Relationship between prion propensity and the rates of individual molecular steps of fibril assembly.

Peptides and proteins possess an inherent propensity to self-assemble into generic fibrillar nanostructures known as amyloid fibrils, some of which are involved in medical conditions such as Alzheimer disease. In certain cases, such structures can self-propagate in living systems as prions and transmit characteristic traits to the host organism. The mechanisms that allow certain amyloid species but not others to function as prions are not fully understood. Much progress in understanding the prion phenomenon has been achieved through the study of prions in yeast as this system has proved to be experimentally highly tractable; but quantitative understanding of the biophysics and kinetics of the assembly process has remained challenging. Here, we explore the assembly of two closely related homologues of the Ure2p protein from Saccharomyces cerevisiae and Saccharomyces paradoxus, and by using a combination of kinetic theory with solution and biosensor assays, we are able to compare the rates of the individual microscopic steps of prion fibril assembly. We find that for these proteins the fragmentation rate is encoded in the structure of the seed fibrils, whereas the elongation rate is principally determined by the nature of the soluble precursor protein. Our results further reveal that fibrils that elongate faster but fracture less frequently can lose their ability to propagate as prions. These findings illuminate the connections between the in vitro aggregation of proteins and the in vivo proliferation of prions, and provide a framework for the quantitative understanding of the parameters governing the behavior of amyloid fibrils in normal and aberrant biological pathways.

A Molecular Dynamics Simulation: the Effect of Finite Size on the Thermal Conductivity in a Single Crystal Silicon

Non-equilibrium molecular dynamics (NEMD) simulations are performed to calculate thermal conductivity. The environment-dependent interatomic potential (EDIP) potential on crystal silicon is adopted as a model system. The issues are related to nonlinear response, local thermal equilibrium and statistical averaging. The simulation results by non-equilibrium molecular dynamics show that the calculated thermal conductivity decreases almost linearly as the film thickness reduced at the nanometre scale. The effect of size on the thermal conductivity is also obtained by a theoretic analysis of the kinetic theory and formulas of the heat capacity. The analysis reveals that the contributions of phonon mean free path (MFP) and phonon number in a finite cell to thermal conductivity are very important.

高温气体反应流中的物理力学问题

从气体动理论(kinetic theory of gases)的原理出发导出了非平衡条件下高温气体反应流基本守恒方程组.讨论了出现在方程组中的各种通量在非平衡条件下的意义,给出了从微观出发的输运系数表达式.介绍各种物理动理论与化学动理论过程的微观理论,讨论了在非平衡条件下现有理论的困难.

Information Preservation (IP) Method in Simulation

This paper reviews firstly methods for treating low speed rarefied gas flows: the linearised Boltzmann equation, the Lattice Boltzmann method (LBM), the Navier-Stokes equation plus slip boundary conditions and the DSMC method, and discusses the difficulties in simulating low speed transitional MEMS flows, especially the internal flows. In particular, the present version of the LBM is shown unfeasible for simulation of MEMS flow in transitional regime. The information preservation (IP) method overcomes the difficulty of the statistical simulation caused by the small information to noise ratio for low speed flows by preserving the average information of the enormous number of molecules a simulated molecule represents. A kind of validation of the method is given in this paper. The specificities of the internal flows in MEMS, i.e. the low speed and the large length to width ratio, result in the problem of elliptic nature of the necessity to regulate the inlet and outlet boundary conditions that influence each other. Through the example of the IP calculation of the microchannel (thousands long) flow it is shown that the adoption of the conservative scheme of the mass conservation equation and the super relaxation method resolves this problem successfully. With employment of the same measures the IP method solves the thin film air bearing problem in transitional regime for authentic hard disc write/read head length ( ) and provides pressure distribution in full agreement with the generalized Reynolds equation, while before this the DSMC check of the validity of the Reynolds equation was done only for short ( ) drive head. The author suggests degenerate the Reynolds equation to solve the microchannel flow problem in transitional regime, thus provides a means with merit of strict kinetic theory for testing various methods intending to treat the internal MEMS flows.

