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PubMed2005

Stochastic transition states: reaction geometry amidst noise.

Classical transition state theory (TST) is the cornerstone of reaction-rate theory. It postulates a partition of phase space into reactant and product regions, which are separated by a dividing surface that reactive trajectories must cross. In order not to overestimate the reaction rate, the dynamics must be free of recrossings of the dividing surface. This no-recrossing rule is difficult (and sometimes impossible) to enforce, however, when a chemical reaction takes place in a fluctuating environment such as a liquid. High-accuracy approximations to the rate are well known when the solvent forces are treated using stochastic representations, though again, exact no-recrossing surfaces have not been available. To generalize the exact limit of TST to reactive systems driven by noise, we introduce a time-dependent dividing surface that is stochastically moving in phase space, such that it is crossed once and only once by each transition path.

Journal Article↗

PubMed1991

On the multiple-minima problem in the conformational analysis of polypeptides. V. Application of the self-consistent electrostatic field and the electrostatically driven Monte Carlo methods to bovine pancreatic trypsin inhibitor.

In connection with the accompanying paper to test various models for the hydration of polypeptides, we have explored a limited portion of the conformational energy hyperspace of the small protein bovine pancreatic trypsin inhibitor (BPTI) with the aid of two search methods developed in this laboratory. A series of low-energy conformations was obtained as a result of this study. These conformations constitute a set of local minima in the conformational energy space of the molecule as described by the ECEPP/2 (Empirical Conformational Energy Program for Peptides) potential energy function, without the inclusion of hydration. Five different initial conformations were used in this exploration: the first corresponds to an energy-refined structure based on the crystallographic coordinates (4PTI) provided by Deisenhofer and Steigemann and reported previously by Meirovitch and Scheraga. The remaining four initial conformations were obtained by using a Variable-Target-Function procedure, applied to the experimental Cartesian coordinates (5PTI) reported by Wlodawer et al. The self-consistent electrostatic field (SCEF) and the electrostatically driven Monte Carlo (EDMC) methods were used to search the conformational space. The SCEF and EDMC methodologies assume that a polypeptide or protein molecule is driven toward the native structure mainly by the action of the electrostatic interactions. Application of these methodologies led to a set of conformations (up to 50 kcal/mol lower than the starting ones) with ECEPP/2 energies lower than any of those that we had previously found. Application of both methods to the initial conformation generated from 4PTI led to a series of low-energy conformations exhibiting similar rms deviations with respect to the experimental data (4PTI) as did the starting conformation. However, statistical analysis of the runs that had started from the conformations generated by using the variable-target-function procedure (and applying the EDMC method) indicated that the rms deviations of the atomic positions of the new low-energy conformations tended to increase as the energy improved, when compared with the X-ray data from which the starting conformations had been generated. The structures with the lowest energies also had radii of gyration smaller than the experimentally observed one. These results indicated a need to include hydration in the potential function, and provided the conformations used in the accompanying paper to test various hydration models.

Animals↗

PubMed2001

First- and second-order phase transitions in a driven lattice gas with nearest-neighbor exclusion.

A lattice gas with infinite repulsion between particles separated by < or = 1 lattice spacing, and nearest-neighbor hopping dynamics, is subject to a drive favoring movement along one axis of the square lattice. The equilibrium (zero drive) transition to a phase with sublattice ordering, known to be continuous, shifts to lower density, and becomes discontinuous for large bias. In the ordered nonequilibrium steady state, both the particle and order-parameter densities are nonuniform, with a large fraction of the particles occupying a jammed strip oriented along the drive. The drive thus induces separation into high- and low-density regions in a system with purely repulsive interactions. Increasing the drive can provoke a transition to the ordered phase, and thereby, a sharp reduction in current.

Journal Article↗

PubMed1998

Molecules, motion, and man.

The application of cell and molecular biology techniques to vestibular research is resulting in rapid changes in our understanding of the fundamental mechanisms of vestibular function. The clinical problems encountered in space travel together with the acute and chronic vestibular dysfunction affecting many of the patients otolaryngologists care for have driven this research at a rapid pace. A review of these methods and highlights of the major advances are discussed.

Animals↗

PubMed1993

The role of infection in juvenile chronic arthritis.

