Anomalous reaction-diffusion as a model of nonexponential DNA escape kinetics

We show that data from recent experiments carried out on the kinetics of DNA escape from alpha-hemolysin nanopores [M. Wiggin, C. Tropini, C. T. Cossa, N. N. Jetha, and A. Marziali, Biophys. J. 95, 5317 (2008)] may be rationalized by a model of chain dynamics based on the anomalous diffusion of a particle moving in a harmonic well in the presence of a delta function sink. The experiments of Wiggin found, among other things, that the occasional occurrence of unusually long escape times in the distribution of chain trapping events led to nonexponential decays in the survival probability, S(t), of the DNA molecules within the nanopore. Wiggin ascribed this nonexponentiality to the existence of a distribution of trapping potentials, which they suggested was theresult of stochastic interactions between the bases of the DNA and the amino acids located on the surface of the nanopore. Based on this idea, they showed that the experimentally determined S(t) could be well fit in both the short and long time regimes by a function of the form (1+t/tau)(-alpha) (the so called Becquerel function). In our model, S(t) is found to be given by a Mittag-Leffler function at short times and by a generalized Mittag-Leffler function at long times. By suitable choice of certain parameter values, these functions are found to fit the experimental S(t) even better than the Becquerel function. Anomalous diffusion of DNA within the trap prior to escape over a barrier of fixed height may therefore provide a second, plausible explanation of the data, and may offer fresh perspectives on similar trapping and escape problems.

A Model of Anomalous Enzyme-Catalyzed Gel Degradation Kinetics

We show that a model of target location involving n noninteracting particles moving subdiffusively along a line segment (a generalization of a model introduced by Sokolov et al. [Biophys. J. 2005, 89, 895.]) provides a basis for understanding recent experiments by Pelta et al. [Phys. Rev. Lett. 2007, 98, 228302.] on the kinetics of diffusion-limited gel degradation. These experiments find that the time t(c) taken by the enzyme thermolysin to completely hydrolyze a gel varies inversely as roughly the 3/2 power of the initial enzyme concentration [E]. In general, however, this time would be expected to vary either as [E](-1) or as [E](-2), depending on whether the Brownian diffusion of the enzyme to the site of cleavage took place along the network chains (1-d diffusion) or through the pore spaces (3-d diffusion). In our model, the unusual dependence of t(c) on [E] is explained in terms of a reaction-diffusion equation that is formulated in terms of fractional rather than ordinary time derivatives.

A singularity-free cosmological model in ECSK theory

In the framework of the ECSK [Einstein-Cartan-Sciama-Kibble] theory of cosmology, a scalar field nonminimally coupled to the gravitational field is considered. For a Robertson-Walker open universe (k=0) in the radiation era, the field equations admit a singularity-free solution for the scale factor. In theory, the torsion is generated through nonminimal coupling of a scalar field to the gravitation field. The nonsingular nature of the cosmological model automatically solves the flatness problem. Further absence of event horizon and particle horizon explains the high degree of isotropy, especially of 2.7-K background radiation.

Solubilization of n-decane into n-decyl-polyoxyethylene surfactants: A cavity forming free energy based model

The present paper reports the results of a theoretical study of the forces and factors driving the solubilization of n-alkane solubilizates into the micellar core of some non-ionic surfactants, based on a micellar model which includes the cavity forming free energy as a component of micellization. The solubilizate is n-decane and the non-ionic surfactants considered are n-decyl-polyoxyethylene surfactants. The extent of solubilization, i.e. the mole fraction of the solubilizate within the core has been calculated. The results indicate that the incorporated solubilizate has more translational and rotational degrees of freedom as compared to those of the tail parts of the surfactants present in the core. This drives the total free energy of aggregation after solubilization into a more favourable direction. The results are in fair agreement with the experimental results.

Mathematical Model of Viral Kinetics In Vitro Estimates the Number of E2-CD81 Complexes Necessary for Hepatitis C Virus Entry

