Diffusive model of protein folding dynamics with Kramers turnover in rate

We study the folding kinetics of a three-helix bundle protein using a coarse polymer model. The folding dynamics can be accurately represented by one-dimensional diffusion along a reaction coordinate selected to capture the transition state. By varying the solvent friction, we show that position-dependent diffusion coefficients are determined by microscopic transitions on a rough energy landscape. A maximum in the folding rate at intermediate friction is explained by "Kramers turnover" in these microscopic dynamics that modulates the rate via the diffusion coefficient; overall folding remains diffusive even close to zero friction. For water friction, we find that the "attempt frequency" (or "speed limit") in a Kramers model of folding is about 2 micros-1, with an activation barrier of about 2kBT, and a folding transition path duration of approximately equal to 100 ns, 2 orders of magnitude less than the folding time of approximately equal to 10 micros.     

Identification and characterization of potential shear transformation zones in metallic glasses

The stability of local atomic configurations in a Ni-Zr metallic glass is studied by molecular dynamics. It is shown that individual atom displacements induce irreversible atomic rearrangements under different glass relaxation, temperature, and strain conditions. The number of regions with an unstable topology depends on the glass relaxation degree. Their time evolution is governed by thermal activation, the activation energy decreasing with elastic strain. It is also shown that unstable regions are located in correspondence of shear transformation zones operating under plastic deformation.     

金属玻璃流变的扩展弹性模型

玻璃-液体转变现象,简称玻璃转变,被诺贝尔物理学奖获得者安德森教授评为最深奥与重要的凝聚态物理问题之一.金属玻璃作为典型的非晶态物质,具有与液体相似的无序原子结构,因此又称为冻结了的液态金属,是研究玻璃转变问题的理想模型材料.当加热至玻璃转变温度,或者加载到力学屈服点附近时,金属玻璃将会发生流动.由于热或应力导致的流动现象对金属玻璃的应用具有重要意义.本文简要回顾了金属玻璃流变现象,综述了流变扩展弹性模型的研究进展和未来发展趋势.     

Slow granular flows: The dominant role of tiny fluctuations

What mechanism governs slow flows of granular media? Microscopically, the grains experience enduring frictional contacts in these flows. However, a straightforward translation to a macroscopic frictional rheology, where the shear stresses are proportional to the normal stresses with a rate-independent friction coefficient, fails to capture important aspects of slow granular flows. There is now overwhelming evidence that agitations, tiny fluctuations of the grain positions, associated with large fluctuation of their contact forces, play a central role for slow granular flows. These agitations are generated in flowing regions, but travel deep inside the quiescent zones, and lead to a nonlocal rheology.     

Importance of shear in the bcc-to-hcp transformation in iron

Iron shows a pressure-induced martensitic phase transformation from the ground state ferromagnetic bcc phase to a nonmagnetic hcp phase at approximately 13 GPa. The exact transformation pressure (TP) and pathway are not known. Here we present a multiscale model containing a quantum-mechanics-based multiwell energy function accounting for the bcc and hcp phases of Fe and a construction of kinematically compatible and equilibrated mixed phases. This model suggests that shear stresses have a significant influence on the bcc<-->hcp transformation. In particular, the presence of modest shear accounts for the scatter in measured TPs. The formation of mixed phases also provides an explanation for the observed hysteresis in TP.     

Rheology of steady-state draining foams

We developed the foam drainage rheology technique in order to perform rheological measurements of aqueous foams at a set liquid fraction epsilon and fixed bubble radius R without the usual difficulties associated with fluid drainage and bubble coarsening. The shear stress exhibits a power-law dependence on strain-rate, tau approximately gamma[over]n where n approximately 0.2. The stress exhibits an inverse dependence on liquid content, tau approximately (1+h'epsilon)(-1), where h'=theta(10) exhibits a diminishing logarithmic trend with gamma[over]. We propose a model based upon film shearing as the dominant source of viscous dissipation.     

