Synthesis of a systolic array genetic algorithm

The paper presents a design for a hardware genetic algorithm which uses a pipeline of systolic arrays. These arrays have been designed using systolic synthesis techniques which involve expressing the algorithm as a set of uniform recurrence relations. The final design divorces the fitness function evaluation from the hardware and can process chromosomes of different lengths, giving the design a generic quality. The paper demonstrates the design methodology by progressively re-writing a simple genetic algorithm, expressed in C code, into a form from which systolic structures can be deduced. This paper extends previous work by introducing a simplification to a previous systolic design for the genetic algorithm. The simplification results in the removal of 2N 2 + 4N cells and reduces the time complexity by 3N + 1 cycles.

The systolic array genetic algorithm, an example of systolic arrays as a reconfigurable design methodology

We advocate the use of systolic design techniques to create custom hardware for Custom Computing Machines. We have developed a hardware genetic algorithm based on systolic arrays to illustrate the feasibility of the approach. The architecture is independent of the lengths of chromosomes used and can be scaled in size to accommodate different population sizes. An FPGA prototype design can process 16 million genes per second.

Controlling a mobile robot with a biological brain

The intelligent controlling mechanism of a typical mobile robot is usually a computer system. Some recent research is ongoing in which biological neurons are being cultured and trained to act as the brain of an interactive real world robot�thereby either completely replacing, or operating in a cooperative fashion with, a computer system. Studying such hybrid systems can provide distinct insights into the operation of biological neural structures, and therefore, such research has immediate medical implications as well as enormous potential in robotics. The main aim of the research is to assess the computational and learning capacity of dissociated cultured neuronal networks. A hybrid system incorporating closed-loop control of a mobile robot by a dissociated culture of neurons has been created. The system is flexible and allows for closed-loop operation, either with hardware robot or its software simulation. The paper provides an overview of the problem area, gives an idea of the breadth of present ongoing research, establises a new system architecture and, as an example, reports on the results of conducted experiments with real-life robots.

Time patterns in UK demand for alcohol and tobacco: an application of the EM algorithm

Capturing the pattern of structural change is a relevant task in applied demand analysis, as consumer preferences may vary significantly over time. Filtering and smoothing techniques have recently played an increasingly relevant role. A dynamic Almost Ideal Demand System with random walk parameters is estimated in order to detect modifications in consumer habits and preferences, as well as changes in the behavioural response to prices and income. Systemwise estimation, consistent with the underlying constraints from economic theory, is achieved through the EM algorithm. The proposed model is applied to UK aggregate consumption of alcohol and tobacco, using quarterly data from 1963 to 2003. Increased alcohol consumption is explained by a preference shift, addictive behaviour and a lower price elasticity. The dynamic and time-varying specification is consistent with the theoretical requirements imposed at each sample point. (c) 2005 Elsevier B.V. All rights reserved.

High-throughput proteomics using matrix-assisted laser desorption/ ionization mass spectrometry

It has become evident that the mystery of life will not be deciphered just by decoding its blueprint, the genetic code. In the life and biomedical sciences, research efforts are now shifting from pure gene analysis to the analysis of all biomolecules involved in the machinery of life. One area of these postgenomic research fields is proteomics. Although proteomics, which basically encompasses the analysis of proteins, is not a new concept, it is far from being a research field that can rely on routine and large-scale analyses. At the time the term proteomics was coined, a gold-rush mentality was created, promising vast and quick riches (i.e., solutions to the immensely complex questions of life and disease). Predictably, the reality has been quite different. The complexity of proteomes and the wide variations in the abundances and chemical properties of their constituents has rendered the use of systematic analytical approaches only partially successful, and biologically meaningful results have been slow to arrive. However, to learn more about how cells and, hence, life works, it is essential to understand the proteins and their complex interactions in their native environment. This is why proteomics will be an important part of the biomedical sciences for the foreseeable future. Therefore, any advances in providing the tools that make protein analysis a more routine and large-scale business, ideally using automated and rapid analytical procedures, are highly sought after. This review will provide some basics, thoughts and ideas on the exploitation of matrix-assisted laser desorption/ ionization in biological mass spectrometry - one of the most commonly used analytical tools in proteomics - for high-throughput analyses.