Interaction between the hepatitis C virus (HCV) envelope protein E2 and the host receptor CD81 is essential for HCV entry into target cells. The number of E2-CD81 complexes necessary for HCV entry has remained difficult to estimate experimentally. Using the recently developed cell culture systems that allow persistent HCV infection in vitro, the dependence of HCV entry and kinetics on CD81 expression has been measured. We reasoned that analysis of the latter experiments using a mathematical model of viral kinetics may yield estimates of the number of E2-CD81 complexes necessary for HCV entry. Here, we constructed a mathematical model of HCV viral kinetics in vitro, in which we accounted explicitly for the dependence of HCV entry on CD81 expression. Model predictions of viral kinetics are in quantitative agreement with experimental observations. Specifically, our model predicts triphasic viral kinetics in vitro, where the first phase is characterized by cell proliferation, the second by the infection of susceptible cells and the third by the growth of cells refractory to infection. By fitting model predictions to the above data, we were able to estimate the threshold number of E2-CD81 complexes necessary for HCV entry into human hepatoma-derived cells. We found that depending on the E2-CD81 binding affinity, between 1 and 13 E2-CD81 complexes are necessary for HCV entry. With this estimate, our model captured data from independent experiments that employed different HCV clones and cells with distinct CD81 expression levels, indicating that the estimate is robust. Our study thus quantifies the molecular requirements of HCV entry and suggests guidelines for intervention strategies that target the E2-CD81 interaction. Further, our model presents a framework for quantitative analyses of cell culture studies now extensively employed to investigate HCV infection.

Defect-Free Hyperbranched Polydithioacetal via Melt Polymerization

Degree of branching (DB) describes the level of structural perfection of a hyperbranched polymer when compared to its defect-free analogue, namely the dendrimer. The strategy most commonly used to achieve high DB values, specifically while using AB(2) type self-condensations, is to design an AB2 monomer wherein the reaction of the first B-group leads to an enhancement of the reactivity of the second one. In the present study, we show that an AB2 monomer carrying a dimethylacetal unit and a thiol group undergoes a rapid self-condensation in the melt under acid-catalysis to yield a hyperbranched polydithioacetal with no linear defects. NMR studies using model systems reveal that the intermediate monothioacetal is relatively unstable under the polymerization conditions and transforms rapidly to the dithioacetal; because this second step occurs irreversibly during polymer formation, it leads to a defect-free hyperbranched polydithioacetal. TGA studies of the polymerization process provided some valuable insights into the kinetics of polymerization. An additional virtue of this approach is that the numerous terminal dimethylacetal groups are very labile and can be quantitatively transformed by treatment with a variety of functional thiols; the terminal dimethylacetals were, thus, reacted with various thiols, such as dodecanethiol, benzyl mercaptan, ethylmercaptopropionate, and so on, to demonstrate the versatility of these systems as sulfur-rich hyperscaffolds to anchor different kinds of functionality on their periphery.

Extracting Three Dimensional Surface Model of Human Kidney from the Visible Human Data Set using Free Software

Three dimensional digital model of a representative human kidney is needed for a surgical simulator that is capable of simulating a laparoscopic surgery involving kidney. Buying a three dimensional computer model of a representative human kidney, or reconstructing a human kidney from an image sequence using commercial software, both involve (sometimes significant amount of) money. In this paper, author has shown that one can obtain a three dimensional surface model of human kidney by making use of images from the Visible Human Data Set and a few free software packages (ImageJ, ITK-SNAP, and MeshLab in particular). Images from the Visible Human Data Set, and the software packages used here, both do not cost anything. Hence, the practice of extracting the geometry of a representative human kidney for free, as illustrated in the present work, could be a free alternative to the use of expensive commercial software or to the purchase of a digital model.

Simulation of Free-Surface Flow in a Tank Using the Navier-Stokes Model and Unstructured Finite Volume Method

Modelling free-surface flow has very important applications in many engineering areas such as oil transportation and offshore structures. Current research focuses on the modelling of free surface flow in a tank by solving the Navier-Stokes equation. An unstructured finite volume method is used to discretize the governing equations. The free surface is tracked by dynamically adapting the mesh and making it always surface conforming. A mesh-smoothing scheme based on the spring analogy is also implemented to ensure mesh quality throughout the computaiton. Studies are performed on the sloshing response of a liquid in an elastic container subjected to various excitation frequencies. Further investigations are also carried out on the critical frequency that leads to large deformation of the tank walls. Another numerical simulation involves the free-surface flow past as submerged obstacle placed in the tank to show the flow separation and vortices. All these cases demonstrate the capability of this numerical method in modelling complicated practical problems.

Chemical kinetics and self-ignition in a model supersonic hydrogen-air combustor

Self-ignition tests of a model scramjet combustor were conducted by using parallel sonic injection of gaseous hydrogen from the base of a blade-like strut into a supersonic vitiated airstream. The range of stagnation pressure and temperature studied varied from 1.0 to 4.5 MPa and from 1300 to 2200 K, respectively. Experimental results show that the self-ignition limit, in terms of either global or local quantities of pressure and temperature, exhibits a nonmonotonic behavior resembling the classical homogeneous explosion limit of the hydrogen-oxygen system. Specifically, for a given temperature, increasing pressure from a low value can render a nonignitable mixture to first become ignitable, then nonignitable again, This correspondence shows that, despite the globally supersonic nonpremixed configuration studied herein, ignition is strongly influenced by the intricate chemical reaction mechanism and thereby exhibits the homogeneous explosion character. Consequently, self-ignition criteria based on a global reaction rate approximating the complex chemistry are inadequate. An auxiliary computational study on counterflow ignition was also conducted to systematically investigate the contamination effects of vitiated air. Results indicate that the net contamination effects for the present experimental data are expected to be substantially smaller than contributions from the individual contamination species because of the counterbalancing influences of the H2O-inhibition and NO-promotion reactions in effecting ignition.

