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At least 1,333 records · Page 74Linked to original sources
PubMed2006

Kinetics of hybridization on surface oligonucleotide microchips: theory, experiment, and comparison with hybridization on gel-based microchips.

The optimal design of oligonucleotide microchips and efficient discrimination between perfect and mismatch duplexes strongly depend on the external transport of target DNA to the cells with immobilized probes as well as on respective association and dissociation rates at the duplex formation. In this paper we present the relevant theory for hybridization of DNA fragments with oligonucleotide probes immobilized in the cells on flat substrate. With minor modifications, our theory also is applicable to reaction-diffusion hybridization kinetics for the probes immobilized on the surface of microbeads immersed in hybridization solution. The main theoretical predictions are verified with control experiments. Besides that, we compared the characteristics of the surface and gel-based oligonucleotide microchips. The comparison was performed for the chips printed with the same pin robot, for the signals measured with the same devices and processed by the same technique, and for the same hybridization conditions. The sets of probe oligonucleotides and the concentrations of probes in respective solutions used for immobilization on each platform were identical as well. We found that, despite the slower hybridization kinetics, the fluorescence signals and mutation discrimination efficiency appeared to be higher for the gel-based microchips with respect to their surface counterparts even for the relatively short hybridization time about 0.5-1 hour. Both the divergence between signals for perfects and the difference in mutation discrimination efficiency for the counterpart platforms rapidly grow with incubation time. In particular, for hybridization during 3 h the signals for gel-based microchips surpassed their surface counterparts in 5-20 times, while the ratios of signals for perfect-mismatch pairs for gel microchips exceeded the corresponding ratios for surface microchips in 2-4 times. These effects may be attributed to the better immobilization efficiency and to the higher thermodynamic association constants for duplex formation within gel pads.

Electrophoresis↗
PubMed1989

On improving the validity of wire screen "unattached" fraction Rn daughter measurements.

Wire screens are commonly used to estimate "unattached" Rn daughter fractions in ambient and mine atmospheres. However, it is now recognized that the "unattached" fraction is in reality an ultrafine cluster mode in the 0.5-3 nm size range and that the collection efficiency versus particle diameter characteristics of wire screens do not permit a distinct separation of the "unattached" and "attached" fractions. Wire screen penetration theory and a semi-empirically corrected diffusion coefficient equation are used to characterize "unattached" fraction measurements as a function of experimental parameters. Collection efficiency curves are estimated for previously published wire screen "unattached" fraction measurements, and improvements in wire screen methods for such measurements are discussed.

Air Pollutants, Radioactive↗
PubMed2001

Scalings of scalar structure functions in a velocity field with coherent vortical structures.

In planar turbulence modeled as an isotropic and homogeneous collection of two-dimensional noninteracting compact vortices, the structure functions S(p)(r) of a statistically stationary passive scalar field have the following scaling behavior in the limit where the Péclet number Pe-->infinity: S(p)(r) approximately const+ln(r/L Pe(-1/3)) for L Pe(-1/3)<<r<<L, S(p)(r) approximately (r/L Pe(-1/3))(6(1-D)) for L Pe(-1/2)<<r<<L Pe(-1/3), where L is a large scale and D is the fractal codimension of the spiral scalar structures generated by the vortices (1/2 < or =D < 2/3). Note that L Pe(-1/2) is the scalar Taylor microscale that stems naturally from our analytical treatment of the advection-diffusion equation. The essential ingredients of our theory are the locality of interscale transfer and Lundgren's time average assumption. A phenomenological theory explicitly based only on these two ingredients reproduces our results and a generalization of this phenomenology to spatially smooth chaotic flows yields (k ln k)(-1) generalized power spectra for the advected scalar fields.

Journal Article↗
PubMed2002

Resonance attractors of spiral waves in excitable media under global feedback.

