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PubMed2000

Identification of reliable spike templates in multi-unit extracellular recordings using fuzzy clustering.

A method for extracting single-unit spike trains from extracellular recordings containing the activity of several simultaneously active cells is presented. The technique is particularly effective when spikes overlap temporally. It is capable of identifying the exact number of neurons contributing to a recording and of creating reliable spike templates. The procedure is based on fuzzy clustering and its performance is controlled by minimizing a cluster-validity index which optimizes the compactness and separation of the identified clusters. Application examples with synthetic spike trains generated from real spikes and segments of background noise show the advantage of the fuzzy method over conventional template-creation approaches in a wide range of signal-to-noise ratios.

Action Potentials↗

PubMed2004

Evolutionary design of a fuzzy classifier from data.

Genetic algorithms show powerful capabilities for automatically designing fuzzy systems from data, but many proposed methods must be subjected to some minimal structure assumptions, such as rule base size. In this paper, we also address the design of fuzzy systems from data. A new evolutionary approach is proposed for deriving a compact fuzzy classification system directly from data without any a priori knowledge or assumptions on the distribution of the data. At the beginning of the algorithm, the fuzzy classifier is empty with no rules in the rule base and no membership functions assigned to fuzzy variables. Then, rules and membership functions are automatically created and optimized in an evolutionary process. To accomplish this, parameters of the variable input spread inference training (VISIT) algorithm are used to code fuzzy systems on the training data set. Therefore, we can derive each individual fuzzy system via the VISIT algorithm, and then search the best one via genetic operations. To evaluate the fuzzy classifier, a fuzzy expert system acts as the fitness function. This fuzzy expert system can effectively evaluate the accuracy and compactness at the same time. In the application section, we consider four benchmark classification problems: the iris data, wine data, Wisconsin breast cancer data, and Pima Indian diabetes data. Comparisons of our method with others in the literature show the effectiveness of the proposed method.

Algorithms↗

PubMed1999

The compact and expanded denatured conformations of apomyoglobin in the methanol-water solvent.

We have performed a detailed study of methanol-induced conformational transitions of horse heart apomyoglobin (apoMb) to investigate the existence of the compact and expanded denatured states. A combination of far- and near-ultraviolet circular dichroism, NMR spectroscopy, and small-angle X-ray scattering (SAXS) was used, allowing a phase diagram to be constructed as a function of pH and the methanol concentration. The phase diagram contains four conformational states, the native (N), acid-denatured (U(A)), compact denatured (I(M)), and expanded helical denatured (H) states, and indicates that the compact denatured state (I(M)) is stable under relatively mild denaturing conditions, whereas the expanded denatured states (U(A) and H) are realized under extreme conditions of pH (strong electric repulsion) or alcohol concentration (weak hydrophobic interaction). The results of this study, together with many previous studies in the literature, indicate the general existence of the compact denatured states not only in the salt-pH plane but also in the alcohol-pH plane. Furthermore, to determine the general feature of the H conformation we used several proteins including ubiquitin, ribonuclease A, alpha-lactalbumin, beta-lactoglobulin, and Streptomyces subtilisin inhibitor (SSI) in addition to apoMb. SAXS studies of these proteins in 60% methanol showed that the H states of these all proteins have expanded and nonglobular conformations. The qualitative agreement of the experimental data with computer-simulated Kratky profiles also supports this structural feature of the H state.

Apoproteins↗

PubMed2005

Structure and stability of small TiO2 nanoparticles.

The effect of the nanostructure on the photochemistry of TiO2 is an active field of research owing to its applications in photocatalysis and photovoltaics. Despite this interest, little is known of the structure of small particles of this oxide with sizes at the nanometer length scale. Here we present a computational study that locates the global minima in the potential energy surface of Ti(n)O2n clusters with n = 1-15. The search procedure does not refer to any of the known TiO2 polymorphs, and is based on a novel combination of simulated annealing and Monte Carlo basin hopping simulations, together with genetic algorithm techniques, with the energy calculated by means of an interatomic potential. The application of several different methods increases our confidence of having located the global minimum. The stable structures are then refined by means of density functional theory calculations. The results from the two techniques are similar, although the methods based on interatomic potentials are unable to describe some subtle effects. The agreement is especially good for the larger particles, with n = 9-15. For these sizes the structures are compact, with a preference for a central octahedron and a surrounding layer of 4- and 5-fold coordinated Ti atoms, although there seems to be some energy penalty for particles containing the 5-fold coordinated metal atoms with square base pyramid geometry and dangling Ti=O bonds. The novel structures reported provide the basis for further computational studies of the effect of nanostructure on adsorption, photochemistry, and nucleation of this material.

Journal Article↗

PubMed2006

On the development and testing of a guided ultrasonic wave array for structural integrity monitoring.

