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At least 739 records · Page 41Linked to original sources
PubMed2005

Photoconductivity and current producing states in molecular semiconductors.

We present a methodology for computing photocurrent production in molecular semiconducting molecules. Our model combines a single-configuration interaction picture with the nonequilibrium Green's function approach to compute the current response of a molecular semiconducting wire following excitation. We give detailed analysis of the essential excitonic, charge transfer, and dipole states for poly-(phenylenevinylene) chains of length 32 and 48 repeat units under an electric field bias and use this to develop a reduced dimensional tunneling model which accounts for chain-length and field-dependent behavior. In this paper, we consider the decay of an excited electron/hole state on a molecular wire under bias attached to semiconducting leads at either end. We find that the current produced by the decay of an excitation depends not only upon the lifetime of the state, as given by the imaginary part of its complex eigenvalue, but also upon the net charge on terminal ends of the molecule. We also find that weakly bound electron/hole charge-transfer pairs can decay into the continuum via field induced tunneling and produce a net current whereas excitonic states decay via tunneling but give no net current contribution.

Journal Article↗
PubMed2005

Application of the constrained fluid lambda-integration path to the calculation of high temperature Au(110) surface free energies.

Recently a method termed constrained fluid lambda-integration was proposed for calculating the free energy difference between bulk solid and liquid reference states via the construction of a reversible thermodynamic integration path; coupling the two states in question. The present work shows how the application of the constrained fluid lambda-integration concept to solid/liquid slab simulation cells makes possible a generally applicable computer simulation methodology for calculating the free energy of any surface and/or surface defect structure, including surfaces requiring variations in surface atom or density number, such as the (1 x 5) Au(100) or (1 x 2) missing row Au(110) reconstructed surfaces or excess adatom/vacancy/step populated surfaces. We evaluate the methodology by calculating the free energy of various disordered high temperature Au(110) embedded atom method surfaces constrained to differing excess surface atom numbers [including those corresponding to the (1 x 2) missing row reconstructed surface] and obtained the interesting result that at 1000 K (as distinct from lower temperatures) the free energy difference between these surfaces is reduced to zero; a result which is consistent with an expected order-disorder phase transition for the Au(110) surface at such high temperatures.

Journal Article↗
PubMed2006

Using massively parallel simulation and Markovian models to study protein folding: examining the dynamics of the villin headpiece.

We report on the use of large-scale distributed computing simulation and novel analysis techniques for examining the dynamics of a small protein. Matters addressed include folding rate, very long time scale kinetics, ensemble properties, and interaction with water. The target system for the study, the villin headpiece, has been of great interest to experimentalists and theorists both. Sampling totaled nearly 500 mus-the most extensive published to date for a system of villin's size in explicit solvent with all atom detail-and was in the form of tens of thousands of independent molecular dynamics trajectories, each several tens of nanoseconds in length. We report on kinetics sensitivity analyses that, using a set of short simulations, probed the role of water in villin's folding and sensitivity to the simulation's electrostatics treatment. By constructing Markovian state models (MSMs) from the collected data, we were able to propagate dynamics to times far beyond those directly simulated and to rapidly compute mean first passage times, long time kinetics (tens of microseconds), and evolution of ensemble property distributions over long times, otherwise currently impossible. We also tested our MSM by using it to predict the structure of villin de novo.

Algorithms↗
PubMed2006

COAST: Controllable approximative stochastic reaction algorithm.

We present an approximative algorithm for stochastic simulations of chemical reaction systems, called COAST, based on three different modeling levels: for small numbers of particles an exact stochastic model; for intermediate numbers an approximative, but computationally more efficient stochastic model based on discrete Gaussian distributions; and for large numbers the deterministic reaction kinetics. In every simulation time step, the subdivision of the reaction channels into the three different modeling levels is done automatically, where all approximations applied can be controlled by a single error parameter for which an appropriate value can easily be found. Test simulations show that the results of COAST simulations agree well with the outcomes of exact algorithms; however, the asymptotic run times of COAST are asymptotically proportional to smaller powers of the particle numbers than exact algorithms.

Algorithms↗
PubMed2002

Automated calculation of the Tei index from signal averaged left ventricular acoustic quantification wave forms.