The dynamics of spiral waves on a circular domain is studied by numerical integration of an excitable reaction-diffusion system with a global feedback. A theory based on the Fourier expansion of the feedback signal is developed to explain the existence and the stability of resonance attractors of spiral waves on domains of different sizes. The theoretical analysis predicts the existence of a discrete set of stable attractors with radii depending on the time delay in the feedback loop. These predictions are in good quantitative agreement with performed numerical simulations.

Journal Article↗
PubMed2003

Functional renormalization group for anisotropic depinning and relation to branching processes.

Using the functional renormalization group, we study the depinning of elastic objects in presence of anisotropy. We explicitly demonstrate how the Kardar-Parisi-Zhang (KPZ) term is always generated, even in the limit of vanishing velocity, except where excluded by symmetry. This mechanism has two steps. First a nonanalytic disorder-distribution is generated under renormalization beyond the Larkin length. This nonanalyticity then generates the KPZ term. We compute the beta function to one loop taking properly into account the nonanalyticity. This gives rise to additional terms, missed in earlier studies. A crucial question is whether the nonrenormalization of the KPZ coupling found at 1-loop order extends beyond the leading one. Using a Cole-Hopf-transformed theory we argue that it is indeed uncorrected to all orders. The resulting flow equations describe a variety of physical situations: We study manifolds in periodic disorder, relevant for charge density waves, as well as in nonperiodic disorder. Further the elasticity of the manifold can either be short range (SR) or long range (LR). A careful analysis of the flow yields several nontrivial fixed points. All these fixed points are transient since they possess one unstable direction towards a runaway flow, which leaves open the question of the upper critical dimension. The runaway flow is dominated by a Landau-ghost mode. For LR elasticity, relevant for contact line depinning, we show that there are two phases depending on the strength of the KPZ coupling. For SR elasticity, using the Cole-Hopf transformed theory we identify a nontrivial 3-dimensional subspace which is invariant to all orders and contains all above fixed points as well as the Landau mode. It belongs to a class of theories which describe branching and reaction-diffusion processes, of which some have been mapped onto directed percolation.

Journal Article↗
PubMed2004

Spatial speckle characterization by Brownian motion analysis.

It is well known that the interactions between coherent monochromatic radiation and a scattering medium induce a speckle phenomenon. The spatial and temporal statistics of this speckle are employed to analyze many applications in laser imaging. The direct exposure of a photographic film, without a lens to the backscattered radiation, gives a speckle pattern. The main problem lies in the determination of those parameters which can efficiently characterize this pattern. In this paper, we present a fractal-theory-based stochastic approach to approximate the diffusion. In our opinion, this method is more appropriate for the classification of this nonlinear and nonstationary phenomenon than the classical frequency-based approach. The paper also presents several applications of this method which have employed for characterization of different test media.

Journal Article↗
PubMed2005

Dynamical susceptibility of glass formers: contrasting the predictions of theoretical scenarios.

We compute analytically and numerically the four-point correlation function that characterizes nontrivial cooperative dynamics in glassy systems within several models of glasses: elastoplastic deformations, mode-coupling theory (MCT), collectively rearranging regions (CRR's), diffusing defects, and kinetically constrained models (KCM's). Some features of the four-point susceptibility chi(4) (t) are expected to be universal: at short times we expect a power-law increase in time as t(4) due to ballistic motion (t(2) if the dynamics is Brownian) followed by an elastic regime (most relevant deep in the glass phase) characterized by a t or sqrt[t] growth, depending on whether phonons are propagative or diffusive. We find in both the beta and early alpha regime that chi(4) approximately t(mu), where mu is directly related to the mechanism responsible for relaxation. This regime ends when a maximum of chi(4) is reached at a time t= t(*) of the order of the relaxation time of the system. This maximum is followed by a fast decay to zero at large times. The height of the maximum also follows a power law chi(4) (t(*)) approximately t(*lambda). The value of the exponents mu and lambda allows one to distinguish between different mechanisms. For example, freely diffusing defects in d=3 lead to mu=2 and lambda=1 , whereas the CRR scenario rather predicts either mu=1 or a logarithmic behavior depending on the nature of the nucleation events and a logarithmic behavior of chi(4) (t(*)) . MCT leads to mu=b and lambda=1/gamma , where b and gamma are the standard MCT exponents. We compare our theoretical results with numerical simulations on a Lennard-Jones and a soft-sphere system. Within the limited time scales accessible to numerical simulations, we find that the exponent mu is rather small, mu<1 , with a value in reasonable agreement with the MCT predictions, but not with the prediction of simple diffusive defect models, KCM's with noncooperative defects, and CRR's. Experimental and numerical determination of chi(4) (t) for longer time scales and lower temperatures would yield highly valuable information on the glass formation mechanism.

