Development and optimisation of a novel genetic algorithm for studying model protein folding

Determination of the native state of a protein from its amino acid sequence is the goal of protein folding simulations, with potential applications in gene therapy and drug design. Location of the global minimum structure for a given sequence, however, is a difficult optimisation problem. In this paper, we describe the development and application of a genetic algorithm (GA) to find the lowest-energy conformations for the 2D HP lattice bead protein model. Optimisation of the parameters of our standard GA program reveals that the GA is most successful (at finding the lowest-energy conformations) for high rates of mating and mutation and relatively high elitism. We have also introduced a number of new genetic operators: a duplicate predator—which maintains population diversity by eliminating duplicate structures; brood selection—where two parent structures undergo crossover and give rise to a brood of (not just two) offspring; and a Monte Carlo based local search algorithm—to explore the neighbourhood of all members of the population. It is shown that these operators lead to significant improvements in the success and efficiency of the GA, both compared with our standard GA and with previously published GA studies for benchmark HP sequences with up to 50 beads.     

Parallelizing of macro-scale pseudo-particle modeling for particle-fluid systems

Particle methods such as SPH (smoothed particlehydrodynamics)[1,2], DEM (distinct-element model)[3],DPD (dissipative particle dynamics)[4— and pseudo- 6]particle modeling (PPM)[7,8] are getting more and morepopular as numerical methods in material science andfluid dynamics, due to their flexibility in simulatingcomplicated phenomena like fluid-solid coupling,multi-phase flow and large deformation and rupture insolid materials. However, a comm…     

Enhanced Optical Image Verification Based on Joint Transform Correlator Adopting Fourier Hologram

In this paper two new architectures for optical image verification are proposed. Both architectures are based on conventional joint transform correlators (JTCs) adopting a Fourier hologram and can significantly improve the recovered image quality. First, an input phase-only function is Fourier transformed and then interferes with a reference wave that is diffracted from a plane wave incident on another random phase mask. Second, two phase-only functions are placed at the two input sides of a beamsplitter such that the interference pattern of their Fourier transforms can be detected. To obtain a predefined target image in the output plane, one of the input phase functions is iteratively retrieved by the use of the projection onto constraint sets algorithm. Simulation results show that the less mean squared error and better image quality are obtained for both the binary and grayscale images.     

Enhancing the accuracy of virtual screening: molecular dynamics with quantum-refined force fields

Summary A methodology aimed at improving the accuracy of current docking–scoring procedures is proposed, and validated through detailed tests of its performance in predicting the activity of HIV-1 protease inhibitors. This methodology is based on molecular dynamics simulations using a force field whose effective charges are refined by means of a novel procedure that relies on quantum-mechanical calculations and preserves the internal consistency of the parameterization scheme.     

Chemistry in microstructured reactors

The application of microstructured reactors in the chemical process industry has gained significant importance in recent years. Companies that offer not only microstructured reactors, but also entire chemical process plants and services relating to them, are already in existence. In addition, many institutes and universities are active within this field, and process-engineering-oriented reviews and a specialized book are available. Microstructured systems can be applied with particular success in the investigation of highly exothermic and fast reactions. Often the presence of temperature-induced side reactions can be significantly reduced through isothermal operations. Although microstructured reaction techniques have been shown to optimize many synthetic procedures, they have not yet received the attention they deserve in organic chemistry. For this reason, this Review aims to address this by providing an overview of the chemistry in microstructured reactors, grouped into liquid-phase, gas-phase, and gas-liquid reactions.     

On the Existence of Solutions of Quasivariational Inclusion Problems

Quasivariational inclusion problems are formulated and sufficient conditions on the existence of solutions are shown. As special cases, we obtain several results on the existence of solutions of general vector ideal, proper, Pareto, weak quasioptimization problems, quasivariational inequalities, and vector quasiequilibrium problems. Further, we prove theorems on the existence for solutions of systems of these inclusions. As a corollary, we obtain an ideal minimax theorem concerning vector functions.     

MODIFIED APPROXIMATE PROXIMAL POINT ALGORITHMS FOR FINDING ROOTS OF MAXIMAL MONOTONE OPERATORS

§1　Introduction and preliminariesA set T Rn×Rnis called a monotone operator on Rn,if T has the property(x,y) ,(x′,y′)∈T 〈x -x′,y -y′〉≥0 ,where〈·,·〉denotes the inner product on Rn.T is maximal if(considered as a graph) itis not strictly contained in any other monotone operator on Rn.It is well known that thetheory of maximal monotone operators plays an important role in the study of convexprogramming and variational inequalities since itcan provide a powerful general framework…     

Finding 2-edge connected spanning subgraphs

This paper studies the NP-hard problem of finding a minimum size 2-edge connected spanning subgraph (2-ECSS). An algorithm is given that on an r-edge connected input graph G=(V,E) finds a 2-ECSS of size at most |V|+(|E|−|V|)/(r−1). For r-regular, r-edge connected input graphs for r=3, 4, 5 and 6, this gives approximation guarantees of and , respectively.     

Randomized on-line scheduling on three processors

We consider a randomized on-line scheduling problem where each job has to be scheduled on any of m identical processors. The objective is to minimize the expected makespan. We show that the competitive ratio of any randomized algorithm for m=3 processors must be strictly greater than .     

The dominating set problem is fixed parameter tractable for graphs of bounded genus

We describe an algorithm for the dominating set problem with time complexity O((4g+40)^kn²) for graphs of bounded genus g1, where k is the size of the set. It has previously been shown that this problem is fixed parameter tractable for planar graphs. We give a simpler proof for the previous O(8^kn²) result for planar graphs. Our method is a refinement of the earlier techniques.