Critical radius of zirconia inclusions in transformation toughening of ceramics

The paper presents a transformation toughening model of ceramics taking into account an energy barrier the overcoming of which results in phase transformation of zirconia inclusions. Methods based on experimental data analysis are proposed for estimating the energy barrier. The size range of zirconia inclusions in Al₂O₃ and WC matrices is defined depending on the energy barrier value, working temperature, and external load. It is shown that the introduction of an energy barrier enables an adequate estimation of the size range of inclusions at which transformation toughening occurs in ceramics. The elastic interaction of inclusions is shown to cause a decrease in their critical radii with the growing volume density, which agrees with experimental data.     

On the problem of activation energy of thermal decay of color centers and similar non-stationary processes

Thermally stimulated process is discussed as a superposition of components with equal activation energy and a distribution of frequency factors. Changes of concentrations of individual components of this process proceed according to first order rate law. A relationship between Laplace transformation of the distribution of frequency factors and the law governing the resulting changes of the concentration is studied. An application on the thermal decay of F-centers indicates that actual activation energy tends to be greater than the energy resulting e.g. from Urbach analysis. Experimental procedures are proposed allowing the actual activation energy and the distribution of frequency factors to be determined.     

Experimental study of different modes of block sliding along interface. Part 2. Field experiments and phenomenological model of the phenomenon

The paper reports the results of field experiments on studying different modes of gravitational sliding of a block on the natural fault surface. Various materials were used as interface filler to model the whole range of deformation events that can be arbitrarily divided into three groups: accelerated creep, slow slip, and dynamic slip. The experiments show that the type of modeled deformation events is defined by both structural parameters of contact between blocks and material composition of the contact filler.Foundations for a new geomechanical model of occurrence of different-type dynamic events were developed. The model is based on the idea that “contact spots” form subnormally to the crack edges during shear deformation; the “spots” are clusters of force mesostructures whose evolution governs the deformation mode. The spatial configuration of “contact spots” remains unchanged during the entire “loading-slip” cycle but changes after the dynamic event occurrence. The destroyed force mesostructures can be replaced by similar structures under intergranular interaction forces when the external influence is fully compensated. Unless “contact spots” are incompletely destroyed, the deformation process dynamics is defined by their rheology. The migration of “contact spots” during deformation of a crack filled with heterogeneous material causes changes in deformation parameters and transformation of the mode itself due to changing rheology of local contact areas between blocks.It is found by fractal analysis that in order for dynamic slip to occur, spatially structured “contact spots” characterized by low fractal dimension must be formed; slow slip events can exist only in a certain parametric domain called the “dome of slow events”. It is found that the probability of slow slip occurrence is higher on fault regions characterized by maximum fractal dimension values: fault tips, fault branching and fault intersection zones.     

Baikal Ice Cover as a Representative Block Medium for Research in Lithospheric Geodynamics

The paper summarizes the results of long-term field research in the dynamics of the Baikal ice cover as a multiscale block medium similar to the lithosphere in structure, rheology, and seismotectonic features. The analysis covers data on deformation, seismicity, and contact interaction modes as well as on meteorological factors responsible for dynamic fracture of ice plates and strong ice shocks with earthquake-like vibrations. Similarity between seismic features in ice interface zones and zones of tectonic subduction, collision, and shear is discussed. Reasoning from dynamic analogies and similarities of destruction processes in the ice and lithosphere, the research data can help solving fundamental and applied problems, particularly those of earthquake prediction and assessment of contact interactions between lithospheric plates in fault zones.     

Thermal quenching of luminescence in erbium doped semiconductors

The nature of the temperature dependence of luminescence intensity from Er⁺ ions in GaInAsP, Si, InP, GaAs, AlGaAs, ZnTe, as observed by Favennecet al [1] has been examined in terms of a double exponential model. The smaller activation energy is found to be 58–100 meV, characteristic of a localized energy barrier at the Er⁺ centre while the higher activation energy is approximately 0.8E _g attributed to an Auger non-radiative process of carrier excitation into bands. This model has been found to describe the observed temperature dependences with reasonably good agreement.     