The prototype of a guided ultrasonic wave array for the structural integrity monitoring of large, plate-like structures has been designed, built, and tested. The development of suitably small transducers for the excitation and measurement of the first antisymmetric Lamb wave mode Ao is described. The array design consists of a ring of 32 transducers, permanently bonded to the structure with a protective membrane, in a compact housing with the necessary multiplexing electronics. Using a phased addition algorithm with dispersion compensation and deconvolution in the wavenumber domain, a good dynamic range can be achieved with a limited number of transducers. Limitations in the transducer design and manufacture restricted the overall dynamic range achieved to 27 dB. Laboratory measurements for a steel plate containing various defects have been performed. The results for standard defects are compared to theoretical predictions and the sensitivity of the array device for defect detection has been established. Simulated corrosion pitting and a defect cut with an angle grinder simulating general corrosion were detected.

Journal Article↗

PubMed2002

Excited state conformational dynamics of semiflexibly bridged electron donor-acceptor systems: a semiempirical CI-study including solvent effects.

Semiempirical (AM1) molecular orbital theory with configuration interaction has been used to investigate the harpooning mechanism proposed from experimental studies on semiflexibly bridged electron donor-acceptor systems. Our calculations on the charge-transfer state of N-phenyl-4-(4-cyano-naphth-1-ylmethyl)-piperidine, 1, confirm the proposed harpooning mechanism including an intermediate loosely folded charge-transfer state and reproduce the thermodynamics obtained from our spectroscopic studies closely. The structural details of the extended (ECT), intermediate (ICT) and compact (CCT) charge-transfer states are discussed, as are the transition states connecting them. Solvent effects have been modeled using self-consistent reaction field (SCRF) calculations within the polarized continuum model. The effect of solvent polarity on the stabilities of the three charge-transfer states is discussed.

Computer Simulation↗

PubMed1987

Structure of the reaction center from Rhodobacter sphaeroides R-26: membrane-protein interactions.

The energetics of membrane-protein interactions are analyzed with the three-dimensional model of the photosynthetic reaction center (RC) from Rhodobacter sphaeroides. The position of the RC in the membrane and the thickness of the membrane were obtained by minimizing the hydrophobic energy with the energy function of Eisenberg and McLachlan. The 2-fold symmetry axis that relates the L and M subunits is, within the accuracy of 5 degrees, parallel to the normal of the membrane. The thickness of the membrane is estimated to be 40-45 A. Residues that are exposed to the membrane are relatively poorly conserved in the sequences of homologous RC proteins. The surface area of the RC is comparable to the surface areas of water-soluble proteins of similar molecular weight. The volumes of interior atoms in the RC are also similar to those of water-soluble proteins, indicating the same compact packing for both types of proteins. The electrostatic potential of the cofactors was calculated. The results show an asymmetry in the potential between the two possible pathways of electron transfer, with the A branch being preferred electrostatically.

Bacteria↗

PubMed1996

Fluorescence and Monte Carlo conformational studies of the (1-15) galanin amide fragment.

Galanin (GAL) is a 29 amino acid C-terminally aminated linear neuropeptide showing diverse biological activities. The N-terminal (1-15)GAL-NH2 fragment was shown to have a very high affinity to the galanin receptor. In this work we describe the results of a combined fluorescence and Monte Carlo studies, the latter carried out using the ECEPP/3 force field with and without including hydration, on the (1-15)GAL-NH2 fragment. Using the time-domain technique we measured fluorescence decay times of the tyrosine residue in position 9. Based on the Forster energy transfer theory we calculated the distance and distance distribution between the Trp2 (acceptor) and Tyr9 (donor) aromatic side chains. The distance obtained was about 10.5 angstrom and half-width, hw, of the distance distribution was 5.6 angstrom. This results were found to be in good agreement with the chromophore distances calculated for the low-energy solution confirmations obtained in Monte Carlo simulations. All the low-energy conformations obtained in the absence of water were almost all-helical with the exception of a few C-terminal residues. In contrast, none of the low-energy solution conformations contained any significant amount of secondary structure. These findings are in agreement with the results of earlier CD and NMR conformational studies of galanin in water and non-aqueous solvents. On the other hand, the conformations obtained in the presence of water turned out to be largely compact in the N-terminal hydrophobic part. This explains the relatively short distance between chromophores and narrow distance distribution obtained in fluorescence measurements.

Amides↗

PubMed2000

Development of computerised procedures for the characterisation of the tableting properties with eccentric machines: extended Heckel analysis.