Juvenile chronic arthritis covers a heterogeneous group of arthritides for which there appears to be a genetically determined susceptibility. The exact events which trigger or perpetuate an arthritic disease have yet to be defined. There is circumstantial clinical evidence that JCA can be initiated by environmental factors such as infection, and indirect laboratory evidence that immune responses to infectious agents are associated with ongoing JCA; such immune responses seem particularly vigorous within the joint space. Although the weight of evidence favours the hypothesis that the intra-articular inflammatory process is antigen-driven, none of the critical antigens have been identified, and it is still unclear whether they are derived from infectious agents or are true auto-antigens. We can however expect progress to be made, since techniques are now available for defining the antigenic specificity and TCR usage of synovial T cell populations, while PCR allows exquisitely sensitive detection of infectious agents deposited in the synovial space. Application of these techniques should lead to an enhanced understanding of whether (or in what circumstances) infectious agents are involved in the pathogenesis of arthritis in children.

Antigens, Bacterial↗

PubMed2006

2 Gbit/s 0.5 microm complementary metal-oxide semiconductor optical transceiver with event-driven dynamic power-on capability.

A 2 Gb/s0.5 microm complementary metal-oxide semiconductor optical transceiver designed for board- or backplane level power-efficient interconnections is presented. The transceiver supports optical wake-on-link (OWL), an event-driven dynamic power-on technique. Depending on external events, the transceiver resides in either the active mode or the sleep mode and switches accordingly. The active-to-sleep transition shuts off the normal, gigabit link and turns on dedicated circuits to establish a low-power (approximately 1.8 mW), low data rate (less than 100 Mbits/s) link. In contrast the normal, gigabit link consumes over 100 mW. Similarly the sleep-to-active transition shuts off the low-power link and turns on the normal, gigabit link. The low-power link, sharing the same optical channel with the normal, gigabit link, is used to achieve transmitter/receiver pair power-on synchronization and greatly reduces the power consumption of the transceiver. A free-space optical platform was built to evaluate the transceiver performance. The experiment successfully demonstrated the event-driven dynamic power-on operation. To our knowledge, this is the first time a dynamic power-on scheme has been implemented for optical interconnects. The areas of the circuits that implement the low-power link are approximately one-tenth of the areas of the gigabit link circuits.

Journal Article↗

PubMed1992

Relation between ventilation and carbon dioxide production in patients with chronic heart failure.

OBJECTIVES: The aim of this study was to analyze the relation between ventilation and carbon dioxide production and the control of ventilation in patients with chronic heart failure. BACKGROUND: Patients with chronic heart failure exhibit an increased ventilatory response to exercise. Ventilation is closely linked to carbon dioxide production, producing a high correlation between the two variables. This relation is nonlinear at high levels of exercise. METHODS: The ventilation/carbon dioxide production ratio during exercise was examined in 29 patients with chronic heart failure and 9 normal volunteers. RESULTS: In the patients with heart failure, there were three patterns: in the least severely affected patients, the pattern was similar to that of the normal subjects, with an initial decrease in the ventilation/carbon dioxide production ratio to a plateau maintained during exercise; in more severely affected patients, there was an increase in the ratio at the end of exercise, and in the most severely affected patients, the ratio increased from the outset of exercise. The ventilation/carbon dioxide relation is not adequately described by a straight line relation. CONCLUSIONS: The ventilation/carbon dioxide ratio is not fixed, and the changes that occur in this ratio reflect either a noncarbon dioxide-driven ventilatory stimulus or an increase in ventilation-perfusion mismatch due to increased dead space ventilation. The different patterns of this ratio may provide clues to the pathophysiologic mechanisms of the excessive ventilation and breathlessness seen during exercise in chronic heart failure.

Adult↗

PubMed2005

The FLUKA code: new developments and application to 1 GeV/n iron beams.

The modeling of ion transport and interactions in matter is a subject of growing interest, driven by the continuous increase of possible application fields. These include hadron therapy, dosimetry, and space missions, but there are also several issues involving fundamental research, accelerator physics, and cosmic ray physics, where a reliable description of heavy ion induced cascades is important. In the present work, the capabilities of the FLUKA code for ion beams will be briefly recalled and some recent developments presented. Applications of the code to the simulation of therapeutic carbon, nitrogen and oxygen ion beams, and of iron beams, which are of direct interest for space mission related experiments, will be also presented together with interesting consideration relative to the evaluation of dosimetric quantities. Both applications involve ion beams in the AGeV range.

Carbon↗

PubMed2005

Diffusion-weighted three-dimensional MP-RAGE MR imaging.

