1,721,423 research outputs found
About Diffusion-processes In Disordered-systems
No full textDifferent diffusion processes can be defined on random networks like the infinite incipient clusters at percolation threshold. The long-time behaviour of two such processes is shown to be the same. In particular the mean-square displacements and the autocorrelation function scale with the same exponents in the two cases
Random-walk and the Ideal Chain Problem On Self-similar Structures
No full textRandom walks and ideal chains (equally weighted trajectories) on self-similar structures are shown to have, in specific examples, drastically different asymptotic behavior. In certain instances localization effects let the end-to-end distance of an ideal chain of length n grow like exp[αlogn)φ] (φ<1) or (logn)ψ for large n. The renormalization-group analysis and the fixed point, giving these behaviors, are of a new type. These results could be of experimental relevance for the migration properties of excitations on fractal structures in the presence of a trapping environment
Exemplars of proteins
No full textA unified framework for understanding proteins is presented, which provides links between the fields of protein science, polymer physics and the physics of liquid crystals
A variational approach to the localization transition of heteropolymers at interfaces
No full textA chain with random hydrophobic-hydrophilic charges is studied in the presence of an interface separating a polar from a non-polar solvent. Within a Gaussian variational approach in replica space, a transition is found, from a high-temperature region, where the chain is delocalized, to a low-temperature region, where the chain is localized at the interface. The transition temperature diverges as the neutrality of the chain is approached. Our results are in agreement with an Imry-Ma type argument by Garel et al. (Europhys. Lett., 8 (1989) 9). The problem of replica symmetry breaking is also addressed, and the replica-symmetric solution is found to be unstable
Phase-diagram of the Frustrated Gauge-invariant Ising-model
No full textThe phase diagram of the Z (2) gauge-invariant Ising model is studied at negative gauge coupling in three dimensions. Exact procedures are applied to establish the ground states and find, at nonzero temperatures, the minima of the local mean-field free energy. The resulting phase diagram exhibits one unfrustrated and two frustrated phases, in good agreement with Monte Carlo results. The interpretation of the various phases in terms of a gas of random surfaces with free edges is also discussed
Crumpled and Flat Regimes In A Random Surface Model
No full textA spherical like model of a D-dimensional random surface embedded in d-dimensional Euclidean space is studied in detail. The embedding weight depends on an attractive term between the nearest neighbours and on a repulsive one between some of the next to the nearest neighbours of the network. The repulsive term mimics an extrinsic curvature energy for surface configurations. Crumpled and flat regimes are found, and, if D less-than-or-equal-to 2, only the former survives in the thermodynamic limit. The model can be seen as the d --> infinity limit of a more realistic model where the 1/d corrections stabilize the flat regime in the thermodynamic limit at least for D = 2
Physics of proteins
No full textPeptides and proteins exhibit a common tendency to assemble into highly ordered fibrillar aggregates, whose formation proceeds in a nucleation-dependent manner that is often preceded by the formation of oligomeric assemblies. This process has received much attention because disordered oligomeric aggregates have been associated with neurodegenerative disorders such as Alzheimer's and Parkinson's disease. Here we describe a self-templated nucleation mechanism that determines the transition between the initial condensation of polypeptide chains into disordered assemblies and their reordering into fibrillar structures. The results that we present show that at the molecular level this transition is due to the ability of polypeptide chains to reorder within oligomers into fibrillar assemblies whose surfaces act as templates that stabilize the disordered assemblies
Knowledge-based scale for amino-acid membrane propensity
No full textIn this article, a membrane-propensity scale for amino acids is derived using only two ingredients: W a set of transmembrane helices segments from membrane protein crystal structures and (ii) the request that each component of the set has a free energy lower than that of a typical soluble protein sequence of the same length. Although the most widely used hydropathy scales satisfy this request, we use an optimization procedure that allows for extraction of an optimal scale, which correlates equally well with those scales. We show that, if the choice of the sequence database is accurate, significant knowledge-based scales, which are robust with respect to changes in the learning set, can be easily derived. The obtained scales can be used for transmembrane helices prediction. The predictive power of one of these scales is tested on membrane proteins, soluble proteins, and signal peptides databases, finding that its performances is comparable with those of the hydropathy scales
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