On induced birefringence in viscoelastic materials

Describing induced birefringence in viscoelastic materials based on constitutive assumptions for stress and dielectric propertie

Hyperelastic cloaking theory: Transformation elasticity with pre-stressed solids

Transformation elasticity, by analogy with transformation acoustics and optics, converts material domains without altering wave properties, thereby enabling cloaking and related effects. By noting the similarity between transformation elasticity and the theory of incremental motion superimposed on finite pre-strain it is shown that the constitutive parameters of transformation elasticity correspond to the density and moduli of small-on-large theory. The formal equivalence indicates that transformation elasticity can be achieved by selecting a particular finite (hyperelastic) strain energy function, which for isotropic elasticity is semilinear strain energy. The associated elastic transformation is restricted by the requirement of statically equilibrated pre-stress. This constraint can be cast as \tr {\mathbf F} = constant, where $\mathbf{F}$ is the deformation gradient, subject to symmetry constraints, and its consequences are explored both analytically and through numerical examples of cloaking of anti-plane and in-plane wave motion.Comment: 20 pages, 5 figure

Dry and wet interfaces: Influence of solvent particles on molecular recognition

We present a coarse-grained lattice model to study the influence of water on the recognition process of two rigid proteins. The basic model is formulated in terms of the hydrophobic effect. We then investigate several modifications of our basic model showing that the selectivity of the recognition process can be enhanced by considering the explicit influence of single solvent particles. When the number of cavities at the interface of a protein-protein complex is fixed as an intrinsic geometric constraint, there typically exists a characteristic fraction that should be filled with water molecules such that the selectivity exhibits a maximum. In addition the optimum fraction depends on the hydrophobicity of the interface so that one has to distinguish between dry and wet interfaces.Comment: 11 pages, 7 figure

Geometrically Reduced Number of Protein Ground State Candidates

Geometrical properties of protein ground states are studied using an algebraic approach. It is shown that independent from inter-monomer interactions, the collection of ground state candidates for any folded protein is unexpectedly small: For the case of a two-parameter Hydrophobic-Polar lattice model for $L$-mers, the number of these candidates grows only as $L^2$. Moreover, the space of the interaction parameters of the model breaks up into well-defined domains, each corresponding to one ground state candidate, which are separated by sharp boundaries. In addition, by exact enumeration, we show there are some sequences which have one absolute unique native state. These absolute ground states have perfect stability against change of inter-monomer interaction potential.Comment: 9 page, 4 ps figures are include

The Origin of the Designability of Protein Structures

We examined what determines the designability of 2-letter codes (H and P) lattice proteins from three points of view. First, whether the native structure is searched within all possible structures or within maximally compact structures. Second, whether the structure of the used lattice is bipartite or not. Third, the effect of the length of the chain, namely, the number of monomers on the chain. We found that the bipartiteness of the lattice structure is not a main factor which determines the designability. Our results suggest that highly designable structures will be found when the length of the chain is sufficiently long to make the hydrophobic core consisting of enough number of monomers.Comment: 17 pages, 2 figure

Human dynamics revealed through Web analytics

When the World Wide Web was first conceived as a way to facilitate the sharing of scientific information at the CERN (European Center for Nuclear Research) few could have imagined the role it would come to play in the following decades. Since then, the increasing ubiquity of Internet access and the frequency with which people interact with it raise the possibility of using the Web to better observe, understand, and monitor several aspects of human social behavior. Web sites with large numbers of frequently returning users are ideal for this task. If these sites belong to companies or universities, their usage patterns can furnish information about the working habits of entire populations. In this work, we analyze the properly anonymized logs detailing the access history to Emory University's Web site. Emory is a medium size university located in Atlanta, Georgia. We find interesting structure in the activity patterns of the domain and study in a systematic way the main forces behind the dynamics of the traffic. In particular, we show that both linear preferential linking and priority based queuing are essential ingredients to understand the way users navigate the Web.Comment: 7 pages, 8 figure

Energetic Components of Cooperative Protein Folding

A new lattice protein model with a four-helix bundle ground state is analyzed by a parameter-space Monte Carlo histogram technique to evaluate the effects of an extensive variety of model potentials on folding thermodynamics. Cooperative helical formation and contact energies based on a 5-letter alphabet are found to be insufficient to satisfy calorimetric and other experimental criteria for two-state folding. Such proteinlike behaviors are predicted, however, by models with polypeptide-like local conformational restrictions and environment-dependent hydrogen bonding-like interactions.Comment: 11 pages, 4 postscripts figures, Phys. Rev. Lett. (in press

Characteristic Temperatures of Folding of a Small Peptide

We perform a generalized-ensemble simulation of a small peptide taking the interactions among all atoms into account. From this simulation we obtain thermodynamic quantities over a wide range of temperatures. In particular, we show that the folding of a small peptide is a multi-stage process associated with two characteristic temperatures, the collapse temperature T_{\theta} and the folding temperature T_f. Our results give supporting evidence for the energy landscape picture and funnel concept. These ideas were previously developed in the context of studies of simplified protein models, and here for the first time checked in an all-atom Monte Carlo simulation.Comment: Latex, 6 Figure

Free Energy Self-Averaging in Protein-Sized Random Heteropolymers

Current theories of heteropolymers are inherently macrpscopic, but are applied to folding proteins which are only mesoscopic. In these theories, one computes the averaged free energy over sequences, always assuming that it is self-averaging -- a property well-established only if a system with quenched disorder is macroscopic. By enumerating the states and energies of compact 18, 27, and 36mers on a simplified lattice model with an ensemble of random sequences, we test the validity of the self-averaging approximation. We find that fluctuations in the free energy between sequences are weak, and that self-averaging is a valid approximation at the length scale of real proteins. These results validate certain sequence design methods which can exponentially speed up computational design and greatly simplify experimental realizations.Comment: 4 pages, 3 figure