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

Coarse grained description of the protein folding

We consider two- and three-dimensional lattice models of proteins which were characterized previously. We coarse grain their folding dynamics by reducing it to transitions between effective states. We consider two methods of selection of the effective states. The first method is based on the steepest descent mapping of states to underlying local energy minima and the other involves an additional projection to maximally compact conformations. Both methods generate connectivity patterns that allow to distinguish between the good and bad folders. Connectivity graphs corresponding to the folding funnel have few loops and are thus tree-like. The Arrhenius law for the median folding time of a 16-monomer sequence is established and the corresponding barrier is related to easily identifiable kinetic trap states.Comment: REVTeX, 9 pages, 15 EPS figures, to appear in Phys. Rev.

Energy landscapes, supergraphs, and "folding funnels" in spin systems

Dynamical connectivity graphs, which describe dynamical transition rates between local energy minima of a system, can be displayed against the background of a disconnectivity graph which represents the energy landscape of the system. The resulting supergraph describes both dynamics and statics of the system in a unified coarse-grained sense. We give examples of the supergraphs for several two dimensional spin and protein-related systems. We demonstrate that disordered ferromagnets have supergraphs akin to those of model proteins whereas spin glasses behave like random sequences of aminoacids which fold badly.Comment: REVTeX, 9 pages, two-column, 13 EPS figures include

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

Localization and Interaction Effects in Strongly Underdoped La2-xSrxCuO4

The in-plane magnetoresistance (MR) in La2-xSrxCuO4 films with 0.03 < x < 0.05 has been studied in the temperature range 1.6 K to 100 K, and in magnetic fields up to 14 T, parallel and perpendicular to the CuO2 planes. The behavior of the MR is consistent with a predominant influence of interaction effects at high temperatures, switching gradually to a regime dominated by spin scattering at low T. Weak localization effects are absent. A positive orbital MR appears close to the boundary between the antiferromagnetic and the spin-glass phase, suggesting the onset of Maki-Thompson superconducting fluctuations deep inside the insulating phase.Comment: 4 pages, 3 figures, to appear in Phys. Rev. Letter

Boundary conditions at a fluid - solid interface

We study the boundary conditions at a fluid-solid interface using molecular dynamics simulations covering a broad range of fluid-solid interactions and fluid densities, and both simple and chain-molecule fluids. The slip length is shown to be independent of the type of flow, but rather is related to the fluid organization near the solid, as governed by the fluid-solid molecular interactions.Comment: REVtex, to appear in Physical Review Letter

Low-Temperature Excitations of Dilute Lattice Spin Glasses

A new approach to exploring low-temperature excitations in finite-dimensional lattice spin glasses is proposed. By focusing on bond-diluted lattices just above the percolation threshold, large system sizes $L$ can be obtained which lead to enhanced scaling regimes and more accurate exponents. Furthermore, this method in principle remains practical for any dimension, yielding exponents that so far have been elusive. This approach is demonstrated by determining the stiffness exponent for dimensions $d=3$, $d=6$ (the upper critical dimension), and $d=7$. Key is the application of an exact reduction algorithm, which eliminates a large fraction of spins, so that the reduced lattices never exceed $\sim10^3$ variables for sizes as large as L=30 in $d=3$, L=9 in $d=6$, or L=8 in $d=7$. Finite size scaling analysis gives $y_3=0.24(1)$ for $d=3$, significantly improving on previous work. The results for $d=6$ and $d=7$, $y_6=1.1(1)$ and $y_7=1.24(5)$, are entirely new and are compared with mean-field predictions made for d>=6.Comment: 7 pages, LaTex, 7 ps-figures included, added result for stiffness in d=7, as to appear in Europhysics Letters (see http://www.physics.emory.edu/faculty/boettcher/ for related information

Phase Transition in a Self-repairing Random Network

We consider a network, bonds of which are being sequentially removed; that is done at random, but conditioned on the system remaining connected (Self-Repairing Bond Percolation SRBP). This model is the simplest representative of a class of random systems for which forming of isolated clusters is forbidden. It qualitatively describes the process of fabrication of artificial porous materials and degradation of strained polymers. We find a phase transition at a finite concentration of bonds $p=p_c$, at which the backbone of the system vanishes; for all $p<p_c$ the network is a dense fractal.Comment: 4 pages, 4 figure

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