Information preservation (IP) method in simulation of internal rarefied gas flows in MEMS

This paper reviews firstly methods for treating low speed rarefied gas flows: the linearised Boltzmann equation, the Lattice Boltzmann method (LBM), the Navier-Stokes equation plus slip boundary conditions and the DSMC method, and discusses the difficulties in simulating low speed transitional MEMS flows, especially the internal flows. In particular, the present version of the LBM is shown unfeasible for simulation of MEMS flow in transitional regime. The information preservation (IP) method overcomes the difficulty of the statistical simulation caused by the small information to noise ratio for low speed flows by preserving the average information of the enormous number of molecules a simulated molecule represents. A kind of validation of the method is given in this paper. The specificities of the internal flows in MEMS, i.e. the low speed and the large length to width ratio, result in the problem of elliptic nature of the necessity to regulate the inlet and outlet boundary conditions that influence each other. Through the example of the IP calculation of the microchannel (thousands m ? long) flow it is shown that the adoption of the conservative scheme of the mass conservation equation and the super relaxation method resolves this problem successfully. With employment of the same measures the IP method solves the thin film air bearing problem in transitional regime for authentic hard disc write/read head length ( 1000 L m ? = ) and provides pressure distribution in full agreement with the generalized Reynolds equation, while before this the DSMC check of the validity of the Reynolds equation was done only for short ( 5 L m ? = ) drive head. The author suggests degenerate the Reynolds equation to solve the microchannel flow problem in transitional regime, thus provides a means with merit of strict kinetic theory for testing various methods intending to treat the internal MEMS flows.

Rarefied gas dynamics: fundamentals, simulations and micro flows

Dislocation nucleation governed softening and maximum strength in nano-twinned metals

In conventional metals, there is plenty of space for dislocations-line defects whose motion results in permanent material deformation-to multiply, so that the metal strengths are controlled by dislocation interactions with grain boundaries(1,2) and other obstacles(3,4). For nano-structured materials, in contrast, dislocation multiplication is severely confined by the nanometre-scale geometries so that continued plasticity can be expected to be source-controlled. Nano-grained polycrystalline materials were found to be strong but brittle(5-9), because both nucleation and motion of dislocations are effectively suppressed by the nanoscale crystallites. Here we report a dislocation-nucleation-controlled mechanism in nano-twinned metals(10,11) in which there are plenty of dislocation nucleation sites but dislocation motion is not confined. We show that dislocation nucleation governs the strength of such materials, resulting in their softening below a critical twin thickness. Large-scale molecular dynamics simulations and a kinetic theory of dislocation nucleation in nano-twinned metals show that there exists a transition in deformation mechanism, occurring at a critical twin-boundary spacing for which strength is maximized. At this point, the classical Hall-Petch type of strengthening due to dislocation pile-up and cutting through twin planes switches to a dislocation-nucleation-controlled softening mechanism with twin-boundary migration resulting from nucleation and motion of partial dislocations parallel to the twin planes. Most previous studies(12,13) did not consider a sufficient range of twin thickness and therefore missed this strength-softening regime. The simulations indicate that the critical twin-boundary spacing for the onset of softening in nano-twinned copper and the maximum strength depend on the grain size: the smaller the grain size, the smaller the critical twin-boundary spacing, and the higher the maximum strength of the material.

Miscibility and crystallization of poly(beta-hydroxybutyrate)/poly(vinyl acetate-co-vinyl alcohol) blends

