1,721,060 research outputs found
The Science of Life
No full textThe advent of powerful computers and algorithms
combined with new, powerful ways of thinking about
problems in statistical physics has created an unprecedented
opportunity for making significant breakthroughs
in a variety of interdisciplinary problems,
most notably in the life sciences
Chaos, Noise, and Synchronization - Reply
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Chaos, Noise, and Synchronization
No full textWe show that a pair of chaotic systems subjected to the same noise may undergo a transition at large enough noise amplitude and follow almost identical trajectories with complete insensitivity to initial conditions. An analytic argument is presented to show that a pair of generic systems in the same potential evolving to equilibrium through standard Langevin dynamics with the same noise collapse into the same trajectory at long times
Comment on the protein folds as platonic forms
No full textDenton et al. (2002) have presented compelling evidence that protein folds ought to be understood as arising from physical laws rather than natural selection. Furthermore, they suggest this could have “implications regarding the origin of proteins, the origin of life and the fundamental nature of organic form.” They do not, however, explain what the physical basis is for understanding the origin of protein folds. Here, we wish to address this key missing ingredient
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
Mean-field theory of sandpiles
No full textWe propose a mean-field theory of sandpiles with dissipation introduced in a clear and physical way. We obtain all exponents for our model by constructing a master equation and mapping the model into a branching process. Two of the exponents are found to depend on a parameter relating the rate of dissipation to that of the addition of sand grains to the system, whereas the others are universal
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
Scoring functions in protein folding and design
No full textWe present an analysis of the assumptions behind some of the most commonly used methods for evaluating the goodness of the fit between a sequence and a structure. Our studies on a lattice model show that methods based on statistical considerations are easy to use and can capture some of the features of protein-like sequences and their corresponding native states, but unfortunately are incapable of recognizing, with certainty, the native-like conformation of a sequence among a set of decoys. Meanwhile, an optimization method, entailing the determination of the parameters of an effective free energy of interaction, is much more reliable in recognizing the native state of a sequence. However, the statistical method is shown to perform quite well in tests of protein design
Scaling behaviour in a nonlocal and nonlinear diffusion equation
No full textWe present the results of analytical studies of a one-dimensional nonlocal and nonlinear diffusion equation describing nonequilibrium processes ranging from aggregation phenomena to the cooperation of individuals. On tuning the initial conditions, a dynamical transition with a universal scaling behavior is observed between two different asymptotic (in time) solutions. The scaling behavior at the transition is also obtained in a self-organized manner, independent of the initial conditions, on temporally evolving the diffusion equation subjected to a mirror symmetry transformation
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