Journal Article↗
PubMed2005

Lévy-Student distributions for halos in accelerator beams.

We describe the transverse beam distribution in particle accelerators within the controlled, stochastic dynamical scheme of stochastic mechanics (SM) which produces time reversal invariant diffusion processes. This leads to a linearized theory summarized in a Schrödinger-like (SL) equation. The space charge effects have been introduced in recent papers by coupling this S-L equation with the Maxwell equations. We analyze the space-charge effects to understand how the dynamics produces the actual beam distributions, and in particular we show how the stationary, self-consistent solutions are related to the (external and space-charge) potentials both when we suppose that the external field is harmonic (constant focusing), and when we a priori prescribe the shape of the stationary solution. We then proceed to discuss a few other ideas by introducing generalized Student distributions, namely, non-Gaussian, Lévy infinitely divisible (but not stable) distributions. We will discuss this idea from two different standpoints: (a) first by supposing that the stationary distribution of our (Wiener powered) SM model is a Student distribution; (b) by supposing that our model is based on a (non-Gaussian) Lévy process whose increments are Student distributed. We show that in the case (a) the longer tails of the power decay of the Student laws and in the case (b) the discontinuities of the Lévy-Student process can well account for the rare escape of particles from the beam core, and hence for the formation of a halo in intense beams.

Journal Article↗
PubMed2006

Nematic-isotropic spinodal decomposition kinetics of rodlike viruses.

We investigate spinodal decomposition kinetics of an initially nematic dispersion of rodlike viruses. Quench experiments are performed from a flow-stabilized homogeneous nematic state at a high shear rate into the two-phase isotropic-nematic coexistence region at a zero shear rate. We present experimental evidence that spinodal decomposition is driven by orientational diffusion, in accordance with a very recent theory.

Journal Article↗
PubMed2000

Hall effect and conduction anisotropy in the organic conductor (TMTSF)2PF6

Both the Hall effect and the ab(')-plane conduction anisotropy are directly addressing the unconventional normal phase properties of the Bechgaard salt (TMTSF)2PF6. We found that the dramatic reduction of the carrier density deduced from recent optical data is not reflected in an enhanced Hall resistance. The pressure and temperature dependence of the b(')-direction resistivity reveal isotropic relaxation time and do not require explanations beyond the Fermi liquid theory. Our results allow a coherent-diffusive transition in the interchain carrier propagation, however the possible crossover to Luttinger liquid behavior is placed at an energy scale above room temperature.

Journal Article↗
PubMed2001

Energy dependence of quasiparticle relaxation in a disordered fermi liquid.

A spectroscopic method is applied to measure the inelastic quasiparticle relaxation rate in a disordered Fermi liquid. The quasiparticle relaxation rate gamma is deduced from the magnitude of fluctuations in the local density of states, which are probed using resonant tunneling through a localized impurity state. We study its dependence on the excitation energy E measured from the Fermi level. In a disordered metal (heavily doped GaAs) we find that gamma~E3/2 within the experimentally accessible energy interval, in agreement with the Altshuler-Aronov theory for electron-electron interactions in diffusive conductors.