The advantages of three-dimensional (3D) acquisition are that you obtain thinner and more slices with better profiles, and better signal-to-noise ratio for an equivalent slice thickness. Three-dimensional acquisition is preferable for obtaining contiguous thin-slice MR images. However, the acquisition time extends compared with the two-dimensional acquisition because the second phase-encode axis is applied by the 3D acquisition. Therefore, 3D acquisition should be a high-speed imaging method. In this paper, a new diffusion-sensitive 3D magnetization-prepared rapid gradient-echo (3D MP-RAGE) sequence was studied. In this sequence, a preparation phase with a 90 degrees RF-motion proving gradient (MPG): MPG-180 degrees RF-MPG-90 degrees RF pulse train (diffusion-weighted driven-equilibrium Fourier transform) was used to sensitize the magnetization to diffusion. Centric k-space acquisition order is necessary to minimize saturation effects from tissues with short relaxation times. From phantom experimental results, the effect of the diffusion weighting was changed by the centric vs. sequential k-space acquisition order. The effect of centric k-space acquisition order was larger than the effect of sequential k-space acquisition order. The contrast of centric k-space acquisition order became equal to the contrast of conventional diffusion-weighted spin echo. From rat experimental results, small isotropic diffusion-weighted image data (voxel size: 0.625 x 0.625 x 0.625 mm3) were obtained. This sequence was useful in vivo.

Acetone↗

PubMed1998

Interpreting the equatorial diffraction pattern of collagenous tissues in the light of molecular motion.

The equatorial diffraction pattern associated with collagenous tissues, particularly type I collagen, is diffuse and clearly unlike that from crystals. Hukins and Woodhead-Galloway proposed a statistical model that they termed a "liquid crystal" for collagen fibers in tendons. Fratzl et al. applied this model to both unmineralized and mineralized turkey leg tendon, a model that ignores the organization imposed by the well-known cross-linking. The justification for adopting this model is that the curve fits the data. It is shown that the data can be equally well matched by fitting a least-squares curve consisting of a second-order polynomial plus a Gaussian. The peak of the Gaussian is taken as the equatorial spacing of the collagen. A physical explanation for this model is given, as is a reason for the changes in the spacing with changes in water content of the tissue. The diffusion is attributed to thermally driven agitation of the molecules, in accordance with the Debye-Waller theory including the Gaussian distribution. The remainder of the diffusion is attributed to other scattering sources like the mineral crystallites.

Animals↗

PubMed2003

Pedestrian injuries in Mexico: a multi-method approach.

UNLABELLED: Studies of road traffic injuries should identify social determinants amenable to intervention, and should attend to the problems of individual drivers and pedestrians. This is especially true in developing nations like Mexico, where traffic fatality rates are high and interventions ineffective. OBJECTIVE: Combine qualitative and quantitative methods to analyze pedestrian injuries from motor vehicles in Mexico City, and identify their social, contextual and environmental determinants. Methods included (1). a cross-sectional analysis of mortality, producing crude and specific mortality rates and standardized mortality ratios (95% CI) by region; (2). Spatial analysis using a geographic information system to generate maps at different aggregation levels; (3). Observation with cameras to identify traffic patterns, spaces, behaviors, and patterned violations of regulations; and 4). Semi-structured in-depth interviews of pedestrians and drivers involved in an accident. RESULTS: The overall crude mortality rate was 7.14/100000, (CI 6.85-7.42), with differences by sex and region. The highest concentration of deaths was observed in 10 neighborhoods, at specific types of street environments. The high-risk environments have wide avenues with abundant vehicular traffic, where spaces supposedly reserved for pedestrians are invaded by cars and vendors. Many pedestrians have never driven a motor vehicle, few know the traffic signs, and almost all events were "hit and run" cases. CONCLUSIONS: The combination of quantitative and qualitative methods allows us to see the specific importance of some determinants of pedestrian injuries. Spatial, epidemiological, and social perspectives help point out the local accident characteristics which must be considered before defining preventive interventions.

Accidents, Traffic↗

PubMed2004

Shear-induced morphology transition and microphase separation in a lamellar phase doped with clay particles.

