196,276 research outputs found
Optimal Paths and Domain-walls In the Strong Disorder Limit
No full textAn optimization problem that may be cast in the context of domain walls in ferromagnets and spin glasses, lattice animals, and percolation is described. Numerical calculations in two and three dimensions show that a new universality class is obtained. In the strong disorder limit interfaces are not self-affine but fractal. Further, the nontrivial ground state of frustrated spin glasses is straightforwardly obtained in this limit
Interfacial geometry and overhanging configurations
No full textSimple optimization and growth models are studied numerically and also using analytic arguments to assess the importance of overhanging configurations of the interface and differences between quenched and annealed disorder
Monte-carlo Mean-field Theory
No full textA Comment on the Letter by R. R. Netz and A. N. Berker, Phys. Rev. Lett. 66, 377 (1991)
Invasion percolation and Eden growth: Geometry and universality
No full textThe mapping of optimal paths in the strong disorder limit to the strands of invasion percolation clusters is shown to lead to a new universal property of these clusters. We suggest that the corresponding strands arising in the annealed Eden growth process are in the same universality class as directed polymers in weak quenched disorder with an upper critical dimension less than or equal to 6
Lattice tube model of proteins
No full textWe present a new lattice model for proteins that incorporates a tubelike anisotropy by introducing a preference for mutually parallel alignments in the conformations. The model is demonstrated to capture many aspects of real proteins
Phase-diagrams of Random-field Ising Systems
No full textWe show that the random-field Ising model may be tuned to obtain two distinct scenarios of phase diagram topology. Explicit evidence for this is presented in a numerically exact analysis in three dimensions and on a Bethe lattice, which allows us to investigate the effects of temperature, coordination number, and asymmetry in the field distribution
Spin-flip Avalanches and Dynamics of 1st-order Phase-transitions
No full textA Comment on the Letter by J. P. Sethna et al., Phys. Rev. Lett. 70, 3347 (1993)
Nematic-isotropic Transition In Porous-media
No full textMotivated by recent experiments on the nematic-isotropic transition in porous media, two simplified models are proposed and studied using mean field theory and Monte Carlo simulations. The results are in qualitative accord with those found in the experiments
Assembly of protein tertiary structures from secondary structures using optimized potentials
No full textWe present a simulated annealing-based method for the prediction of the tertiary structures of proteins given knowledge of the secondary structure associated with each amino acid in the sequence. The backbone is represented in a detailed fashion whereas the sidechains and pair-wise interactions are modeled in a simplified way, following the LINUS model of Srinivasan and Rose. A perceptron-based technique is used to optimize the interaction potentials for a training set of three proteins. For these proteins, the procedure is able to reproduce the tertiary structures to below 3 Angstrom in root mean square deviation (rmsd) from the PDB targets. We present the results of tests on twelve other proteins. For half of these, the lowest energy decoy has a rmsd from the native state below 6 Angstrom and, in 9 out of 12 cases, we obtain decoys whose rmsd from the native states are also well below 5 Angstrom
Prediction of protein secondary structures from conformational biases
No full textWe use LINUS (the "Local Independently Nucleated Units of Structure"), a procedure developed by Srinivasan and Rose, to provide a physical interpretation of and. predict the secondary structures of proteins. The secondary structure type at a given site is identified by the largest conformational bias during short simulations. We examine the rate of successful prediction as a function of temperature and the interaction window. At high temperatures, there is a large propensity for the establishment of beta-strands whereas a-helices appear only when the temperature is lower than a certain threshold value. It is found that there exists an optimal temperature at which the correct secondary structures are predicted most accurately. We find that this temperature is close to the peak temperature of the specific heat. Changing the interaction window or carrying out longer simulations approaching equilibrium lead to little change in the optimal success rate. Our findings are in accord with the observation by Srinivasan and Rose that the secondary structures are mainly determined by local interactions and appear in the early stage of folding
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