Heckel plots are a suitable and valuable method for analysis of powder compaction with very small amounts of powder. The determination is based upon a non-linear transformation of compression data and thus the signal errors that might be introduced into the analysis might be enlarged and become critical. The method of determination of true density affects the results dramatically as does the accuracy of the powder height determination. The porosity should be corrected for compression of the solid fraction. The accuracy of the powder height detection is the most demanding parameter. The statements are proven by simulations based on real data and analytic calculation. According to these highly corrected Heckel plots, the shape of the plots during the compression phase gives the information about fragmentation and plasticity and additionally about the time dependency of the compression behaviour within one compression on an eccentric press.

Algorithms↗

PubMed2003

Development of an implantable high-energy and compact battery system for artificial heart.

The purpose of this study was to demonstrate the feasibility of the use of an implantable, high-energy, and compact battery system for an undulation pump total artificial heart (UPTAH). The implantable battery system tested consists of six lithium-ion batteries in series, a charge unit, and a charge/discharge control unit. A lithium-ion battery is currently the best energy-storage device because it has more energy density, a better life cycle, and a smaller temperature rise than those of other secondary batteries. The performance of the implantable battery system was evaluated in an in vitro experiment using an electric load that simulated the UPTAH. Also, sufficiently reliable operation of a system for supplying energy to a UPTAH consisting of a transcutaneous energy transmission system (TETS) and an implantable battery system was confirmed in three experiments using goats. The results of the in vitro and in vivo experiments showed that the implantable battery system supplied sufficient current to the UPTAH for maintenance of physiological conditions in the goat with maximum rise in temperature to less than 43 degrees C.

Animals↗

PubMed2000

Molecular dynamics study of the behavior of a single long chain polyethylene on a solid surface

A molecular dynamics simulation has been used in exploring the behavior of a single long chain polyethylene (PE) on a solid surface. We have established how varying the intermolecular (polymer-surface) van der Waals (vdW) interaction force effects the structural and dynamic properties of the polymer chain. For a high intermolecular vdW force, the starting PE chain absorbs on to solid surface, and develops into a stretched monolayerlike structure. However, for a low intermolecular vdW force, segments in the PE chain avoid the surface and fold into a compact lamellalike structure. However, for a moderate intermolecular vdW force, the PE chain forms into a polylayerlike structure where stems align parallel to the surface. Unlike the short chain molecules, the overall conformations developed by the long chain PE possess a degree of intramolecular (intrachain) order. In addition to these, we have systematically analyzed the changes in components of the square of the radius of gyration parallel and orthogonal to the surface, as well as the intermolecular and intramolecular vdW energy of the PE chain when it transforms to monolayerlike, lamellalike, and polylayerlike configurations. Results show that the structural change is in phase with the variation of parallel and orthogonal components of the square of the radius of gyration, and has a corresponding relation with the intermolecular and intramolecular vdW energy. The intermolecular vdW force drags the PE chain lying on the surface and stretching into a loose monolayer. The intramolecular vdW force, rather than any of the other intramolecular interactions, drives the PE chain folding into a compact, ordered lamella.

Journal Article↗

PubMed2003

Photonic crystal horn and array antennas.

We introduce a defect-based horn antenna in a two-dimensional photonic crystal. Our numerical simulations demonstrate the efficient, highly directional nature of the antenna. It has a large operating bandwidth, low loss, and an operating frequency that is scalable to various regions of the electromagnetic spectrum. We also show that the photonic crystal horn antenna can be successfully used in an array configuration that uses a feed network made from photonic crystal waveguide circuits. The feed network and antennas have been integrated into a single photonic crystal device. This photonic crystal array antenna is shown to have high directivity and compact size while retaining the advantages of the photonic crystal horn antenna.

Journal Article↗

PubMed1997

Protein structure prediction force fields: parametrization with quasi-newtonian dynamics.

We present an unusual method for parametrizing low-resolution force fields of the type used for protein structure prediction. Force field parameters were determined by assigning each a fictitious mass and using a quasi-molecular dynamics algorithm in parameter space. The quasi-energy term favored folded native structures and specifically penalized folded nonnative structures. The force field was generated after optimizing less than 70 adjustable parameters, but shows a strong ability to discriminate between native structures and compact misfolded alternatives. The functional form of the force field was chosen as in molecular mechanics and is not table-driven. It is continuous with continuous derivatives and is thus suitable for use with algorithms such as energy minimization or newtonian dynamics.

Algorithms↗

PubMedDate not supplied

Electrophoretic charge density and persistence length of DNA as measured by fluorescence microscopy.

Individual ethidium-stained DNA molecules, embedded in an agarose gel made with electrophoresis buffer (0.05 molar salt), are observed using a fluorescence microscope. In the first experiment, open circular 66 kilobase pair (kbp) plasmids, immobilized by agarose fibers threaded through their centers, display entropic "rubber" elasticity. The charged molecules extend in an electric field of several volts per centimeter and contract to a compact random coil when the field is removed. The extension of the plasmids as a function of field strength is consistent with the freely jointed chain model when the effective electrophoretic charge density is set at 15 e-per persistence length. In a second experiment, stained linear 48.5 kbp DNA molecules are observed as random coils immobilized in agarose. A measure of their size, here named the "maximal-X-extent," is taken for 100 molecules and found to average 1.47 mu. A Monte Carlo computer simulation of random coils (freely jointed chain model) gives the same maximal-X-extent value when the persistence length is set at 0.08 mu.