Poly(vinyl acetate-co-vinyl alcohol) copolymers (P(VAc-co-VA)) were synthesized by hydrolysis-alcoholysis of PVAc. The miscibility, crystallization, and morphology of poly(P-hydroxybutyrate) (PHB) and P(VAc-co-VA) blends were studied by differential scanning calorimetry, optical microscopy (OM), and SAXS. It is found that the P(VAc-co-VA)s with vinyl alcohol content of 9, 15, and 22 mol % will form a miscible phase with the amorphous part of PHB in the solution-cast samples. The melting-quenched samples of PHB/P(VAc-co-VA) blends with different vinyl alcohol content show different phase behavior. PHB and P(VAc-co-VA9) with low vinyl alcohol content (9% mel) will form a miscible blend in the melt state. PHB and P(VAc-co-VA15) with 15 mol % vinyl alcohol will not form miscible blends while PHB/P(VAc-co-VA15) blend with 20/80 composition will form a partially miscible blend in the melt state. PHB and P(VAc-co-VA22) with 22 mol % vinyl alcohol are not miscible in the whole composition range. The single glass transition temperature of the blends within the whole composition range suggests that PHB and P(VAc-co-VA9) are totally miscible in the melt. The crystallization kinetics was studied from the whole crystallization and spherulite growth for the miscible blends. The equilibrium melting point of PHB in the PHB/P(VAc-co-VA9) blends, which was obtained from DSC results using the Hoffman-Weeks equation, decreases with the increase in P(VAc-co-VA9) content. The negative value of the interaction parameter determined from the equilibrium melting point depression supports the miscibility between the components. The kinetics of spherulitic crystallization of PHB in the blends was analyzed according to nucleation theory in the temperature range studied in this work. The best fit of the data to the kinetic theory is obtained by employing WLF parameters and the equilibrium melting points obtained by DSC. The addition of P(VAc-co-VA) did not affect the crystalline structure of PHB, as shown by the WAXD results. The long periods of blends obtained from SAXS increase with the increase in P(VAc-co-VA) content. It indicates that the amorphous P(VAc-co-VA) was rejected to interlamellar phase corporating with the amorphous part of PHB.

Biodegradation and biosorption of acid anthraquinone dye

The acid anthraquinone dye Tectilon Blue (TB4R) is a major coloured component from the aqueous effluent of a carpet printing plant in Northern Ireland. The aerobic biodegradation of TB4R has been investigated experimentally in batch systems, using three strains of bacteria, namely, Bacillus gordonae (NCIMB 12553), Bacillus benzeovorans (NCIMB 12555) and Pseudomonas putida (NCIMB 9776). All three strains successfully decolourised the dye, and results were correlated using Michaelis-Menten kinetic theory. A recalculation of the reaction rate constants, to account for biosorption, gave an accurate simulation of the colour removal over a 24-h period. Up to 19% of the decolorisation was found to be caused by biosorption of the dye onto the biomass, with the majority of the decolorisation caused by utilisation of the dye by the bacteria. The reaction rate was found to be intermediate between zero and first order at dye concentrations of 200-1000 mg/l. (C) 2000 Elsevier Science Ltd. All rights reserved.

Propagation regimes for an electromagnetic beam in magnetized plasma

The propagation of a Gaussian electromagnetic beam along the direction of magnetic field in a plasma is investigated. The extraordinary (E-x+iE(y)) mode is explicitly considered in the analysis, although the results for the ordinary mode can be obtained upon replacing the electron cyclotron frequency omega(c) by -omega(c). The propagating beam electric field is coupled to the surrounding plasma via the dielectric tensor, taking into account the existence of a stationary magnetic field. Both collisionless and collisional cases are considered, separately. Adopting an established methodological framework for beam propagation in unmagnetized plasmas, we extend to magnetized plasmas by considering the beam profile for points below the critical curve in the beam-power versus beam-width plane, and by employing a relationship among electron concentration and electron temperature, provided by kinetic theory (rather than phenomenology). It is shown that, for points lying above the critical curve in the beam-power versus beam-width plane, the beam experiences oscillatory convergence (self-focusing), while for points between the critical curve and divider curve, the beam undergoes oscillatory divergence and for points on and below the divider curve the beam suffers a steady divergence. For typical values of parameters, numerical results are presented and discussed. (C) 2008 American Institute of Physics.

