Informatica

Ligand-Based Virtual Screening accelerates and cheapens the design of new drugs. However, it needs efficient optimizers because of the size of compound databases. This work proposes a new method called Tangram CW. The proposal also encloses a knowledge-based filter of compounds. Tangram CW achieves comparable results to the state-of-the-art tools OptiPharm and 2L-GO-Pharm using about a tenth of their computational budget without filtering. Activating it discards more than two thirds of the database while keeping the desired compounds. Thus, it is possible to consider molecular flexibility despite increasing the options. The implemented software package is public.

This paper deals with the two-stage transportation problem with fixed charges, denoted by TSTPFC. We propose a fast solving method, designed for parallel environments, that allows solving real-world applications efficiently. The proposed constructive heuristic algorithm is iterative and its primary feature is that the solution search domain is reduced at each iteration. Our achieved computational results were compared with those of the existing solution approaches. We tested the method on two sets of instances available in literature. The outputs prove that we have identified a very competitive approach as compared to the methods than one can find in literature.

We know the necessity for information security becomes more widespread in these days, especially for hardware-based implementations such as smart cards chips for wireless applications and cryptographic accelerators. Fast modular exponentiation algorithms are often considered of practical significance in public-key cryptosystems. The RSA cryptosystem is one of the most widely used technologies for achieving information security. The main task of the encryption and decryption engine of RSA cryptosystem is to compute M^E mod N. Because the bit-length of the numbers M, E, and N would be about 512 to 1024 bits now, the computations for RSA cryptosystem are time-consuming. In this paper, an efficient technique for parallel computation of the modular exponentiation is proposed and our algorithm can reduce time complexity. We can have the speedup ratio as 1.06 or even 2.75 if the proposed technique is used. In Savas–Tenca–Koc algorithm, they design a multiplier with an insignificant increase in chip area (about 2.8%) and no increase in time delay. Our proposed technique is faster than Savas–Tenca–Koc algorithm in time complexity and improves efficiency for RSA cryptosystem.

The paper describes the development and performance of parallel algorithms for the discrete element method (DEM) software. Spatial domain decomposition strategy and message passing inter-processor communication have been implemented in the DEMMAT code for simulation of visco-elastic frictional granular media. The novel algorithm combining link-cells for contact detection, the static domain decomposition for parallelization and MPI data transfer for processors exchanging particles has been developed for distributed memory PC clusters. The parallel software DEMMAT_PAR has been applied to model compacting of spherical particles in the rectangular box. Two benchmark problems with different numbers of particles have been solved in order to measure parallel efficiency of the code. The inter-processor communication has been examined in order to improve domain decomposition topology and to achieve better load balancing. The speed-up equal to 11 has been obtained on 16 processors. The parallel performance study has been performed on the PC cluster VILKAS of Vilnius Gediminas Technical University, Lithuania.

The present paper describes the development and the performance of parallel FEM software for solving various CFD problems. Domain decomposition strategy and parallel iterative GMRES solver have been adapted to the universal space‐time FEM code FEMTOOL, which allows implementation of any partial differential equation with minor expenses. The developed data structures, the static load balancing and the inter‐processor communication algorithms have been particularly suited for homogeneous distributed memory PC clusters. The universality of the considered parallel algorithms has been validated solving applications described by the Poisson equation, by the convective transport equation and by the Navier–Stokes equations. Three typical benchmark problems have been solved in order to perform the efficiency study. The performance of parallel computations, the speed‐up and the efficiency have been measured on three BEOWULF PC clusters as well as on the cluster of IBM RISC workstations and on the IBM SP2 supercomputer.

The analysis of the method for multiple criteria optimization problems applying a computer network has been presented in the paper. The essence of the proposed method is the distribution of the concrete optimization problem into the network rather than the parallelization of some optimization method. The aim of the authors is to design and investigate the interactive strategies to solve complex multiple criteria problems by applying a computer network. The optimized objective function is the weight sum of the criteria. The multiple criteria problem is iterated by selecting interactively different weight coefficients of the criteria. Therefore, the process is organized by designating the computers as the master (that coordinates the process of other computers) and the slaves (that execute different tasks). In the beginning of the process the researcher allocates a certain number of optimization problems to the network. The objective function optimization problems differ only in weight coefficients of the criteria. As soon as the task of a slave has been executed, the result is sent to the master. Every computer of the network behaves in analogous way. Whenever the researcher receives an immediate result from one of the computers, he gives a decision taking into consideration the latter and all the previous results, i.e., he selects new weight coefficients for the criteria and assigns a new task to the network. Likewise the multiple criteria problem is solved until the result is acceptable for the researcher. The application of the proposed method is illustrated on the basis of the problem for the selection of the optimal nutritive value. Message Passing Interface (MPI) software has been used. The trials have been carried out with the network of computers under the operation system Windows NT.

We consider a possibility of automating the analysis of a computer program realizing the objective function of an extremal problem, and of distributing the calculation of the function value into parallel processes on the basis of results of the analysis. The first problem is to recognize the constituent parts of the function. The next one is to determine their computing times. The third problem is to distribute the calculation of these parts among independent processes. A special language similar to PASCAL has been used to describe the objective function. A new scheduling algorithm, seeking to minimize the maximal finishing time of processing units, was proposed and investigated. Experiments are performed using a computer network.