Liquid ultraviolet matrix-assisted laser desorption/ionization - mass spectrometry for automated proteomic analysis

We have combined several key sample preparation steps for the use of a liquid matrix system to provide high analytical sensitivity in automated ultraviolet -- matrix-assisted laser desorption/ionisation -- mass spectrometry (UV-MALDI-MS). This new sample preparation protocol employs a matrix-mixture which is based on the glycerol matrix-mixture described by Sze et al. The low-femtomole sensitivity that is achievable with this new preparation protocol enables proteomic analysis of protein digests comparable to solid-state matrix systems. For automated data acquisition and analysis, the MALDI performance of this liquid matrix surpasses the conventional solid-state MALDI matrices. Besides the inherent general advantages of liquid samples for automated sample preparation and data acquisition the use of the presented liquid matrix significantly reduces the extent of unspecific ion signals in peptide mass fingerprints compared to typically used solid matrices, such as 2,5-dihydroxybenzoic acid (DHB) or alpha-cyano-hydroxycinnamic acid (CHCA). In particular, matrix and low-mass ion signals and ion signals resulting from cation adduct formation are dramatically reduced. Consequently, the confidence level of protein identification by peptide mass mapping of in-solution and in-gel digests is generally higher.

Use of a novel Hill-climbing genetic algorithm in protein folding simulations

We have developed a novel Hill-climbing genetic algorithm (GA) for simulation of protein folding. The program (written in C) builds a set of Cartesian points to represent an unfolded polypeptide's backbone. The dihedral angles determining the chain's configuration are stored in an array of chromosome structures that is copied and then mutated. The fitness of the mutated chain's configuration is determined by its radius of gyration. A four-helix bundle was used to optimise simulation conditions, and the program was compared with other, larger, genetic algorithms on a variety of structures. The program ran 50% faster than other GA programs. Overall, tests on 100 non-redundant structures gave comparable results to other genetic algorithms, with the Hill-climbing program running from between 20 and 50% faster. Examples including crambin, cytochrome c, cytochrome B and hemerythrin gave good secondary structure fits with overall alpha carbon atom rms deviations of between 5 and 5.6 Angstrom with an optimised hydrophobic term in the fitness function. (C) 2003 Elsevier Ltd. All rights reserved.

Rhodium assisted C-H activation of N-(2 '-hydroxyphenyl)benzaldimines. Synthesis, structure and electrochemical properties of a group of organorhodium complexes

Reaction of a group of N-(2'-hydroxyphenyl)benzaldimines, derived from 2-aminophenol and five para-substituted benzaldehydes (the para substituents are OCH3, CH3, H, Cl and NO2), with [Rh(PPh3)(3)Cl] in refluxing toluene in the presence of a base (NEW afforded a family of organometallic complexes of rhodium(III). The crystal structure of one complex has been determined by X-ray crystallography. In these complexes the benzaldimine ligands are coordinated to the metal center, via dissociation of the phenolic proton and the phenyl proton at the ortho position of the phenyl ring in the imine fragment, as dianionic tridentate C,N,O-donors, and the two PPh3 ligands are trans. The complexes are diamagnetic (low-spin d(6), S = 0) and show intense MLCT transitions in the visible region. Cyclic voltammetry shows a Rh(III)-Rh(IV) oxidation within 0.63-0.93 V vs SCE followed by an oxidation of the coordinated benzaldimine ligand. A reduction of the coordinated benzaldimine is also observed within -0.96 to -1.04 V vs SCE. Potential of the Rh(Ill)-Rh(IV) oxidation is found to be sensitive to the nature of the para-substituent. (c) 2006 Elsevier B.V. All rights reserved.

Liquid ultraviolet matrix-assisted laser desorption/ionization mass spectrometry for automated proteomic analysis

We have combined several key sample preparation steps for the use of a liquid matrix system to provide high analytical sensitivity in automated ultraviolet - matrix-assisted laser desorption/ ionisation - mass spectrometry (UV-MALDI-MS). This new sample preparation protocol employs a matrix-mixture which is based on the glycerol matrix-mixture described by Sze et al. U. Am. Soc. Mass Spectrom. 1998, 9, 166-174). The low-ferntomole sensitivity that is achievable with this new preparation protocol enables proteomic analysis of protein digests comparable to solid-state matrix systems. For automated data acquisition and analysis, the MALDI performance of this liquid matrix surpasses the conventional solid-state MALDI matrices. Besides the inherent general advantages of liquid samples for automated sample preparation and data acquisition the use of the presented liquid matrix significantly reduces the extent of unspecific ion signals in peptide mass fingerprints compared to typically used solid matrices, such as 2,5-dihydrox-ybenzoic acid (DHB) or alpha-cyano-hydroxycinnamic acid (CHCA). In particular, matrix and lowmass ion signals and ion signals resulting from cation adduct formation are dramatically reduced. Consequently, the confidence level of protein identification by peptide mass mapping of in-solution and in-gel digests is generally higher.