A Modified Free Volume Model For Characterizing Of Rate Effect In Bulk Metallic Glasses

We investigate the plastic deformation and constitutive behaviour of bulk metallic glasses (BMGs). A dimensionless Deborah number De(ID) = t(r)/t(i) is proposed to characterize the rate effect in BMGs, where t(r) is the structural relaxing characteristic time of BMGs under shear load, t(i) is the macroscopic imposed characteristic time of applied stress or the characteristic time of macroscopic deformation. The results demonstrate that the modified free volume model can characterize the strain rate effect in BMGs effectively.

Semi-gas kinetics model for performance modeling of flowing chemical oxygen-iodine lasers (COIL)

A semi-gas kinetics (SGK) model for performance analyses of flowing chemical oxygen-iodine laser (COIL) is presented. In this model, the oxygen-iodine reaction gas flow is treated as a continuous medium, and the effect of thermal motions of particles of different laser energy levels on the performances of the COIL is included and the velocity distribution function equations are solved by using the double-parameter perturbational method. For a premixed flow, effects of different chemical reaction systems, different gain saturation models and temperature, pressure, yield of excited oxygen, iodine concentration and frequency-shift on the performances of the COIL are computed, and the calculated output power agrees well with the experimental data. The results indicate that the power extraction of the SGK model considering 21 reactions is close to those when only the reversible pumping reaction is considered, while different gain saturation models and adjustable parameters greatly affect the output power, the optimal threshold gain range, and the length of power extraction.

A unified model for dislocation nucleation, dislocation emission and dislocation free zone

In this paper, a unified model for dislocation nucleation, emission and dislocation free zone is proposed based on the Peierls framework. Three regions are identified ahead of the crack tip. The emitted dislocations, located away from the crack tip in the form of an inverse pileup, define the plastic zone. Between that zone and the cohesive zone immediately ahead of the crack tip, there is a dislocation free zone. With the stress field and the dislocation density field in the cohesive zone and plastic zone being, respectively, expressed in the first and second Chebyshev polynomial series, and the opening and slip displacements in trigonometric series, a set of nonlinear algebraic equations can be obtained and solved with the Newton-Raphson Method. The results of calculations for pure shearing and combined tension and shear loading after dislocation emission are given in detail. An approximate treatment of the dynamic effects of the dislocation emission is also developed in this paper, and the calculation results are in good agreement with those of molecular dynamics simulations.

A consistent model of isolated force-free magnetic arches

The magnetic flux tube concentrating strong magnetic field is the basic configuration of magneticfield in the solar atmosphere. In the present paper, the equilibrium of isolated magnetic flux tube inthe solar atmosphere is discussed. In the viewpoint of mathematics, the boundary condition is nonlinearand the position of boundary needs to be determined by the physical condition although the equation ofmagnetic potential is linear for the linear force-free field. Analytical solutions to the arches of bothuniform circular cross-section and non-uniform cross section have been obtained. The results show thatthe nonlinear problem may have or not have any solution according to different azimuthal components of the magnetic field; the number of solutions to the nonlinear problem is four at most, and two in some cases. In the present paper, the analytical solutions to the approximations of both fat and slender arches are given in detail, and the general features of magnetic arch structure are shown.

Experimental Studies on Model Scramjet in a Mach 6 High Enthalpy Free-Jet Wind Tunnel

A side-wall compression scramjet model with different combustor geometries has been tested in a propulsion tunnel that typically provides the testing flow with Mach number of 5.8, total temperature of 1800K, total pressure of 4.5MPa and mass flow rate of 4kg/s. This kerosene-fueled scramjet model consists of a side-wall compression inlet, a combustor and a thrust nozzle. A strut was used to increase the contraction ratio and to inject fuels, as well as a mixing enhancement device. Several wall cavities were also employed for flame-holding. In order to shorten the ignition delay time of the kerosene fuel, a little amount of hydrogen was used as a pilot flame. The pressure along the combustor has an evident raise after ignition occurred. Consequently thrust was observed during the fuel-on period. However, the thrust was still less than the drag of the scramjet model. For this reason, the drag variation produced by different strut and cavities was tested. Typical results showed that the cavities do not influence the drag so much, but the length of the strut does.