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We develop a small distance expansion for the radiative heat transfer between gently curved objects, in terms of the ratio of distance to radius of curvature. A gradient expansion allows us to go beyond the lowest order proximity transfer approximation. The range of validity of such expansion depends on temperature as well as material properties. Generally, the expansion converges faster for the derivative of the transfer than for the transfer itself, which we use by introducing a near-field adjusted plot. For the case of a sphere and a plate, the logarithmic correction to the leading term has a very small prefactor for all materials investigated., Comment: 5 pages, 3 figures

We develop a unified scattering approach to dynamical Casimir problems which can be applied to both accelerating boundaries, as well as dispersive objects in relative motion. A general (trace) formula is derived for the radiation from accelerating boundaries. Applications are provided for objects with different shapes in various dimensions, and undergoing rotational or linear motion. Within this framework, photon generation is discussed in the context of a modulated optical mirror. For dispersive objects, we find general results solely in terms of the scattering matrix. Specifically, we discuss the vacuum friction on a rotating object, and the friction on an atom moving parallel to a surface., Comment: References added

The number of configurations of a polymer is reduced in the presence of a barrier or an obstacle. The resulting loss of entropy adds a repulsive component to other forces generated by interaction potentials. When the obstructions are scale invariant shapes (such as cones, wedges, lines or planes) the only relevant length scales are the polymer size R_0 and characteristic separations, severely constraining the functional form of entropic forces. Specifically, we consider a polymer (single strand or star) attached to the tip of a cone, at a separation h from a surface (or another cone). At close proximity, such that h<

We present a detailed derivation of heat radiation, heat transfer and (Casimir) interactions for N arbitrary objects in the framework of fluctuational electrodynamics in thermal non-equilibrium. The results can be expressed as basis-independent trace formulae in terms of the scattering operators of the individual objects. We prove that heat radiation of a single object is positive, and that heat transfer (for two arbitrary passive objects) is from the hotter to a colder body. The heat transferred is also symmetric, exactly reversed if the two temperatures are exchanged. Introducing partial wave-expansions, we transform the results for radiation, transfer and forces into traces of matrices that can be evaluated in any basis, analogous to the equilibrium Casimir force. The method is illustrated by (re)deriving the heat radiation of a plate, a sphere and a cylinder. We analyze the radiation of a sphere for different materials, emphasizing that a simplification often employed for metallic nano-spheres is typically invalid. We derive asymptotic formulae for heat transfer and non-equilibrium interactions for the cases of a sphere in front a plate and for two spheres, extending previous results. As an example, we show that a hot nano-sphere can levitate above a plate with the repulsive non-equilibrium force overcoming gravity -- an effect that is not due to radiation pressure., Comment: 29 pages, 6 figures (v2: Sentence added in Sec. 1)

We study the quantum electrodynamics (QED) vacuum in the presence of a body rotating along its axis of symmetry and show that the object spontaneously emits energy if it is lossy. The radiated power is expressed as a general trace formula solely in terms of the scattering matrix, making an explicit connection to the conjecture of Zel'dovich [JETP Lett. 14, 180 (1971)] on rotating objects. We further show that a rotating body drags along nearby objects while making them spin parallel to its own rotation axis.

We study Casimir interactions between cylinders in thermal non-equilibrium, where the objects as well as the environment are held at different temperatures. We provide the general formula for the force, in a one reflection approximation, for cylinders of arbitrary radii and optical properties. As is the case for equilibrium, we find that the force for optically diluted cylinders can be obtained by appropriate summation of the corresponding result for spheres. We find that the non-equilibrium forces are generally larger than their equilibrium counterpart at separations greater than the thermal wavelength. They may also exhibit oscillations as function of separation, leading to stable points of zero net force. These effects are particularly pronounced for thin conducting cylinders (e.g. 40nm diameter nano-wires of tungsten) due to their large emissivity., Comment: 10 pages, 5 figures

We consider polymers attached to the tip of a cone, and the resulting force due to entropy loss on approaching a plate (or another cone). At separations shorter than the polymer radius of gyration R_g, the only relevant length scale is the tip-plate (or tip-tip) separation h, and the entropic force is given by F=A kT/h. The universal amplitude A can be related to (geometry dependent) correlation exponents of long polymers. We compute A for phantom polymers, and for self-avoiding (including star) polymers by epsilon-expansion, as well as by numerical simulations in 3 dimensions.