We report on the influence of shear on a nonionic lamellar phase of tetraethyleneglycol monododecyl ether (C12E4) in D2O containing clay particles (Laponite RD). The system was studied by means of small-angle light scattering (SALS) and small-angle neutron scattering (SANS) under shear. The SANS experiments were conducted using a H2O/D2O mixture of the respective scattering length density to selectively match the clay scattering. The rheological properties show the familiar shear thickening regime associated with the formation of multilamellar vesicles (MLVs) and a shear thinning regime at higher stresses. The variation of viscosity is less pronounced as commonly observed. In the shear thinning regime, depolarized SALS reveals an unexpectedly strong variation of the MLV size. SANS experiments using the samples with lamellar contrast reveal a change in interlamellar spacing of up to 30% at stresses that lead to MLV formation. This change is much more pronounced than the change observed, when shear suppresses thermal bilayer undulations. Microphase separation occurs, and as a consequence, the lamellar spacing decreases drastically. The coincidence of the change in lamellar spacing and the onset of MLV formation is a strong indication for a morphology-driven microphase separation.

Journal Article↗

PubMed2002

Salmeterol for the prevention of high-altitude pulmonary edema.

BACKGROUND: Pulmonary edema results from a persistent imbalance between forces that drive water into the air space and the physiologic mechanisms that remove it. Among the latter, the absorption of liquid driven by active alveolar transepithelial sodium transport has an important role; a defect of this mechanism may predispose patients to pulmonary edema. Beta-adrenergic agonists up-regulate the clearance of alveolar fluid and attenuate pulmonary edema in animal models. METHODS: In a double-blind, randomized, placebo-controlled study, we assessed the effects of prophylactic inhalation of the beta-adrenergic agonist salmeterol on the incidence of pulmonary edema during exposure to high altitudes (4559 m, reached in less than 22 hours) in 37 subjects who were susceptible to high-altitude pulmonary edema. We also measured the nasal transepithelial potential difference, a marker of the transepithelial sodium and water transport in the distal airways, in 33 mountaineers who were prone to high-altitude pulmonary edema and 33 mountaineers who were resistant to this condition. RESULTS: Prophylactic inhalation of salmeterol decreased the incidence of high-altitude pulmonary edema in susceptible subjects by more than 50 percent, from 74 percent with placebo to 33 percent (P=0.02). The nasal potential-difference value under low-altitude conditions was more than 30 percent lower in the subjects who were susceptible to high-altitude pulmonary edema than in those who were not susceptible (P<0.001). CONCLUSIONS: Prophylactic inhalation of a beta-adrenergic agonist reduces the risk of high-altitude pulmonary edema. Sodium-dependent absorption of liquid from the airways may be defective in patients who are susceptible to high-altitude pulmonary edema. These findings support the concept that sodium-driven clearance of alveolar fluid may have a pathogenic role in pulmonary edema in humans and therefore represent an appropriate target for therapy.

Administration, Inhalation↗

PubMed2002

Statistical theory for the Kardar-Parisi-Zhang equation in (1+1) dimensions.

The Kardar-Parisi-Zhang (KPZ) equation in (1+1) dimensions dynamically develops sharply connected valley structures within which the height derivative is not continuous. We develop a statistical theory for the KPZ equation in (1+1) dimensions driven with a random forcing that is white in time and Gaussian-correlated in space. A master equation is derived for the joint probability density function of height difference and height gradient P(h-h*, partial differential(x)h,t) when the forcing correlation length is much smaller than the system size and much larger than the typical sharp valley width. In the time scales before the creation of the sharp valleys, we find the exact generating function of h-h* and partial differential(x)h. The time scale of the sharp valley formation is expressed in terms of the force characteristics. In the stationary state, when the sharp valleys are fully developed, finite-size corrections to the scaling laws of the structure functions left angle bracket(h-h*)(n)(partial differential(x)h)(m)right angle bracket are also obtained.

Journal Article↗

PubMed2003

Brownian dynamics simulations of aging colloidal gels.

The aging of colloidal gels is investigated using very long duration Brownian dynamics simulations. The Asakura-Oosawa description of the depletion interaction is used to model a simple colloid polymer mixture. Several regimes are identified during gel formation. The intermediate scattering function displays a double decay characteristic of systems where some kinetic processes are frozen. The beta relaxation at short times is explained in terms of the Krall-Weitz model for the decorrelation due to the elastic modes present. The alpha relaxation at long times is well described by a stretched exponential, showing a wide spectrum of relaxation times for which the q dependence is tau(alpha)=q(-2.2), lower than for diffusion. For the shortest waiting times, a combination of two stretched exponentials is used, suggesting a bimodal distribution. The extracted relaxation times vary with waiting time as tau(alpha)=tau(0.66)(w), more slowly than in the simple aging case. The real space displacements are found to be strongly non-Gaussian, correlated in space and time. We were unable to find clear evidence that the gel aging was driven by internal stresses. Rather, we hypothesize that in this case of weakly interacting gels, the aging behavior arises due to the thermal diffusion of strands, constrained by the percolating network, which ruptures discontinuously. Although the mechanisms differ, the similarity of some of the results to aging of glasses is striking.

