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At least 721 records · Page 40Linked to original sources
PubMed2003

A deoxyribozyme-based molecular automaton.

We describe a molecular automaton, called MAYA, which encodes a version of the game of tic-tac-toe and interactively competes against a human opponent. The automaton is a Boolean network of deoxyribozymes that incorporates 23 molecular-scale logic gates and one constitutively active deoxyribozyme arrayed in nine wells (3x3) corresponding to the game board. To make a move, MAYA carries out an analysis of the input oligonucleotide keyed to a particular move by the human opponent and indicates a move by fluorescence signaling in a response well. The cycle of human player input and automaton response continues until there is a draw or a victory for the automaton. The automaton cannot be defeated because it implements a perfect strategy.

Algorithms↗
PubMed2004

In silico simulation of biological network dynamics.

Realistic simulation of biological networks requires stochastic simulation approaches because of the small numbers of molecules per cell. The high computational cost of stochastic simulation on conventional microprocessor-based computers arises from the intrinsic disparity between the sequential steps executed by a microprocessor program and the highly parallel nature of information flow within biochemical networks. This disparity is reduced with the Field Programmable Gate Array (FPGA)-based approach presented here. The parallel architecture of FPGAs, which can simulate the basic reaction steps of biological networks, attains simulation rates at least an order of magnitude greater than currently available microprocessors.

Algorithms↗
PubMed2004

Analysis of the transcriptional complexity of Arabidopsis thaliana by massively parallel signature sequencing.

Large-scale sequencing of short mRNA-derived tags can establish the qualitative and quantitative characteristics of a complex transcriptome. We sequenced 12,304,362 tags from five diverse libraries of Arabidopsis thaliana using massively parallel signature sequencing (MPSS). A total of 48,572 distinct signatures, each representing a different transcript, were expressed at significant levels. These signatures were compared to the annotation of the A. thaliana genomic sequence; in the five libraries, this comparison yielded between 17,353 and 18,361 genes with sense expression, and between 5,487 and 8,729 genes with antisense expression. An additional 6,691 MPSS signatures mapped to unannotated regions of the genome. Expression was demonstrated for 1,168 genes for which expression data were previously unknown. Alternative polyadenylation was observed for more than 25% of A. thaliana genes transcribed in these libraries. The MPSS expression data suggest that the A. thaliana transcriptome is complex and contains many as-yet uncharacterized variants of normal coding transcripts.

Arabidopsis↗
PubMed2005

A sound barrier for silicon?

For the first time in thirty five years, the clockspeed of the fastest commercial computer chips has not increased. Is the semiconductor industry just pausing for breath or about to suffer a fate similar to that of aerospace?

Computing Methodologies↗
PubMed2006

An approach for estimating exposure to ambient concentrations.

The degree of certainty in epidemiological studies is probably limited more by estimates of exposure than by any other component. We present a methodology for computing daily pollutant concentration fields that reduces exposure uncertainty and bias by taking account of spatial variation in air quality. This approach, using elliptical influence functions, involves the optimum blending of observations from a monitoring network with gridded pollution fields predicted by the complex air quality model TAPM. Such fields allow more information to be incorporated in the exposure fields used in epidemiological studies, rather than having to assume that ambient exposure is the same across a whole city and/or that individuals remain at the one location for the duration of a study.

Air Pollutants↗
PubMed2003

Two-dimensional analysis of ventricular fibrillation in the guinea pig.

Cardiac arrhythmias are undesirable electrical activity in the heart. Ventricular fibrillation (VF) is a fatal cardiac arrhythmia and is characterized by the breakdown of organized electrical activity in the ventricular myocardium. However, little is known about VF, partially because it is difficult to study and understand an apparently disorganized activity. One method for discovering the nature of VF is processing the epicardial electrical signals by using cardiac mapping techniques. These techniques involve the study of propagation patterns seen in VF. In this project, we used guinea pigs to study the spatial organization of the epicardial electrical activity during VF. VF was induced in 9 open chest guinea pigs and epicardial electrode data were acquired by using a square array of 192 electrodes for 4 seconds every minute. The mean correlation length and dominant frequency were measured in each recorded segment. Correlation length is a measure of the spatial order in a system and dominant frequency is the frequency corresponding to the spectral maximum. The mean correlation length was found to vary between 1-7 mm and the dominant frequency was in the range of 1-14 Hz. This study suggests that guinea pig VF exhibits a level of organization equivalent to or greater than that seen in previous studies.

Analysis of Variance↗
PubMed2004

Coupled reference interaction site model/simulation approach for thermochemistry of solvation: theory and prospects.

We present a new methodology for computing solvation free energy, which is based upon the reference interaction site model (RISM)/hypernetted chain (HNC) solvation free energy expression, but which substitutes radial distribution functions taken from simulations for those calculated by simultaneous solution of the RISM and HNC equations. Consequently, solvation free energy can be obtained from a single molecular dynamics or Monte Carlo simulation. Here we describe in detail the coupled RISM/simulation approach, and offer some error analysis. Finally we give the results of its application to a set of small test molecules in aqueous solution. The success shown in some of our results demonstrates that the coupled RISM/simulation approach is worth considering further as a potentially useful tool in studies of solvated systems, such as aqueous molecular biosystems.

Journal Article↗
PubMed2004

Mixed-sector intermediate Hamiltonian Fock-space coupled cluster approach.

An alternative formulation of the intermediate Hamiltonian Fock-space coupled cluster scheme developed before is presented. The methodological and computational advantages of the new formulation include the possibility of using a model space with determinants belonging to different Fock-space sectors. This extends the scope of application of the multireference coupled cluster method, and makes possible the use of quasiclosed shells (e.g., p2, d4) as reference states. Representative applications are described, including electron affinities of group-14 atoms, ionization potentials of group-15 elements, and ionization potentials and excitation energies of silver and gold. Excellent agreement with experiment (a few hundredths of an electronvolt) is obtained, with significant improvement (by a factor of 5-10 for p3 states) over Fock-space coupled cluster results. Many states not reachable by the Fock-space approach can now be studied.

Journal Article↗