High-throughput proteomics using matrix-assisted laser desorption/ionization mass spectrometry

It has become evident that the mystery of life will not be deciphered just by decoding its blueprint, the genetic code. In the life and biomedical sciences, research efforts are now shifting from pure gene analysis to the analysis of all biomolecules involved in the machinery of life. One area of these postgenomic research fields is proteomics. Although proteomics, which basically encompasses the analysis of proteins, is not a new concept, it is far from being a research field that can rely on routine and large-scale analyses. At the time the term proteomics was coined, a gold-rush mentality was created, promising vast and quick riches (i.e., solutions to the immensely complex questions of life and disease). Predictably, the reality has been quite different. The complexity of proteomes and the wide variations in the abundances and chemical properties of their constituents has rendered the use of systematic analytical approaches only partially successful, and biologically meaningful results have been slow to arrive. However, to learn more about how cells and, hence, life works, it is essential to understand the proteins and their complex interactions in their native environment. This is why proteomics will be an important part of the biomedical sciences for the foreseeable future. Therefore, any advances in providing the tools that make protein analysis a more routine and large-scale business, ideally using automated and rapid analytical procedures, are highly sought after. This review will provide some basics, thoughts and ideas on the exploitation of matrix-assisted laser desorption/ionization in biological mass spectrometry - one of the most commonly used analytical tools in proteomics - for high-throughput analyses.

Novel solid networks containing Sn-H as a greener replacement for soluble alkyl Sn-H reagents in radical assisted organic synthesis

DiGrignard reagents of the form XMg(CH2)(n)MgX, where X = Br or I and n = 6, 8, 10 or 12, were allowed to react with PhSnCl3 to produce highly cross-linked Ph-Sn polymeric networks. The Sn-H moiety was incorporated into these insoluble network polymers by treatment with Br-2 and NaBH4. Excellent accessibility of the Sn-H was displayed by these solvent penetrable but insoluble networks, giving them higher Sn-H loadings than all previously reported supported reagents. These reagents were totally regenerable in NaBH4 for radical assisted organic synthesis and no detectable leaching of the Sn into solution was observed during these reactions.

Solvent-Assisted Formation of Vesicles by a Self-Assembling Ni-3-Schiff Base Complex

A linear trinuclear Ni-Schiff base complex [Ni-3(salpen)(2)(PhCH2COO)(2)(EtOH)] has been synthesized by combining Ni(ClO4)(2)center dot 6H(2)O, phenyl acetic acid (C6H5CH2COOH), and the Schiff base ligand, N,N'-bis(salicylidene)-1,3-pentanediamine (H(2)salpen). This complex is self-assembled through hydrogen bonding and C-H-g interaction in the solid state to generate a sheet-like architecture, while in organic solvent (CH2Cl2), it forms vesicles with a mean diameter of 290 nm and fused vesicles, depending upon the concentration of the solution. These vesicles act as an excellent carrier of dye molecules in CH2Cl2. The morphology of the complex has been determined by scanning electron microscopy and transmission electron microscopy experiments, and the encapsulation of dye has been examined by confocal microscopic image and electronic absorption spectra.

Light-assisted synthesis of a Ru(VI) nitrido complex by the reaction of azide with a Ru(III) complex

Reaction of Ru(III)(L)(dmf)Cl-3 (1) (L = 4,4,4',4'-tetramethyl-2,2'- bisoxazoline, dmf = N,N-dimethylformamide) with an excess of sodium azide in a methanol-water mixture leads to the isolation of the sodium salt of a Ru( VI) nitrido complex of the tetraanion of N,N'-bis-(2,2-dimethyl-1-hydroxyethyl)-1,2-ethanediamide ( L'H-4; H a dissociable proton) of the formulation Na[Ru(L')(N)(H2O)].1.4H(2)O (2). Complex 2 is not generated in the absence of light. A tentative mechanism for the reaction is proposed and a Ru(IV) intermediate, Na[Ru(L')(N-3)(H2O)] . 2CH(3)OH.2H(2)O (3), isolated.