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At least 1,351 records · Page 75Linked to original sources
PubMed2004

Viscosity-dependent relaxation significantly modulates the kinetics of CO recombination in the truncated hemoglobin TrHbN from Mycobacterium tuberculosis.

Kinetic traces were generated for the nanosecond and slower rebinding of photodissociated CO to trHbN in solution and in porous sol-gel matrices as a function of viscosity, conformation, and mutation. TrHbN is one of the two truncated hemoglobins from Mycobacterium tuberculosis. The kinetic traces were analyzed in terms of three distinct phases. These three phases are ascribed to rebinding: (i) from the distal heme pocket, (ii) from the adjacent apolar tunnel prior to conformational relaxation, and (iii) from the apolar tunnel subsequent to conformational relaxation. The fractional content of each of these phases was shown to be a function of the viscosity and, in the case of the sol-gel-encapsulated samples, sample preparation history. The observed kinetic patterns support a model consisting of the following elements: (i) the viscosity and conformation-sensitive dynamics of the Tyr(B10) side chain facilitate diffusion of the dissociated ligand from the distal heme pocket into the adjacent tunnel; (ii) the distal heme pocket architecture determines ligand access from the tunnel back to the heme iron; (iii) the distal heme pocket architecture is governed by a ligand-dependent hydrogen bonding network that limits the range of accessible side chain positions; and (iv) the apolar tunnel linking the heme site to the solvent biases the competition between water and ligand for occupancy of the vacated polar distal heme pocket greatly toward the nonpolar ligand. Implications of these finding with respect to biological function are discussed.

Binding Sites↗
PubMed2003

Development of a nutritious low viscosity weaning mix using natural ingredients and microbial amylases.

A nutritious weaning food was developed using natural ingredients; namely, staple cereals and pulses, groundnut, Spirulina and gooseberry. The nutritive value of the developed weaning mix was found to be better than a commercial mix. The viscosity of the mixes was reduced by the addition of bacterial and fungal amylases. Addition of amylases at a concentration of 0.1-0.4% drastically reduced the viscosity in all the formulated mixes. The maximum viscosity reduction effect was evident at 0.2% for bacterial amylase and at 0.4% for fungal amylases.

Arachis↗
PubMed2004

VisCoSe: visualization and comparison of consensus sequences.

We introduce visualization and comparison of consensus sequences (VisCoSe) as a WWW service and a stand-alone command line Perl script for visualizing and comparing consensus sequences of protein and nucleotide sequences. VisCoSe is the only interface available that simultaneously calculates consensus sequences of multiple data sets and automatically compares these consensus sequences. Furthermore, VisCoSe allows visualization of chemical properties of amino acids.

Algorithms↗
PubMedDate not supplied

Quantitative structure-activity relationships of perfluorinated hetero-hydrocarbons as potential respiratory media. Application to oxygen solubility, partition coefficient, viscosity, vapor pressure, and density.

It has been extensively reported that liquid-assisted ventilation, using inert perfluorocarbon liquids (PFCs), can reduce interfacial surface tension and allow for improved ventilation at decreased alveolar pressures. PFCs are bioinert, minimally absorbed, and have no deleterious histologic, cellular, or biochemical effects when used as respiratory media. Although several types of PFCs have been characterized, a select few are considered to be compatible with life. Compatibility is often related to the physicochemical profile inherent to the PFC liquids. It is essential that certain physical properties such as respiratory gas solubility, vapor pressure, density, viscosity, and tissue permeability be within a narrow, acceptable range for a PFC to be considered as a possible candidate for respiratory media. The current study sought to characterize the physicochemical profile of commercially available PFCs. This was accomplished by creating a method for accurate, rapid prediction of a host of unknown physical characteristics of PFCs. The physicochemical properties of 16 perfluorinated hetero-hydrocarbons were catalogued from the literature. The input data were categorized into three major groups: empiric properties, geometric indices, and quantum mechanical descriptors, to generate a database. Algorithms were then developed, one for each dependent variable (FUNCTION), including oxygen solubility, partition coefficient (logP), vapor pressure, viscosity, and density, that related the values of these physical properties of potential breathable PFC liquids to the parameters listed in the database. The general form of the algorithm can be written as follows: FUNCTION = sigma (CiPi/magnitude of Pi) + constant; where the FUNCTIONS are oxygen solubility, logP, vapor pressure, viscosity, and density. Ci is a coefficient that weights the relative contribution of each parameter. Each independent parameter, Pi, was normalized by the average value of the parameter used in the analysis, magnitude of Pi. Residual analysis demonstrated validity with all five equations. This method is expected to assist in the prediction of physical properties of PFC liquids with acceptable accuracy, such that PFC production and selection from currently available liquids can be optimized for each liquid ventilation application.