Rapid and localized electron internal-transport-barrier formation during shear inversion in fully noninductive TCV discharges

Clear evidence is reported for the first time of a rapid localized reduction of core electron energy diffusivity during the formation of an electron internal-transport barrier. The transition occurs rapidly (approximately = 3 ms), during a slow (approximately = 200 ms) self-inductive evolution of the magnetic shear. This crucial observation, and the correlation of the transition with the time and location of the magnetic shear reversal, lend support to models attributing the reduced transport to the local properties of a zero-shear region, in contrast to models predicting a gradual reduction due to a weak or negative shear.     

Simultaneous attainment of high electron and ion temperatures in discharges with internal transport barriers in ASDEX upgrade

Internal transport barriers have been demonstrated to exist also under conditions with T(e) approximately T(i) approximately 10 keV and predominant electron heating of the tokamak core region. Central electron cyclotron heating was added to neutral beam injection-heated ASDEX Upgrade discharges with a preexisting internal transport barrier, established through programmed current ramping leading to shear reversal. Compared to a reference internal transport barrier discharge without electron cyclotron resonance heating, the electron heat conductivity in the barrier region was found not to increase, in spite of a fivefold increase in electron heat flux, and also angular momentum and ion energy transport did not deteriorate.     

Modelling of dislocation-induced martensitic transformation in anisotropic crystals

The structural transformation caused by dislocation-induced heterogeneous nucleation in the fcc?→?bcc martensitic transformation in elastically anisotropic crystals is investigated by using the phase field microelasticity model. The three-dimensional microstructure of the dislocation-induced martensitic embryos is obtained. It is found that the embryos are not single-domain particles as is usually assumed but rather a complex self-organized assemblage of stress-accommodating twin-related microdomains. Sessile metastable martensitic embryos around the dislocation loops form in the prototype Fe–Ni alloy system above the temperatures of the martensitic transformation. A possibility that the presence of these pre-existing embryos could be responsible, at least, for a part of the elastic modulus softening with the temperature decrease observed in many martensitic systems is discussed. The effects of elastic anisotropy, the “chemical” energy barrier and structural anisotropy of the Landau free energy on the formation and growth of martensitic embryos are investigated. The assumptions of elastic isotropy and a choice of the anisotropic term in Landau polynomial do not significantly affect the microstructure of martensitic embryos but may appreciably change the undercooling that is necessary to eliminate the total nucleation barrier and start the athermal martensitic transformation.     

Cross-correlation tomography: measuring dark energy evolution with weak lensing

A cross-correlation technique of lensing tomography is developed to probe dark energy in the Universe. The variation of weak shear with redshift around foreground galaxies depends only on the angular distances and is robust to the dominant systematic error in lensing. We estimate the margin-alized accuracies that deep lensing surveys with photometric redshifts can provide on the dark energy density Omega(de), the equation of state parameter w, and its evolution w('): sigma(w) approximately equal 0.01f(-1/2)(sky) and sigma(w(')) approximately equal 0.03f(-1/2)(sky), where a prior of sigma(Omega(de))=0.03 is assumed in the marginalization.     