Journal Article↗
PubMed2002

Dynamic behavior of anisotropic nonequilibrium driving lattice gases.

It is shown that intrinsically anisotropic nonequilibrium systems relaxing by a dynamic process exhibit universal critical behavior during their evolution toward nonequilibrium stationary states. An anisotropic scaling ansatz for the dynamics is proposed and tested numerically. Relevant critical exponents can be evaluated self-consistently using both the short- and long-time dynamics frameworks. The obtained results allow us to clarify a long-standing controversy about the theoretical description, the universality, and the origin of the anisotropy of driven diffusive systems, showing that the standard field theory does not hold and supporting a recently proposed alternative theory.

Journal Article↗
PubMed2005

Electron emission from diamondoids: a diffusion quantum Monte Carlo study.

We present density-functional theory (DFT) and quantum Monte Carlo (QMC) calculations designed to resolve experimental and theoretical controversies over the optical properties of H-terminated C nanoparticles (diamondoids). The QMC results follow the trends of well-converged plane-wave DFT calculations for the size dependence of the optical gap, but they predict gaps that are 1-2 eV higher. They confirm that quantum confinement effects disappear in diamondoids larger than 1 nm, which have gaps below that of bulk diamond. Our QMC calculations predict a small exciton binding energy and a negative electron affinity (NEA) for diamondoids up to 1 nm, resulting from the delocalized nature of the lowest unoccupied molecular orbital. The NEA suggests a range of possible applications of diamondoids as low-voltage electron emitters.

Journal Article↗
PubMed1999

Surfactant-spreading and surface-compression disturbance on a thin viscous film.

Spreading of a new surfactant in the presence of a pre-existing surfactant distribution is investigated both experimentally and theoretically for a thin viscous substrate. The experiments are designed to provide a better understanding of the fundamental interfacial and fluid dynamics for spreading of surfactants instilled into the lung. Quantitative measurements of spreading rates were conducted using a fluorescent new surfactant that was excited by argon laser light as it spread on an air-glycerin interface in a petri dish. It is found that pre-existing surfactant impedes surfactant spreading. However, fluorescent microspheres used as surface markers show that pre-existing surfactant facilitates the propagation of a surface-compression disturbance, which travels faster than the leading edge of the new surfactant. The experimental results compare well with the theory developed using lubrication approximations. An effective diffusivity of the thin film system is found to be Deff = (E*gamma)/(mu/H), which indicates that the surface-compression disturbance propagates faster for larger background surfactant concentration, gamma, larger constant slope of the sigma*-gamma* relation, -E*, and smaller viscous resistance, mu/H. Note that sigma* and gamma* are the dimensional surface tension and concentration, respectively, mu is fluid viscosity, and H is the unperturbed film thickness.

4-Chloro-7-nitrobenzofurazan↗
PubMed1995

Tracheal gas exchange: perfusion-related differences in inert gas elimination.

Exchange of inert gases across the conducting airways has been demonstrated by using an isolated dog tracheal preparation and has been characterized by using a mathematical model (E. R. Swenson, H. T. Robertson, N. L. Polissar, M. E. Middaugh, and M. P. Hlastala, J. Appl. Physiol. 72: 1581-1588, 1992). Theory predicts that gas exchange is both diffusion and perfusion dependent, with gases with a higher blood-gas partition coefficient exchanging more efficiently. The present study evaluated the perfusion dependence of airway gas exchange in an in situ canine tracheal preparation. Eight dogs were studied under general anesthesia with the same isolated tracheal preparation. Tracheal perfusion (Q) was altered from control blood flow (Qo) by epinephrine or papaverine instilled into the trachea and was measured with fluorescent microspheres. Six inert gases of differing blood-gas partition coefficients were used to measure inert gas elimination. Gas exchange was quantified as excretion (E), equal to exhaled partial pressure divided by arterial partial pressure. Data were plotted as ln [E/(l-E)] vs. In (Q/Qo), and the slopes were determined by least squares. Excretion was a positive function of Q, and the magnitude of the response of each gas to changes in Q was similar and highly significant (P < or = 0.0002). These results confirm a substantial perfusion dependence of airway gas exchange.