Journal Article↗

PubMed2003

Pattern formation at the bicritical point of the Faraday instability.

We present measurements on parametrically driven surface waves (Faraday waves) performed in the vicinity of a bicritical point in parameter space, where modes with harmonic and subharmonic time dependence interact. The primary patterns are squares in the subharmonic and hexagons in the harmonic regime. If the primary instability is harmonic we observe a hysteretic secondary transition from hexagons to squares without a perceptible variation of the fundamental wavelength. The transition is understood in terms of a set of coupled Landau equations and related to other canonical examples of phase transitions in nonlinear dissipative systems. Moreover, the subharmonic-harmonic mode competition gives rise to a variety of new superlattice states. These structures are interpreted as mediator modes involved in the transition between patterns of fourfold and sixfold rotational symmetry.

Journal Article↗

PubMed2004

Nonequilibrium critical dynamics of the relaxational models C and D.

We investigate the critical dynamics of the n-component relaxational models C and D, which incorporate the coupling of a nonconserved and conserved order parameter S, respectively, to the conserved energy density rho, under nonequilibrium conditions by means of the dynamical renormalization group. Detailed balance violations can be implemented isotropically by allowing for different effective temperatures for the heat baths coupling to the slow modes. In the case of model D with conserved order parameter, the energy density fluctuations can be integrated out, leaving no trace of the nonequilibrium perturbations in the asymptotic regime. For model C with scalar order parameter, in equilibrium governed by strong dynamic scaling (z(S)=z(rho)), we find no genuine nonequilibrium fixed point either. The nonequilibrium critical dynamics of model C with n=1 thus follows the behavior of other systems with nonconserved order parameter wherein detailed balance becomes effectively restored at the phase transition. For n> or =4, the energy density generally decouples from the order parameter. However, for n=2 and n=3, in the weak dynamic scaling regime (z(S)< or =z(rho)) entire lines of genuine nonequilibrium model C fixed points emerge to one-loop order, which are characterized by continuously varying static and dynamic critical exponents. Similarly, the nonequilibrium model C with spatially anisotropic noise and n<4 allows for continuously varying exponents, yet with strong dynamic scaling. Subjecting model D to anisotropic nonequilibrium perturbations leads to genuinely different critical behavior with softening only in subsectors of momentum space and correspondingly anisotropic scaling exponents. Similar to the two-temperature model B (randomly driven diffusive systems) the effective theory at criticality can be cast into an equilibrium model D dynamics, albeit incorporating long-range interactions of the uniaxial dipolar or ferroelastic type.

Journal Article↗

PubMed2003

Single-nanowire electrically driven lasers.

Electrically driven semiconductor lasers are used in technologies ranging from telecommunications and information storage to medical diagnostics and therapeutics. The success of this class of lasers is due in part to well-developed planar semiconductor growth and processing, which enables reproducible fabrication of integrated, electrically driven devices. Yet this approach to device fabrication is also costly and difficult to integrate directly with other technologies such as silicon microelectronics. To overcome these issues for future applications, there has been considerable interest in using organic molecules, polymers, and inorganic nanostructures for lasers, because these materials can be fashioned into devices by chemical processing. Indeed, amplified stimulated emission and lasing have been reported for optically pumped organic systems and, more recently, inorganic nanocrystals and nanowires. However, electrically driven lasing, which is required in most applications, has met with several difficulties in organic systems, and has not been addressed for assembled nanocrystals or nanowires. Here we investigate the feasibility of achieving electrically driven lasing from individual nanowires. Optical and electrical measurements made on single-crystal cadmium sulphide nanowires show that these structures can function as Fabry-Perot optical cavities with mode spacing inversely related to the nanowire length. Investigations of optical and electrical pumping further indicate a threshold for lasing as characterized by optical modes with instrument-limited linewidths. Electrically driven nanowire lasers, which might be assembled in arrays capable of emitting a wide range of colours, could improve existing applications and suggest new opportunities.

Journal Article↗