The Tei index is a combined measurement of systolic and diastolic left ventricular (LV) performance and may be more useful for the diagnosis of global cardiac dysfunction than either systolic or diastolic measures alone. We sought to determine whether the Tei index could be accurately calculated from LV area waveforms generated with automated border detection. Twenty-four patients were studied in 3 groups: systolic dysfunction, diastolic dysfunction, and normal. The Tei index was calculated both from Doppler tracings and from analysis of LV area waveforms. Excellent agreement was found between Doppler-derived timing intervals and the Tei index with those obtained from averaged LV area waveforms. A significant difference was seen in the Tei index, computed with both Doppler and automated border detection techniques, between the normal group and those with LV systolic dysfunction and subjects with isolated diastolic dysfunction. This study validates the use of LV area waveforms for the automated calculation of the Tei index.

Acoustics↗
PubMed2004

Stochastic computing with biomolecular automata.

Stochastic computing has a broad range of applications, yet electronic computers realize its basic step, stochastic choice between alternative computation paths, in a cumbersome way. Biomolecular computers use a different computational paradigm and hence afford novel designs. We constructed a stochastic molecular automaton in which stochastic choice is realized by means of competition between alternative biochemical pathways, and choice probabilities are programmed by the relative molar concentrations of the software molecules coding for the alternatives. Programmable and autonomous stochastic molecular automata have been shown to perform direct analysis of disease-related molecular indicators in vitro and may have the potential to provide in situ medical diagnosis and cure.

Calibration↗
PubMed2005

A quasi-Monte Carlo Metropolis algorithm.

This work presents a version of the Metropolis-Hastings algorithm using quasi-Monte Carlo inputs. We prove that the method yields consistent estimates in some problems with finite state spaces and completely uniformly distributed inputs. In some numerical examples, the proposed method is much more accurate than ordinary Metropolis-Hastings sampling.

Algorithms↗
PubMed2003

DNA molecule provides a computing machine with both data and fuel.

The unique properties of DNA make it a fundamental building block in the fields of supramolecular chemistry, nanotechnology, nano-circuits, molecular switches, molecular devices, and molecular computing. In our recently introduced autonomous molecular automaton, DNA molecules serve as input, output, and software, and the hardware consists of DNA restriction and ligation enzymes using ATP as fuel. In addition to information, DNA stores energy, available on hybridization of complementary strands or hydrolysis of its phosphodiester backbone. Here we show that a single DNA molecule can provide both the input data and all of the necessary fuel for a molecular automaton. Each computational step of the automaton consists of a reversible software molecule input molecule hybridization followed by an irreversible software-directed cleavage of the input molecule, which drives the computation forward by increasing entropy and releasing heat. The cleavage uses a hitherto unknown capability of the restriction enzyme FokI, which serves as the hardware, to operate on a noncovalent software input hybrid. In the previous automaton, software input ligation consumed one software molecule and two ATP molecules per step. As ligation is not performed in this automaton, a fixed amount of software and hardware molecules can, in principle, process any input molecule of any length without external energy supply. Our experiments demonstrate 3 x 10(12) automata per microl performing 6.6 x 10(10) transitions per second per microl with transition fidelity of 99.9%, dissipating about 5 x 10(-9) W microl as heat at ambient temperature.

Adenosine Triphosphate↗
PubMed1997

Ensemble quantum computing by NMR spectroscopy.

A quantum computer (QC) can operate in parallel on all its possible inputs at once, but the amount of information that can be extracted from the result is limited by the phenomenon of wave function collapse. We present a new computational model, which differs from a QC only in that the result of a measurement is the expectation value of the observable, rather than a random eigenvalue thereof. Such an expectation value QC can solve nondeterministic polynomial-time complete problems in polynomial time. This observation is significant precisely because the computational model can be realized, to a certain extent, by NMR spectroscopy on macroscopic ensembles of quantum spins, namely molecules in a test tube. This is made possible by identifying a manifold of statistical spin states, called pseudo-pure states, the mathematical description of which is isomorphic to that of an isolated spin system. The result is a novel NMR computer that can be programmed much like a QC, but in other respects more closely resembles a DNA computer. Most notably, when applied to intractable combinatorial problems, an NMR computer can use an amount of sample, rather than time, which grows exponentially with the size of the problem. Although NMR computers will be limited by current technology to exhaustive searches over only 15 to 20 bits, searches over as much as 50 bits are in principle possible, and more advanced algorithms could greatly extend the range of applicability of such machines.