Absorption↗
PubMed2000

Viscosity of liquid water from computer simulations with a polarizable potential model

The longitudinal and shear viscosity of water are calculated by molecular dynamics simulation with a polarizable potential model at room temperature. To overcome the difficulty of evaluating directly the stress autocorrelation function of a system with intrinsically many-body forces, we have resorted to the analysis of the wave-vector-dependent longitudinal and transverse-current correlation functions. In a memory function formalism, the generalized viscosity can be evaluated as a function of the wave vector k. By extrapolating to k=0, we find longitudinal and shear viscosity values in better agreement with the experimental value than the corresponding quantities evaluated by making use of a nonpolarizable potential model. This result points out that for a realistic reproduction of transport quantities, it is crucial to take into account many-body contributions to the interaction potential.

Journal Article↗
PubMed2001

Two-state protein model with water interactions: influence of temperature on the intrinsic viscosity of myoglobin.

We describe a single-domain protein as a two-state system with water interactions. Around the unfolded apolar parts of the protein we incorporate the hydration effect by introducing hydrogen bonds between the water molecules in order to mimic the "icelike" shell structure. Intrinsic viscosity, proportional to the effective hydrodynamic volume, for sperm whale metmyoglobin is assigned from experimental data in the folded and in the denaturated state. By weighing statistically the two states against the degree of folding, we express the total intrinsic viscosity. The temperature dependence of the intrinsic viscosity, for different chemical potentials, is in good correspondence with experimental data [P. L. Privalov et al., J. Mol. Biol. 190, 487 (1986)]. Cold and warm unfolding, common to small globular proteins, is also a result of the model.

Animals↗
PubMed2001

Bulk and shear viscosities in lattice Boltzmann equations.

Lattice Boltzmann equations (LBE) are a useful tool for simulating the incompressible Navier-Stokes equations. However, LBE actually simulate a compressible but usually isothermal fluid at some small but finite Mach number. There has been recent interest in using LBE at larger, but still subsonic, Mach numbers, for which the viscous terms in the resulting momentum equation depart appreciably from those in the compressible Navier-Stokes equations. In particular, the isothermal constraint implies a nonzero "bulk" viscosity in addition to the usual shear viscosity. This difficulty arises at the level of the isothermal continuum Boltzmann equation prior to discretization. A remedy is proposed, and tested in numerical experiments with decaying sound waves. Conversely, an enhanced bulk viscosity is found useful for identifying or suppressing artifacts in under-resolved simulations of supposedly incompressible shear flows.

Journal Article↗
PubMed2002

Viscosity and transient electric birefringence study of clay colloidal aggregation.

We study a synthetic clay suspension of laponite at different particle and NaCl concentrations by measuring stationary shear viscosity and transient electrically induced birefringence (TEB). On one hand the viscosity data are consistent with the particles being spheres and the particles being associated with large amount bound water. On the other hand the viscosity data are also consistent with the particles being asymmetric, consistent with single laponite platelets associated with a very few monolayers of water. We analyze the TEB data by employing two different models of aggregate size (effective hydrodynamic radius) distribution: (1) bidisperse model and (2) log-normal distributed model. Both models fit, in the same manner, fairly well to the experimental TEB data and they indicate that the suspension consists of polydisperse particles. The models also appear to confirm that the aggregates increase in size vs increasing ionic strength. The smallest particles at low salt concentrations seem to be monomers and oligomers.

Journal Article↗
PubMed2002

Nature of the divergence in low shear viscosity of colloidal hard-sphere dispersions.