Chemical Phenomena↗

PubMed2004

A molecular dynamics study of monolayers of nonionic poly(ethylene oxide) based surfactants.

Molecular dynamics simulations of monolayers of nonionic, poly(ethylene oxide) based surfactants are reported. Specifically, alcohol ethoxylates and alkylphenol ethoxylates are compared in terms of the varying architecture of the molecules for the development of a structure-behavior relationship. Interfacial density profiles are used to assess the structure of the monolayers, the penetration of water and oil into the monolayers, and the solvation of the hydrophiles and hydrophobes. Chain conformational descriptors are used to examine the molecular structure of the surfactants. The simulations revealed that monolayers of alcohol ethoxylates are considerably more diffuse than their alkylphenol counterparts, with the packing being governed by the size of the hydrophile. With the exception of the branched alcohol ethoxylate, the intermixing of the bulk phases within monolayers of alcohol ethoxylates increases with increasing hydrophile length. By comparison, the packing of alkylphenol ethoxylates within the monolayer is governed by the aromatic nucleus in the molecule. No specific interaction is observed between the aromatic rings of neighboring molecules. Monolayers of alkylphenol ethoxylates are more compact than their alcohol counterparts, resulting in more effective separation of the bulk water and oil phases.

Journal Article↗

PubMed2000

Modelling the static and dynamic responses of total heat production of broiler chickens to step changes in air temperature and light intensity.

1. The objective of this work was to explore the possibilities of modelling the static and dynamic responses of total heat production of broiler chickens to step changes in temperature and light intensity (light-dark alterations) using compact dynamic model structures. 2. Seventy-seven experiments were performed in an open-circuit respiration chamber to measure the dynamic response of heat production to step variations in temperature and light (on/off). The animal responses were modelled using transfer function model structures. 3. It was demonstrated that the complex process of the dynamic response of heat production of broiler chickens to step changes in air temperature and light-dark alterations can be modelled assuming 1st order dynamics. The coefficient of determination between measured and simulated heat production was on average 0.83 for responses to air temperature and 0.93 for responses to light-dark alterations.

Animals↗

PubMed2000

A multiply substituted G-H loop from foot-and-mouth disease virus in complex with a neutralizing antibody: a role for water molecules.

The crystal structure of a 15 amino acid synthetic peptide, corresponding to the sequence of the major antigenic site A (G-H loop of VP1) from a multiple variant of foot-and-mouth disease virus (FMDV), has been determined at 2.3 A resolution. The variant peptide includes four amino acid substitutions in the loop relative to the previously studied peptide representing FMDV C-S8c1 and corresponds to the loop of a natural FMDV isolate of subtype C(1). The peptide was complexed with the Fab fragment of the neutralizing monoclonal antibody 4C4. The peptide adopts a compact fold with a nearly cyclic conformation and a disposition of the receptor-recognition motif Arg-Gly-Asp that is closely related to the previously determined structure for the viral loop, as part of the virion, and for unsubstituted synthetic peptide antigen bound to neutralizing antibodies. New structural findings include the observation that well-defined solvent molecules appear to play a major role in stabilizing the conformation of the peptide and its interactions with the antibody. Structural results are supported by molecular-dynamic simulations. The multiply substituted peptide developed compensatory mechanisms to bind the antibody with a conformation very similar to that of its unsubstituted counterpart. One water molecule, which for steric reasons could not occupy the same position in the unsubstituted antigen, establishes hydrogen bonds with three peptide amino acids. The constancy of the structure of an antigenic domain despite multiple amino acid substitutions has implications for vaccine design.

Amino Acid Substitution↗

PubMed2005

Persistence length changes dramatically as RNA folds.

We determine the persistence length l(p) for a bacterial group I ribozyme as a function of concentration of monovalent and divalent cations by fitting the distance distribution functions P(r) obtained from small angle x-ray scattering intensity data to the asymptotic form of the calculated P(WLC)(r) for a wormlike chain. The l(p) values change dramatically over a narrow range of Mg(2+) concentration from approximately 21 Angstroms in the unfolded state (U) to approximately 10 Angstroms in the compact (I(C)) and native states. Variations in l(p) with increasing Na(+) concentration are more gradual. In accord with the predictions of polyelectrolyte theory we find l(p) alpha 1/kappa(2) where kappa is the inverse Debye-screening length.

Computer Simulation↗