Hybridization of a class of "second order" models of traffic flow

Despite the simultaneous progress of traffic modelling both on the macroscopic and microscopic front, recent works [E. Bourrel, J.B. Lessort, Mixing micro and macro representation of traffic flow: a hybrid model based on the LWR theory, Transport. Res. Rec. 1852 (2003) 193–200; D. Helbing, M. Treiber, Critical discussion of “synchronized flow”, Coop. Transport. Dyn. 1 (2002) 2.1–2.24; A. Hennecke, M. Treiber, D. Helbing, Macroscopic simulations of open systems and micro–macro link, in: D. Helbing, H.J. Herrmann, M. Schreckenberg, D.E. Wolf (Eds.), Traffic and Granular Flow ’99, Springer, Berlin, 2000, pp. 383–388] highlighted that one of the most promising way to simulate efficiently traffic flow on large road networks is a clever combination of both traffic representations: the hybrid modelling. Our focus in this paper is to propose two hybrid models for which the macroscopic (resp. mesoscopic) part is based on a class of second order model [A. Aw, M. Rascle, Resurection of second order models of traffic flow?, SIAM J. Appl. Math. 60 (2000) 916–938] whereas the microscopic part is a Follow-the Leader type model [D.C. Gazis, R. Herman, R.W. Rothery, Nonlinear follow-the-leader models of traffic flow, Oper. Res. 9 (1961) 545–567; R. Herman, I. Prigogine, Kinetic Theory of Vehicular Traffic, American Elsevier, New York, 1971]. For the first hybrid model, we define precisely the translation of boundary conditions at interfaces and for the second one we explain the synchronization processes. Furthermore, through some numerical simulations we show that the waves propagation is not disturbed and the mass is accurately conserved when passing from one traffic representation to another.

Electron localization function at the correlated level

The electron localization function (ELF) has been proven so far a valuable tool to determine the location of electron pairs. Because of that, the ELF has been widely used to understand the nature of the chemical bonding and to discuss the mechanism of chemical reactions. Up to now, most applications of the ELF have been performed with monodeterminantal methods and only few attempts to calculate this function for correlated wave functions have been carried out. Here, a formulation of ELF valid for mono- and multiconfigurational wave functions is given and compared with previous recently reported approaches. The method described does not require the use of the homogeneous electron gas to define the ELF, at variance with the ELF definition given by Becke. The effect of the electron correlation in the ELF, introduced by means of configuration interaction with singles and doubles calculations, is discussed in the light of the results derived from a set of atomic and molecular systems

Conservative force fields in non-Gaussian statistics

In this Letter, we determine the kappa-distribution function for a gas in the presence of an external field of force described by a potential U(r). In the case of a dilute gas, we show that the kappa-power law distribution including the potential energy factor term can rigorously be deduced in the framework of kinetic theory with basis on the Vlasov equation. Such a result is significant as a preliminary to the discussion on the role of long range interactions in the Kaniadakis thermostatistics and the underlying kinetic theory. (C) 2008 Elsevier B.V. All rights reserved.

CONSTRAINING THE NONEXTENSIVE MASS FUNCTION OF HALOS FROM BAO, CMB AND X-RAY DATA

Clusters of galaxies are the most impressive gravitationally-bound systems in the universe, and their abundance (the cluster mass function) is an important statistic to probe the matter density parameter (Omega(m)) and the amplitude of density fluctuations (sigma(8)). The cluster mass function is usually described in terms of the Press-Schecther (PS) formalism where the primordial density fluctuations are assumed to be a Gaussian random field. In previous works we have proposed a non-Gaussian analytical extension of the PS approach with basis on the q-power law distribution (PL) of the nonextensive kinetic theory. In this paper, by applying the PL distribution to fit the observational mass function data from X-ray highest flux-limited sample (HIFLUGCS), we find a strong degeneracy among the cosmic parameters, sigma(8), Omega(m) and the q parameter from the PL distribution. A joint analysis involving recent observations from baryon acoustic oscillation (BAO) peak and Cosmic Microwave Background (CMB) shift parameter is carried out in order to break these degeneracy and better constrain the physically relevant parameters. The present results suggest that the next generation of cluster surveys will be able to probe the quantities of cosmological interest (sigma(8), Omega(m)) and the underlying cluster physics quantified by the q-parameter.