Megavariate Analysis of Environmental QSAR Data. Part II – Investigating Very Complex Problem Formulations Using Hierarchical, Non-Linear and Batch-Wise Extensions of PCA and PLS

Summary Three extensions of the basic PCA and PLS methodologies are described. These extensions are hierarchical, non-linear and batch-based in nature. The objectives of these methods are to assist in problem understanding and problem solving in very complex (QSAR) problem formulations. The method extensions are illustrated using two example QSAR data sets containing many X- and Y-variables.     

Scheduling elective surgery under uncertainty and downstream capacity constraints

The objective of this study is to generate an optimal surgery schedule of elective surgery patients with uncertain surgery operations, which includes uncertainty in surgery durations and the availability of downstream resources such as surgical intensive care unit (SICU) over multi-periods. The stochastic optimization is adapted and the sample average approximation (SAA) method is proposed for obtaining an optimal surgery schedule with respect to minimizing the total cost of patient costs and overtime costs. A computational experiment is presented to evaluate the performance of the proposed method.     

Parallel Implementation of Successive Convex Relaxation Methods for Quadratic Optimization Problems

As computing resources continue to improve, global solutions for larger size quadrically constrained optimization problems become more achievable. In this paper, we focus on larger size problems and get accurate bounds for optimal values of such problems with the successive use of SDP relaxations on a parallel computing system called Ninf (Network-based Information Library for high performance computing).     

Simulation of Optical Devices Using Parallel FDTD Method

On this paper, we investigate the algorithm and efficiency of simulation of optical devices using parallel computing method, implement some real wavelength division multiplexing (WDM) components such as resonators to test the method's possibility and efficiency.     

JACOB: An enterprise framework for computational chemistry

Here, we present just a collection of beans (JACOB): an integrated batch‐based framework designed for the rapid development of computational chemistry applications. The framework expedites developer productivity by handling the generic infrastructure tier, and can be easily extended by user‐specific scientific code. Paradigms from enterprise software engineering were rigorously applied to create a scalable, testable, secure, and robust framework. A centralized web application is used to configure and control the operation of the framework. The application‐programming interface provides a set of generic tools for processing large‐scale noninteractive jobs (e.g., systematic studies), or for coordinating systems integration (e.g., complex workflows). The code for the JACOB framework is open sourced and is available at: www.wallerlab.org/jacob . © 2013 Wiley Periodicals, Inc.     

Fast parallel detection of feline panleukopenia virus DNA by multi‐channel microchip electrophoresis with programmed step electric field strength

A multi‐channel microchip electrophoresis using a programmed step electric field strength (PSEFS) method was investigated for fast parallel detection of feline panleukopenia virus (FPV) DNA. An expanded laser beam, a 10× objective lens, and a charge‐coupled device camera were used to simultaneously detect the separations in three parallel channels using laser‐induced fluorescence detection. The parallel separations of a 100‐bp DNA ladder were demonstrated on the system using a sieving gel matrix of 0.5% poly(ethylene oxide) (M_r = 8 000 000) in the individual channels. In addition, the PSEFS method was also applied for faster DNA separation without loss of resolving power. A DNA size marker, FPV DNA sample, and a negative control were simultaneously analyzed with single‐run and one‐step detection. The FPV DNA was clearly distinguished within 30 s, which was more than 100 times faster than with conventional slab gel electrophoresis. The proposed multi‐channel microchip electrophoresis with PSEFS was demonstrated to be a simple and powerful diagnostic method to analyze multiple disease‐related DNA fragments in parallel with high speed, throughput, and accuracy.     

电场对(4, 0)Zigzag模型单壁碳纳米管的影响

The structural and electronic properties of a (4, 0) zigzag single-walled carbon nanotube (SWCNT) under parallel and transverse electric fields with strengths of 0-1.4×10~(-2) a.u. Were studied using the density functional theory (DFT) B3LYP/6-31G~* method. Results show that the properties of the SWCNT are dependent on the external electric field. The applied external electric field strongly affects the molecular dipole moments. The induced dipole moments increase linearly with increase in the electrical field intensities. This study shows that the application of parallel and transverse electric fields results in changes in the occupied and virtual molecular orbitals (Mos) but the energy gap between the highest occupied MO (HOMO) and the lowest unoccupied MO (LUMO) of this SWCNT is less sensitive to the electric field strength. The electronic spatial extent (ESE) and length of the SWCNT show small changes over the entire range of the applied electric field strengths. The natural bond orbital (NBO) electric charges on the atoms of the SWCNT show that increase in the external electric field strength increases the separation of the center of the positive and negative electric charges of the carbon nanotube.     

One pot solid phase synthesis of 2-substituted 2,3-dihydropyridin-4(1H)-ones on Rinkamide-resin

A novel solid phase synthesis of 2-substituted 2,3-dihydropyridin-4(1H)-ones using Rinkamide-polystyrene-resin is described. The key step involves a hetero-Diels-Alder reaction of Danishefsky's diene with solid phase bound imines, which was carefully optimized. Using this method even ketones are transformed into 2,2-disubstituted dihydropyridones.     

Statistical assertion: A more powerful method for debugging scientific applications

Traditional debuggers are of limited value for modern scientific codes that manipulate large complex data structures. Current parallel machines make this even more complicated, because the data structure may be distributed across processors, making it difficult to view/interpret and validate its contents. Therefore, many applications’ developers resort to placing validation code directly in the source program. This paper discusses a novel debug-time assertion, called a “Statistical Assertion”, that allows using extracted statistics instead of raw data to reason about large data structures, therefore help locating coding defects. In this paper, we present the design and implementation of an ‘extendable’ statistical-framework which executes the assertion in parallel by exploiting the underlying parallel system. We illustrate the debugging technique with a molecular dynamics simulation. The performance is evaluated on a 20,000 processor Cray XE6 to show that it is useful for real-time debugging.     

Solving Large Quadratic Assignment Problems in Parallel

Quadratic Assignment problems are in practice among the mostdifficult to solve in the class of NP-complete problems. Theonly successful approach hitherto has been Branch-and-Bound-basedalgorithms, but such algorithms are crucially dependent on good boundfunctions to limit the size of the space searched. Much work hasbeen done to identify such functions for the QAP, but with limitedsuccess.Parallel processing has also been used in order to increase the sizeof problems solvable to optimality. The systems used have, however, oftenbeen systems with relatively few, but very powerful vector processors, andhave hence not been ideally suited for computations essentially involving non-vectorizable computations on integers.In this paper we investigate the combination of one of the best bound functions for a Branch-and-Bound algorithm (the Gilmore-Lawler bound) and various testing, variable binding and recalculation of bounds between branchings when used in aparallel Branch-and-Bound algorithm. The algorithm has been implemented on a 16-processor MEIKO Computing Surface with Intel i860processors. Computational results from the solution of a number of large QAPs, including the classical Nugent 20 are reported.