The Born-model and the effects of hydrostatic and non-hydrostatic stresses on rubidium halide structural phase transitions

An analytic Born-model, with the same set of repulsive parameters for both phases in each salt, has been used to calculate the properties of the NaCl-CaCl structural phase transformation in three rubidium halides. The treatment required a careful evaluation of the three repulsive parameters by comparison with equilibrium conditions in both phases and measured bulk moduli, and involved a self consistent analysis which takes into account the experimental uncertainties in reported values of CsCl-phase lattice parameters. Calculated values for the equilibrium transition pressure, lattice parameters and lattice energies are in satisfactory agreement with reported experimental results. The model has also been used to calculate the lattice energy continuously from the NaCl to the CsCl phases, as a function of both hydrostatic and non-hydrostatic stresses. These calculations give a semiquantitative estimate of an energy barrier between the two stable structures, which is consistent with reported measurements of elastic constant and hysteresis effects near the transition pressure. The calculated effects of a uniaxial stress are found to be as much as three times larger than those of a hydrostatic stress, and the effects of the uniaxial stress on the barrier height are found to be approximately the same as the effects on the equilibrium energy differences. Measurements of the effect of this uniaxial stress on the forward transition pressure of RbI were carried out and the measured variations were found to be in excellent agreement with the calculated change in equilibrium transition pressure—as expected from the energy barrier calculations.     

Cross-slip in face centred cubic metals: a general full stress-field dependent activation energy line-tension model

Cross-slip is a thermally activated process by which a screw dislocation changes its slip plane. Understanding and modelling the activation barrier of the cross-slip process as a free-energy barrier that depends on the stress conditions at the vicinity of the dislocation is crucial. In this work, we employ the line-tension model for the cross-slip of screw dislocations in face-centred cubic (FCC) metals in order to calculate the energy barrier when both Escaig stresses are applied on the primary and cross-slip planes and Schmid stress is applied on the cross-slip plane. We propose a closed-form expression for the activation energy for cross-slip in a large range of stresses, without any fitting parameters. The results of the proposed model are in good agreement with previous numerical results and atomistic simulations. We also show that, when Schmid stress is applied on the cross-slip plane, the energy barrier is decreased, and in particular, cross-slip can occur even when the Escaig stress in the primary plane is smaller than that on the cross-slip plane. The proposed closed-form expression for the activation energy can be easily implemented in dislocation dynamics simulations, owing to its simplicity and universality. This will allow cross-slip to be more accurately related to macroscopic plasticity.     

Age-dependent transient shear banding in soft glasses

We study numerically the formation of long-lived transient shear bands during shear startup within two models of soft glasses (a simple fluidity model and an adapted "soft glassy rheology" model). The degree and duration of banding depends strongly on the applied shear rate, and on sample age before shearing. In both models the ultimate steady flow state is homogeneous at all shear rates, consistent with the underlying constitutive curve being monotonic. However, particularly in the soft glassy rheology case, the transient bands can be extremely long lived. The banding instability is neither "purely viscous" nor "purely elastic" in origin, but is closely associated with stress overshoot in startup flow.     

Rheology of giant micelles

Giant micelles are elongated, polymer-like objects created by the self-assembly of amphiphilic molecules (such as detergents) in solution. Giant micelles are typically flexible, and can become highly entangled even at modest concentrations. The resulting viscoelastic solutions show fascinating flow behaviour (rheology) which we address theoretically in this article at two levels. First, we summarize advances in understanding linear viscoelastic spectra and steady-state nonlinear flows, based on microscopic constitutive models that combine the physics of polymer entanglement with the reversible kinetics of self-assembly. Such models were first introduced two decades ago, and since then have been shown to explain robustly several distinctive features of the rheology in the strongly entangled regime, including extreme shear thinning. We then turn to more complex rheological phenomena, particularly involving spatial heterogeneity, spontaneous oscillation, instability and chaos. Recent understanding of these complex flows is based largely on grossly simplified models which capture in outline just a few pertinent microscopic features, such as coupling between stresses and other order parameters such as concentration. The role of ‘structural memory’ (the dependence of structural parameters such as the micellar length distribution on the flow history) in explaining these highly nonlinear phenomena is addressed. Structural memory also plays an intriguing role in the little-understood shear thickening regime, which occurs in a concentration regime close to but below the onset of strong entanglement, and which is marked by a shear-induced transformation from an inviscid to a gelatinous state.