Simulation-based transfer function modeling for transient analysis of general queueing systems

This paper is concerned with characterizing the transient behavior of general queueing systems, which is widely known to be notoriously difficult. The objective is to develop a statistical methodology, integrated with extensive offline simulation and preliminary queueing analysis, for the estimation of a small number of transfer function models (TFMs) that quantify the input–output dynamics of a general queueing system. The input here is the time-varying arrival rate of jobs to the system; the time-dependent output performances include the departure rate of jobs and the mean of the work in process (i.e., number of jobs in the system). The resulting TFMs are difference equations, like the discrete approximations of the ordinary differential equations provided by an analytical approach, while possessing the high fidelity of simulation. Our method is expected to overcome the shortcomings of the existing transient analysis approaches, i.e., the computational burden of simulation and the lack of fidelity of analytical queueing models.     

Statistical mixture design selective extraction of compounds with antioxidant activity and total polyphenol content from Trichilia catigua

Statistical design mixtures of water, methanol, acetone and ethanol were used to extract material from Trichilia catigua (Meliaceae) barks to study the effects of different solvents and their mixtures on its yield, total polyphenol content and antioxidant activity. The experimental results and their response surface models showed that quaternary mixtures with approximately equal proportions of all four solvents provided the highest yields, total polyphenol contents and antioxidant activities of the crude extracts followed by ternary design mixtures. Principal component and hierarchical clustering analysis of the HPLC–DAD spectra of the chromatographic peaks of 1:1:1:1 water–methanol–acetone–ethanol mixture extracts indicate the presence of cinchonains, gallic acid derivatives, natural polyphenols, flavanoids, catechins, and epicatechins.     

Automatic Computerized Analysis of Multi-Exponential Decay Curves

Abstract

A prototype method is described which automatically analyzes exponential decay curves by using nonlinear regression analysis and deviation pattern recognition. Lifetimes and preexponential factors are computed for the proper model. The program successfully classified simulated data consisting of one, two, or three exponentials when noise followed a Poisson distribution. However, for real luminescence decay data, systematic instrumental noise of higher frequency tended to obscure low frequency deviations from incorrect models in smoothed deviation plots. This factor complicated classification of multi-exponential data, although the program easily distinguished between single and multiple exponential behavior.     

Modeling of Low Concentrations of Reactive Species in Kinetic Monte Carlo Simulations

A new method for determination of contributions of species present in low concentration in kinetic Monte Carlo (MC) simulations of chemical processes is proposed. It allows, for instance, to calculate of exact concentrations when species being of interest appear in MC experiments only for short time intervals. The method is based on monitoring of the cumulative life‐time of the investigated species under consideration as a function of the reaction time and subsequent differentiation of the resulting curve. It is especially useful for determination of distributions of low‐concentration active propagation species in radical polymerizations, both free and controlled ones. The method enables to reduce significantly a simulation scale required for determination of the concentrations of investigated species.

     

Characterization of Pressure Effects on the Cohesive Properties and Structure of Hexane and Polyethylene Using Molecular Dynamics Simulations

Molecular dynamics (MD) simulations using the OPLS‐AA force field are conducted to compute pressure‐ and molecular‐weight‐dependence of Hildebrand's solubility parameters of hexane and high‐density polyethylene (HDPE) at high pressures. The pressure dependence investigation also captures density data computed at high temperature and for external pressures ranging from 100 to 3000 bar. The effect of electrostatic potential energy contribution to cohesive energy and density is investigated and it is shown that the solubility parameter increases monotonically with increasing external pressure for both molecular mechanical models with and without electrostatic terms. Analysis of the pair distribution function is carried out versus pressure together with the influence of electrostatic energy contribution reflecting structural change of the condensed phase.

     

Modeling Corrosion of Archaeological Silver‐Copper Coins Using the Voltammetry of Immobilized Particles

Two complementary models to describe the long‐term corrosion of silver‐copper coins, based on potential rate laws for smooth corrosion and those combined with diffusive law, for gross corrosion, are proposed. Theoretical kinetics can be tested using signatures of copper and silver corrosion products using the voltammetry of immobilized particles technique. The method is applied to silver coins minted during the 13^th–14^th centuries from the Libertad street hoard in Valencia (Spain) using non‐invasive one‐touch graphite pencil sampling. Voltammetric features yield functional dependences in agreement with the proposed model potentially useful for distinguishing between different mints.     

Extension of the CHARMM general force field to sulfonyl‐containing compounds and its utility in biomolecular simulations

Presented is an extension of the CHARMM General Force Field (CGenFF) to enable the modeling of sulfonyl‐containing compounds. Model compounds containing chemical moieties such as sulfone, sulfonamide, sulfonate, and sulfamate were used as the basis for the parameter optimization. Targeting high‐level quantum mechanical and experimental crystal data, the new parameters were optimized in a hierarchical fashion designed to maintain compatibility with the remainder of the CHARMM additive force field. The optimized parameters satisfactorily reproduced equilibrium geometries, vibrational frequencies, interactions with water, gas phase dipole moments, and dihedral potential energy scans. Validation involved both crystalline and liquid phase calculations showing the newly developed parameters to satisfactorily reproduce experimental unit cell geometries, crystal intramolecular geometries, and pure solvent densities. The force field was subsequently applied to study conformational preference of a sulfonamide based peptide system. Good agreement with experimental IR/NMR data further validated the newly developed CGenFF parameters as a tool to investigate the dynamic behavior of sulfonyl groups in a biological environment. CGenFF now covers sulfonyl group containing moieties allowing for modeling and simulation of sulfonyl‐containing compounds in the context of biomolecular systems including compounds of medicinal interest. © 2012 Wiley Periodicals, Inc.     

HolT Hunter: Software for identifying and characterizing low‐strain DNA holliday triangles

Synthetic DNA nanostructures are most commonly held together via Holliday junctions. These junctions allow for a wide variety of different angles between the double helices they connect. Nevertheless, only constructs with a very limited selection of angles have been built, to date, because of the computational complexity of identifying structures that fit together with low strain at odd angles. I have developed an algorithm that finds over 95% of the possible solutions by breaking the problem down into two portions. First, there is a problem of how smooth rods can form triangles by lying across one another. This problem is easily handled by numerical computation. Second, there is the question of how distorted DNA double helices would need to be to fit onto the rod structure. This strain is calculated directly. The algorithm has been implemented in a Mathematica 8 notebook called Holliday Triangle Hunter. A large database of solutions has been identified. Additional interface software is available to facilitate drawing and viewing models. © 2012 Wiley Periodicals, Inc.