We propose steps toward enhancing evolutionary computation via mechanisms from molecular biology, in particular the ideas of regulatory networks and embryogenesis. First we survey key facts and developments in bioinformatics and molecular genetics, followed by speculations on future implementations in evolutionary computation. We then focus on computational implementations of the mechanisms of ...

Quantum correlations are central to the foundations of quantum physics and form basis technologies. Here, our goal is connect computation: using as a resource for computation - vice versa, test correlations. We derive Bell-type inequalities that capacity states computing Boolean functions experimentally investigate them 4-photon Greenberger-Horne-Zeilinger (GHZ) states. Further, we show how gen...

Ab initio molecular orbital calculations are usually limited to smalland medium-size molecular systems. The obstacle lies in the rapid increase of computational cost as the systems become larger and more complex. For the ground state, a number of linear scaling computational methods are proposed. Here the locality of the ground state density matrix was the key to achieve the linear scaling comp...

Biomolecular computing is the computational method that uses the potential of DNA as a parallel computing device. DNA computing can be used to solve NP-complete problems. An appropriate application of DNA computation is large-scale evaluation of parallel computation models such as Boolean Circuits. In this study, we present a molecular-based algorithm for evaluation of Nand-based Boolean Circui...

In this paper, we consider a parallel method for computing interior eigenvalues and corresponding eigenvectors of generalized eigenvalue problems which arise from molecular orbital computation of biochemistry applications. Matrices in such applications are sparse but often have relatively large number of nonzero elements, and we may require some eigenpairs in a specific part of the spectrum. We...

for October 2004 CEGS Grantee Meeting Roger Brent, Molecular Sciences Institute P50 HG02370 Center for Genomic Experimentation and Computation Awarded September 2002 The mission of the Center for Genomic Experimentation and Computation at the Molecular Sciences Institute (MSI) is to combine genomic and computational research to make predictive models of biological systems. Its flagship activity...

Abstract Molecular science is governed by the dynamics of electrons and atomic nuclei, their interactions with electromagnetic fields. A faithful physicochemical understanding these processes crucial for design synthesis chemicals materials value our society economy. Although some problems in this field can be adequately addressed classical mechanics, many demand an explicit quantum mechanical ...

This paper describes a scheme for implementing a binary counter with chemical reactions. The value of the counter is encoded by logical values of "0" and "1" that correspond to the absence and presence of specific molecular types, respectively. It is incremented when molecules of a trigger type are injected. Synchronization is achieved with reactions that produce a sustained three-phase oscilla...

Electrostatics plays a fundamental role in virtually all processes involving biomolecules in solution. The Poisson-Boltzmann equation constitutes one of the most fundamental approaches to treat electrostatic effects in solution. The theoretical basis of the Poisson-Boltzmann equation is reviewed and a wide range of applications is presented, including the computation of the electrostatic potent...