Measurements of the low-shear viscosity eta(o) with a Zimm-Crothers viscometer for dispersions of colloidal hard spheres are reported as a function of volume fraction phi up to 0.56. Nonequilibrium theories based on solutions to the two-particle Smoluchoski equation or ideal mode coupling approximations do not capture the divergence. However, the nonhydrodynamic contribution to the relative viscosity Deltaeta(o) is correlated over a wide range of volume fractions by the Doolittle and Adam-Gibbs equations, indicating an exponential divergence at phi(m)=0.625+/-0.015. The data extend the previously proposed master curve, providing a test for improved theories for the many-body thermodynamic and hydrodynamic interactions that determine the viscosity of hard-sphere dispersions.

Journal Article↗
PubMed2002

Density matrix renormalization group studies of the effect of constraint release on the viscosity of polymer melts.

The scaling of the viscosity of polymer melts is investigated with regard to the molecular weight. We present a generalization of the Rubinstein-Duke model, which takes constraint releases into account and calculates the effects on the viscosity by the use of the density matrix renormalization group algorithm. Using input from Rouse theory, the rates for the constraint releases are determined in a self-consistent way. We conclude that shape fluctuations of the tube caused by constraint release are not a likely candidate for improving Doi's crossover theory for the scaling of the polymer viscosity.

Journal Article↗
PubMed2003

Bulk viscosity in the case of the interatomic potential depending on density.

We derive a formula for the bulk viscosity zeta in a density-dependent-potential system. This is a generalization of the bulk-viscosity formula for the density-independent-potential system which has been proposed recently by us. In our formulas, the bulk viscosity is expressed by using microscopic quantities such as interatomic potentials and pair distribution functions. This has an outstanding advantage of providing the relation between such microscopic information and a macroscopic quantity zeta. On the other hand, in all formulas proposed previously, zeta is expressed in terms of pressure, a macroscopic quantity, and it is difficult to discuss this relation. We apply our formula to a model liquid metal in which the interatomic potential varies with density. Our calculated results show that zeta increases in the density region where the interatomic potential changes from one type to another. These results agree qualitatively with the experimental results about liquid mercury.

Journal Article↗
PubMed2003

Stabilization of hydrodynamic flows by small viscosity variations.

Motivated by the large effect of turbulent drag reduction by minute concentrations of polymers, we study the effects of a weakly space-dependent viscosity on the stability of hydrodynamic flows. In a recent paper [Phys. Rev. Lett. 87, 174501, (2001)], we exposed the crucial role played by a localized region where the energy of fluctuations is produced by interactions with the mean flow (the "critical layer"). We showed that a layer of a weakly space-dependent viscosity placed near the critical layer can have a very large stabilizing effect on hydrodynamic fluctuations, retarding significantly the onset of turbulence. In this paper we extend these observations in two directions: first we show that the strong stabilization of the primary instability is also obtained when the viscosity profile is realistic (inferred from simulations of turbulent flows with a small concentration of polymers). Second, we analyze the secondary instability (around the time-dependent primary instability) and find similar strong stabilization. Since the secondary instability develops around a time-dependent solution and is three dimensional, this brings us closer to the turbulent case. We reiterate that the large effect is not due to a modified dissipation (as is assumed in some theories of drag reduction), but due to reduced energy intake from the mean flow to the fluctuations. We propose that similar physics act in turbulent drag reduction.

Journal Article↗
PubMed2003

Comment on "Computation of the viscosity of a liquid from time averages of stress fluctuations".

In a recent paper, Hess and Evans [Phys. Rev. E 64, 011207 (2001)] propose a method different from the conventional Green-Kubo and Einstein methods to calculate viscosity in equilibrium molecular dynamics simulations. For a comparison, we calculate the shear viscosity of SPC/E water at 303 K using these three different methods. We find that the Hess-Evans method is not as good as the other two in practical application, especially for the fluids with high viscosity and complicated relaxation.

Comment↗
PubMed2003

Shear viscosity of liquid mixtures: mass dependence.

The expressions for zeroth, second, and fourth sum rules of the transverse stress autocorrelation function of a two-component fluid have been derived. These sum rules and Mori's memory function formalism have been used to study the shear viscosity of Ar-Kr and isotopic mixtures. It has been found that the theoretical result is in good agreement with the computer simulation result for the Ar-Kr mixture. The mass dependence of shear viscosity for different mole fractions shows that deviation from ideal linear model comes even from the mass difference in two species of the fluid mixture. At higher mass ratio, shear viscosity of the mixture is not explained by any of the empirical models.

