Chirality and Protein Folding

There are several simple criteria of folding to a native state in model proteins. One of them involves crossing of a threshold value of the RMSD distance away from the native state. Another checks whether all native contacts are established, i.e. whether the interacting amino acids come closer than some characteristic distance. We use Go-like models of proteins and show that such simple criteria may prompt one to declare folding even though fragments of the resulting conformations have a wrong sense of chirality. We propose that a better condition of folding should augment the simple criteria with the requirement that most of the local values of the chirality should be nearly native. The kinetic discrepancy between the simple and compound criteria can be substantially reduced in the Go-like models by providing the Hamiltonian with a term which favors native values of the local chirality. We study the effects of this term as a function of its amplitude and compare it to other models such as with the side groups and with the angle-dependent potentials.Comment: To be published in a special issue of J. Phys.: Cond. Mat. (Bedlewo Workshop

Delineation of the Native Basin in Continuum Models of Proteins

We propose two approaches for determining the native basins in off-lattice models of proteins. The first of them is based on exploring the saddle points on selected trajectories emerging from the native state. In the second approach, the basin size can be determined by monitoring random distortions in the shape of the protein around the native state. Both techniques yield the similar results. As a byproduct, a simple method to determine the folding temperature is obtained.Comment: REVTeX, 6 pages, 5 EPS figure

Scaling of folding properties in simple models of proteins

Scaling of folding properties of proteins is studied in a toy system -- the lattice Go model with various two- and three- dimensional geometries of the maximally compact native states. Characteristic folding times grow as power laws with the system size. The corresponding exponents are not universal. Scaling of the thermodynamic stability also indicates size-related deterioration of the folding properties.Comment: REVTeX, 4 pages, 4 EPS figures, PRL (in press

Folding in two-dimenensional off-lattice models of proteins

Model off-lattice sequences in two dimensions are constructed so that their native states are close to an on-lattice target. The Hamiltonian involves the Lennard-Jones and harmonic interactions. The native states of these sequences are determined with a high degree of certainty through Monte Carlo processes. The sequences are characterized thermodynamically and kinetically. It is shown that the rank-ordering-based scheme of the assignment of contact energies typically fails in off-lattice models even though it generates high stability of on-lattice sequences. Similar to the on-lattice case, Go-like modeling, in which the interaction potentials are restricted to the native contacts in a target shape, gives rise to good folding properties. Involving other contacts deteriorates these properties.Comment: REVTeX, 9 pages, 8 EPS figure

Conductance fluctuations in the presence of spin scattering

Electron transport through disordered systems that include spin scatterers is studied numerically. We consider three kinds of magnetic impurities: the Ising, the XY and the Heisenberg. By extending the transfer matrix method to include the spin degree of freedom, the two terminal conductance is calculated. The variance of conductance is halved as the number of spin components of the magnetic impurities increases. Application of the Zeeman field in the lead causes a further halving of the variance under certain conditions.Comment: to be published in Phys. Rev.

Influence of Hydrodynamic Interactions on Mechanical Unfolding of Proteins

We incorporate hydrodynamic interactions in a structure-based model of ubiquitin and demonstrate that the hydrodynamic coupling may reduce the peak force when stretching the protein at constant speed, especially at larger speeds. Hydrodynamic interactions are also shown to facilitate unfolding at constant force and inhibit stretching by fluid flows.Comment: to be published in Journal of Physics: Condensed Matte

Vortex glass transition and thermal creep in niobium films

The evolution of the vortex glass (VG) phase transition and vortex creep with decreasing film thickness is studied in ultrathin, polycrystalline niobium films, with thickness in the range 7.4 nm to 44 nm, using current-voltage characteristics measurements in perpendicular magnetic field. Standard methods, including scaling laws, allow to identify VG transition in the thickest film, while in thinner films creep produces large uncertainty in the putative VG transition temperature and scaling exponents. Using strong pinning theory we perform analysis of the creep, and extract the dependence of the activation energy for vortex pinning on temperature, magnetic field, and film thickness. This analysis provides more information on vortex dynamics than the standard evaluation of critical current density. The results reveal two distinct regimes of pinning, which we propose to identify with $\delta l$ or $\delta T_c$-types of pinning (due to spacial fluctuation of mean free path $l$ or spacial fluctuation of superconducting transition temperature $T_c$, respectively). In the thickest film $\delta l$ pinning is observed, but with the decrease of film thickness the second pinning regime appears, and becomes dominant in the thinnest film. We link these pinning regimes with the structural disorder due to grain boundaries, which produce charge carrier scattering in the thickest film, but with decreasing film thickness gradually evolve into amorphous inclusions, producing fluctuations in the $T_c$

Disorder-induced critical behavior in driven diffusive systems

Using dynamic renormalization group we study the transport in driven diffusive systems in the presence of quenched random drift velocity with long-range correlations along the transport direction. In dimensions $d\mathopen< 4$ we find fixed points representing novel universality classes of disorder-dominated self-organized criticality, and a continuous phase transition at a critical variance of disorder. Numerical values of the scaling exponents characterizing the distributions of relaxation clusters are in good agreement with the exponents measured in natural river networks

Impurity and strain effects on the magnetotransport of La1.85Sr0.15Cu(1-y)Zn(y)O4 films

The influence of zinc doping and strain related effects on the normal state transport properties(the resistivity, the Hall angle and the orbital magneto- resistance(OMR) is studied in a series of La1.85Sr0.15Cu(1-y)Zn(y)O4 films with values of y between 0 and 0.12 and various degrees of strain induced by the mismatch between the films and the substrate. The zinc doping affects only the constant term in the temperature dependence of cotangent theta but the strain affects both the slope and the constant term, while their ratio remains constant.OMR is decreased by zinc doping but is unaffected by strain. The ratio delta rho/(rho*tan^2 theta) is T-independent but decreases with impurity doping. These results put strong constraints on theories of the normal state of high- temperature superconductors