153 research outputs found
Diffusion, peer pressure and tailed distributions
We present a general, physically motivated non-linear and non-local advection
equation in which the diffusion of interacting random walkers competes with a
local drift arising from a kind of peer pressure. We show, using a mapping to
an integrable dynamical system, that on varying a parameter, the steady state
behaviour undergoes a transition from the standard diffusive behavior to a
localized stationary state characterized by a tailed distribution. Finally, we
show that recent empirical laws on economic growth can be explained as a
collective phenomenon due to peer pressure interaction.Comment: RevTex: 4 pages + 3 eps-figures. Minor Revision and figure 3
replaced. To appear in Phys. Rev. Letter
Organization of Ecosystems in the Vicinity of a Novel Phase Transition
It is shown that an ecosystem in equilibrium is generally organized in a
state which is poised in the vicinity of a novel phase transition.Comment: 4 pages, 2 figure
Real Space Renormalization Group for Langevin Dynamics in Absence of Translational Invariance
A novel exact dynamical real space renormalization group for a Langevin
equation derivable from a Euclidean Gaussian action is presented. It is
demonstrated rigorously that an algebraic temporal law holds for the Green
function on arbitrary structures of infinite extent. In the case of fractals it
is shown on specific examples that two different fixed points are found at
variance with periodic structures. Connection with growth dynamics of
interfaces is also discussed.Comment: 22 pages, RevTex 3.0, 5 figures available upon request from
[email protected], to be published in J.Stat.Phy
Protein design in a lattice model of hydrophobic and polar amino acids
A general strategy is described for finding which amino acid sequences have
native states in a desired conformation (inverse design). The approach is used
to design sequences of 48 hydrophobic and polar aminoacids on three-dimensional
lattice structures. Previous studies employing a sequence-space Monte-Carlo
technique resulted in the successful design of one sequence in ten attempts.
The present work also entails the exploration of conformations that compete
significantly with the target structure for being its ground state. The design
procedure is successful in all the ten cases.Comment: RevTeX, 12 pages, 1 figur
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
Role of Secondary Motifs in Fast Folding Polymers: A Dynamical Variational Principle
A fascinating and open question challenging biochemistry, physics and even
geometry is the presence of highly regular motifs such as alpha-helices in the
folded state of biopolymers and proteins. Stimulating explanations ranging from
chemical propensity to simple geometrical reasoning have been invoked to
rationalize the existence of such secondary structures. We formulate a
dynamical variational principle for selection in conformation space based on
the requirement that the backbone of the native state of biologically viable
polymers be rapidly accessible from the denatured state. The variational
principle is shown to result in the emergence of helical order in compact
structures.Comment: 4 pages, RevTex, 4 eps figure
Steric constraints in model proteins
A simple lattice model for proteins that allows for distinct sizes of the
amino acids is presented. The model is found to lead to a significant number of
conformations that are the unique ground state of one or more sequences or
encodable. Furthermore, several of the encodable structures are highly
designable and are the non-degenerate ground state of several sequences. Even
though the native state conformations are typically compact, not all compact
conformations are encodable. The incorporation of the hydrophobic and polar
nature of amino acids further enhances the attractive features of the model.Comment: RevTex, 5 pages, 3 postscript figure
Protein structures and optimal folding emerging from a geometrical variational principle
Novel numerical techniques, validated by an analysis of barnase and
chymotrypsin inhibitor, are used to elucidate the paramount role played by the
geometry of the protein backbone in steering the folding to the correct native
state. It is found that, irrespective of the sequence, the native state of a
protein has exceedingly large number of conformations with a given amount of
structural overlap compared to other compact artificial backbones; moreover the
conformational entropies of unrelated proteins of the same length are nearly
equal at any given stage of folding. These results are suggestive of an
extremality principle underlying protein evolution, which, in turn, is shown to
be associated with the emergence of secondary structures.Comment: Revtex, 5 pages, 5 postscript figure
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