Gikhman nature of the SDEs. The consistency of the FDF approach, the convergence of its Monte Carlo solution and the performance of the closures employed in the FDF transport equation are assessed by comparisons with results obtained by direct numerical simulation (DNS) and by conventional LES procedures in which the first two SGS scalar moments are obtained by a finite difference method (LES-FD). These comparative assessments are conducted by implementations of all three schemes (FDF, DNS and LES-FD) in a temporally developing mixing layer and a spatially developing planar jet under both non-reacting and reacting conditions. In non-reacting flows, the Monte Carlo solution of the FDF yields results similar to those via LES-FD. The advantage of the FDF is demonstrated by its use in reacting flows. In the absence of a closure for the SGS scalar fluctuations, the LES-FD results are significantly different from those based on DNS. The FDF results show a much closer agreement with filtered DNS results. © 1998 American Institute of Physics.

Simulation of RNA silencing pathway for time-dependent transgene transcription rate

The synthesis of dsRNA is analyzed using a pathway model with amplifications caused by the aberrant RNAs. The transgene influx rate is assumed time-decaying considering the fact that the number of transgenes can not be infinite. The dynamics of the transgene induced RNA silencing is investigated using a system of coupled nonautonomous ordinary nonlinear differential equations which describe the model phenomenologically. The silencing phenomena are detected after a period of transcription. Important contributions of certain parameters are discussed with several numerical examples.

Real-time Computer Simulation of Three Dimensional Elastostatics using the Finite Point Method

Real-time simulation of deformable solids is essential for some applications such as biological organ simulations for surgical simulators. In this work, deformable solids are approximated to be linear elastic, and an easy and straight forward numerical technique, the Finite Point Method (FPM), is used to model three dimensional linear elastostatics. Graphics Processing Unit (GPU) is used to accelerate computations. Results show that the Finite Point Method, together with GPU, can compute three dimensional linear elastostatic responses of solids at rates suitable for real-time graphics, for solids represented by reasonable number of points.

Stochastic Algorithms for Discrete Parameter Simulation Optimization

We present two efficient discrete parameter simulation optimization (DPSO) algorithms for the long-run average cost objective. One of these algorithms uses the smoothed functional approximation (SFA) procedure, while the other is based on simultaneous perturbation stochastic approximation (SPSA). The use of SFA for DPSO had not been proposed previously in the literature. Further, both algorithms adopt an interesting technique of random projections that we present here for the first time. We give a proof of convergence of our algorithms. Next, we present detailed numerical experiments on a problem of admission control with dependent service times. We consider two different settings involving parameter sets that have moderate and large sizes, respectively. On the first setting, we also show performance comparisons with the well-studied optimal computing budget allocation (OCBA) algorithm and also the equal allocation algorithm. Note to Practitioners-Even though SPSA and SFA have been devised in the literature for continuous optimization problems, our results indicate that they can be powerful techniques even when they are adapted to discrete optimization settings. OCBA is widely recognized as one of the most powerful methods for discrete optimization when the parameter sets are of small or moderate size. On a setting involving a parameter set of size 100, we observe that when the computing budget is small, both SPSA and OCBA show similar performance and are better in comparison to SFA, however, as the computing budget is increased, SPSA and SFA show better performance than OCBA. Both our algorithms also show good performance when the parameter set has a size of 10(8). SFA is seen to show the best overall performance. Unlike most other DPSO algorithms in the literature, an advantage with our algorithms is that they are easily implementable regardless of the size of the parameter sets and show good performance in both scenarios.

Fluctuation quench and hydrophobic collapse of polymers and biopolymers in water-DMSO binary mixture at low DMSO concentration

Binary mixtures have strong influence on activities of polymers and biopolymers even at low cosolvent concentration. Among the several aqueous binary mixtures studied, water-DMSO especially stands out for its unusual behavior at certain specific concentrations of DMSO. In the present work, we study the effect of water-DMSO binary mixture on polymers and biopolymers by taking a simple linear hydrocarbon chain of intermediate length (n = 30) and the protein lysozyme, respectively. We find that at a mole fraction of 0.05 of DMSO (x(DMSO) = 0.05) in aqueous solution, the hydrocarbon chain adopts the collapsed conformation as the most stable and rigid state. In this case of 0.05 mole fraction of DMSO in bulk, the DMSO concentration in the first hydration layer around the polymer is found to be as large as 17%. Formation of such hydrophobic environment around the polymer is the reason for the collapsed state gaining so much stability. Interestingly, similar quench of conformational fluctuation is also observed for the protein investigated. It is observed that in the case of alkane polymer chains, long wavelength fluctuation gets easily quenched, the polymer being purely hydrophobic. However, in case of the protein, quench of fluctuation is prominent only at the hydrophobic surface, and quench of long wavelength fluctuation becomes insignificant for the full protein. As protein contains both hydrophobic and hydrophilic moieties, the extent of quench of conformational fluctuation with respect to that in pure water is almost half for the biopolymer complex (16.83%) than the same for pure hydrophobic polymer chain (32.43%).