Animals↗
PubMed2004

Calcium dynamics in dendritic spines and spine motility.

A dendritic spine is an intracellular compartment in synapses of central neurons. The role of the fast twitching of spines, brought about by a transient rise of internal calcium concentration above that of the parent dendrite, has been hitherto unclear. We propose an explanation of the cause and effect of the twitching and its role in the functioning of the spine as a fast calcium compartment. Our molecular model postulates that rapid spine motility is due to the concerted contraction of calcium-binding proteins. The contraction induces a stream of cytoplasmic fluid in the direction of the dendritic shaft, thus speeding up the time course of spine calcium dynamics, relative to pure diffusion. Simulations indicate that chemical reaction rate theory at the molecular level can explain spine motility. They reveal two time periods in calcium dynamics, as measured recently by other researchers. It appears that rapid motility in dendritic spines increases the efficiency of calcium conduction to the dendrite and speeds up the emptying of the spine. This could play a major role in the induction of synaptic plasticity. A prediction of the model is that alteration of spine motility will modify the time course of calcium in the dendritic spine and could be tested experimentally.

Animals↗
PubMedDate not supplied

A comparative analysis of mass transport models in peritoneal dialysis.

To better understand the differences in published estimates of peritoneal mass transport coefficients, a comparative analysis of seven mathematical models of peritoneal transport was performed. Uniform investigation involving measurements of solute concentrations and accurate determination of peritoneal dialysate volume was undertaken in twenty-eight 6 hour dwell studies using 3.86% glucose dialysate in non-diabetic patients undergoing continuous ambulatory peritoneal dialysis (CAPD). The investigated models were all based on the theory of transport across a homogeneous membrane. Diffusive mass transport coefficients (KBD) calculated during a period of dialysate isovolemia served as reference values in the comparative analysis. The evaluation of models involved calculations of transport coefficients and comparison of calculated dialysate-to-plasma concentration ratios (D/P) with experimental D/P. The best fit of theoretically predicted D/P to experimental D/P was obtained with Pyle-Popovich's model, which accounts for both the diffusive (KBD) and convective (sieving coefficient [S]) characteristics of the peritoneal membrane. Garred's model, assuming S = 1, yielded acceptable results for small solutes (except sodium), whereas Henderson's model, in which convective transport is neglected, proved to be surprisingly accurate for KBD for both small solutes (except sodium) and protein. S values (mean +/- SD) calculated using Pyle-Popovich's model were found to be out of the physically interpretable range for glucose (S = -0.38 +/- 0.48) and potassium (S = 1.57 +/- 0.19), and therefore these S values should be treated as phenomenologic rather than physical quantities.

Biological Transport↗
PubMedDate not supplied

[Nonlinear laser photomodification of nucleic acids induced by intercalating dyes].

Results of a cycle of investigations of two-quantum affinity modification of nucleic acids (NA) are presented. The modification is induced by laser excitation of chromophoric molecules which are in intercalative complexes with NA. The following subjects are considered: theoretical basis of the two-quantum affinity modification: experimental investigation of nonlinear scission of DNA; theory and experiment on the light--induced diffusion of DNA. The latter is an effect which accompanies the scission and allows one to obtain information on it. The modification specificity and universality in a dye type are established experimentally. Influence of free radicals, oxygen, heating and hydrodynamical phenomena in bulk are excluded. The modification has been shown to be dependent on NA structure (secondary and tertiary) and to provide information on it. Total aggregate of the data obtained is in agreement with the suggested modification mechanism which is based on the radiationless transfer of two-quantum excitation energy from the chromophore to NA.

Coloring Agents↗