Journal Article↗
PubMed2003

Shear viscosity for a moderately dense granular binary mixture.

The shear viscosity for a moderately dense granular binary mixture of smooth hard spheres undergoing uniform shear flow is determined. The basis for the analysis is the Enskog kinetic equation, solved first analytically by the Chapman-Enskog method up to first order in the shear rate for unforced systems as well as for systems driven by a Gaussian thermostat. As in the elastic case, practical evaluation requires a Sonine polynomial approximation. In the leading order, we determine the shear viscosity in terms of the control parameters of the problem: solid fraction, composition, mass ratio, size ratio, and restitution coefficients. Both kinetic and collisional transfer contributions to the shear viscosity are considered. To probe the accuracy of the Chapman-Enskog results, the Enskog equation is then numerically solved for systems driven by a Gaussian thermostat by means of an extension to dense gases of the well-known direct simulation Monte Carlo method for dilute gases. The comparison between theory and simulation shows, in general, an excellent agreement over a wide region of the parameter space.

Journal Article↗
PubMed2003

Theory of the viscosity of supercooled liquids and the glass transition: fragile liquids.

A statistical mechanical theory is presented for viscosity of relatively low molecular weight organic liquids which are supercooled down to the glass transition temperature. In this theory a relation resembling the Stokes-Einstein relation between the viscosity and self-diffusion coefficient of supercooled liquids and an expression for the self-diffusion coefficient are augmented by a suitably constructed semiempirical generic van der Waals equation of state that makes it possible to calculate the free volume. The theory accounts in excellent accuracy for viscosities and self-diffusion coefficients of fragile liquids over the entire range of temperature experimentally investigated. According to the theory, vitrification occurs when the free volume available for translational molecular motion falls below a critical value.

Journal Article↗
PubMed2003

Clustering and viscosity in a shear flow of a particulate suspension.

A shear flow of particulate suspension is analyzed for the qualitative effect of particle clustering on viscosity using a simple kinetic clustering model and direct numerical simulations. The clusters formed in a Couette flow can be divided into rotating chainlike clusters and layers of particles at the channel walls. The size distribution of the rotating clusters is scale invariant in the small-cluster regime and decreases rapidly above a characteristic length scale that diverges at a jamming transition. The behavior of the suspension can qualitatively be divided into three regimes. For particle Reynolds number Re(p) less than or approximately equal 0.1, viscosity is controlled by the characteristic cluster size deduced from the kinetic clustering model. For Re(p) approximately 1, clustering is maximal, but the simple kinetic model becomes inapplicable presumably due to onset of instabilities. In this transition regime viscosity begins to increase. For Re(p) greater than or approximately equal 10, inertial effects become important, clusters begin to breakup, and suspension displays shear thickening. This phenomenon may be attributed to enhanced contribution of solid phase in the total shear stress.

Journal Article↗
PubMed2004

Role of liquid compressional viscosity in the dynamics of a sonoluminescing bubble.

The well-known Rayleigh-Plesset ( RP ) equation is the basis of almost all hydrodynamical descriptions of single-bubble sonoluminescence ( SBSL ). A major deficiency of the RP equation is that it accounts for viscosity of an incompressible liquid and compressibility, separately. By removing this approximation, a new modification of the RP equation is presented considering effect of compressional viscosity of the liquid. This modification leads to addition of a new viscous term to the traditional bubble boundary equation. Influence of this new term in the dynamics of a sonoluminescing bubble has numerically been studied considering effects of heat transfer at the bubble wall, nonequilibrium evaporation and condensation of water vapor, chemical reactions, and diffusion of the reactions products in the liquid. The results show that the new term has a significant damping role in the bubble motion at the end of collapse and during the rebounds, so that its consideration dramatically reduces amplitude of the afterbounces. Dependence of this new damping mechanism on the driving pressure amplitude and on the ambient radius has been investigated. The results indicate that the more intense the collapse, the more important the damping of the liquid compressional viscosity.

Journal Article↗