Chemical Phenomena↗
PubMed1999

The two-dimensional IR nonlinear spectroscopy of a cyclic penta-peptide in relation to its three-dimensional structure.

A form of two-dimensional (2D) vibrational spectroscopy, which uses two ultrafast IR laser pulses, is used to examine the structure of a cyclic penta-peptide in solution. Spectrally resolved cross peaks occur in the off-diagonal region of the 2D IR spectrum of the amide I region, analogous to those in 2D NMR spectroscopy. These cross peaks measure the coupling between the different amide groups in the structure. Their intensities and polarizations relate directly to the three-dimensional structure of the peptide. With the help of a model coupling Hamiltonian, supplemented by density functional calculations, the spectra of this penta-peptide can be regenerated from the known solution phase structure. This 2D-IR measurement, with an intrinsic time resolution of less than 1 ps, could be used in all time regimes of interest in biology.

Amino Acid Sequence↗
PubMed1988

Null hypothesis disrespect in neuropsychology: dangers of alpha and beta errors.

To understand why there are so many inconsistencies and contradictory findings among hemispheric-asymmetry studies, data were analyzed from a large study of 300 left-handers. These data included information on familial sinistrality (FS), handwriting posture (HPO), a measure of cognitive performance, and five measures of hemispheric specialization. Using computer simulation methodology, 40 independent samples of 36 to 65 subjects each were drawn randomly with replacement. The sample data were analyzed and the results compared to those of the parent "population." Often, the samples poorly reflected the parent "population," and some procedures substantially inflated error rates. These procedures are discussed and specific guidelines suggested. These results are also discussed in the broader context of the necessity for investigators in neuropsychology to differentiate between the statistical and clinical significance of research findings; and to develop a more positive attitude toward the design, execution, and publication of replication studies.

Adult↗
PubMed2002

Parallel computing in microwave heating analysis.

The use of parallel computing in the finite element analysis of microwave heating applicators is discussed. Numerical results for a multiple feed cavity at 896 MHz and a cavity with a mode stirrer at 2.45 GHz are presented, and it is shown that for the two structures parallelism is most effectively introduced at different levels in the analysis.

Algorithms↗
PubMed2002

Multigrid block preconditioning for a coupled system of partial differential equations modeling the electrical activity in the heart.

The electrical activity of the heart may be modeled with a system of partial differential equations (PDEs) known as the bidomain model. Computer simulations based on these equations may become a helpful tool to understand the relationship between changes in the electrical field and various heart diseases. Because of the rapid variations in the electrical field, sufficiently accurate simulations require a fine-scale discretization of the equations. For realistic geometries this leads to a large number of grid points and consequently large linear systems to be solved for each time step. In this paper, we present a fully coupled discretization of the bidomain model, leading to a block structured linear system. We take advantage of the block structure to construct an efficient preconditioner for the linear system, by combining multigrid with an operator splitting technique.

Action Potentials↗
PubMed2000

Implementing store-and-forward telemedicine: organizational issues.

This article documents a study of an organization's cultural readiness for successful implementation of a store-and-forward telemedicine system in a military health care environment. The study focused on the organization's cultural attributes that reflect its learning propensity and thereby its capability to adapt effectively and utilize the new technology. Results suggest that the organization did not possess the most favorable attributes for the utilization of a new technology, and the utilization of the new system was significantly lower than expected during the first 6 months of implementation.

Computing Methodologies↗
PubMed1997

Protein structure and energy landscape dependence on sequence using a continuous energy function.

We have recently described a new conformational search strategy for protein folding algorithms called the CGU (convex global underestimator) method. Here we use a simplified protein chain representation and a differentiable form of the Sun/Thomas/Dill energy function to test the CGU method. Standard search methods, such as Monte Carlo and molecular dynamics are slowed by kinetic traps. That is, the computer time depends more strongly on the shape of the energy landscape (dictated by the amino acid sequence) than on the number of degrees of freedom (dictated by the chain length). The CGU method is not subject to this limitation, since it explores the underside of the energy landscape, not the top. We find that the CGU computer time is largely independent of the monomer sequence for different chain folds and scales as O(n4) with chain length. By using different starting points, we show that the method appears to find global minima. Since we can currently find stable states of 36-residue chains in 2.4 hours, the method may be practical for small proteins.

Algorithms↗