The heat radiated by objects small or comparable to the thermal wavelength can be very different from the classical blackbody radiation as described by the laws of Planck and Stefan-Boltzmann. We use methods based on scattering of electromagnetic waves to explore the dependence on size, shape, as well as material properties. In particular, we explore the radiation from a long cylinder at uniform temperature, discussing in detail the degree of polarization of the emitted radiation. If the radius of the cylinder is much smaller than the thermal wavelength, the radiation is polarized parallel to the cylindrical axis and becomes perpendicular when the radius is comparable to the thermal wavelength. For a cylinder of uniaxial material (a simple model for carbon nanontubes), we find that the influence of uniaxiality on the polarization is most pronounced if the radius is larger than a few microns, and quite small for submicron sizes typical for nanotubes., Comment: 16 pages, 13 figures

T cells orchestrate adaptive immune responses upon activation. T cell activation requires sufficiently strong binding of T cell receptors on their surface to short peptides derived from foreign proteins bound to protein products of the major histocompatibility (MHC) gene products, which are displayed on the surface of antigen presenting cells. T cells can also interact with peptide-MHC complexes, where the peptide is derived from host (self) proteins. A diverse repertoire of relatively self-tolerant T cell receptors is selected in the thymus. We study a model, computationally and analytically, to describe how thymic selection shapes the repertoire of T cell receptors, such that T cell receptor recognition of pathogenic peptides is both specific and degenerate. We also discuss the escape probability of autoimmune T cells from the thymus., Comment: 12 pages, 7 figures

In equilibrium, forces induced by fluctuations of the electromagnetic field between electrically polarizable objects (microscopic or macroscopic) in vacuum are always attractive. The force may, however, become repulsive for microscopic particles coupled to thermal baths with different temperatures. We demonstrate that this non-equilibrium repulsion can be realized also between macroscopic objects, as planar slabs, if they are kept at different temperatures. It is shown that repulsion can be enhanced by (i) tuning of material resonances in the thermal region, and by (ii) reducing the dielectric contrast due to "dilution". This can lead to stable equilibrium positions. We discuss the realization of these effects for aerogels, yielding repulsion down to sub-micron distances at realistic porosities., Comment: 5 pages, 4 figures

We discuss non-equilibrium extensions of the Casimir force (due to electromagnetic fluctuations), where the objects as well as the environment are held at different temperatures. While the formalism we develop is quite general, we focus on a sphere in front of a plate, as well as two spheres, when the radius is small compared to separation and thermal wavelengths. In this limit the forces can be expressed analytically in terms of the lowest order multipoles, and corroborated with results obtained by diluting parallel plates of vanishing thickness. Non-equilibrium forces are generally stronger than their equilibrium counterpart, and may oscillate with separation (at a scale set by material resonances). For both geometries we obtain stable points of zero net force, while two spheres may have equal forces in magnitude and direction resulting in a self-propelling state., Comment: 6 pages, 6 figures

An exact calculation of electromagnetic scattering from a perfectly conducting parabolic cylinder is employed to compute Casimir forces in several configurations. These include interactions between a parabolic cylinder and a plane, two parabolic cylinders, and a parabolic cylinder and an ordinary cylinder. To elucidate the effect of boundaries, special attention is focused on the "knife-edge" limit in which the parabolic cylinder becomes a half-plane. Geometrical effects are illustrated by considering arbitrary rotations of a parabolic cylinder around its focal axis, and arbitrary translations perpendicular to this axis. A quite different geometrical arrangement is explored for the case of an ordinary cylinder placed in the interior of a parabolic cylinder. All of these results extend simply to nonzero temperatures., Comment: 17 pages, 10 figures, uses RevTeX 4

The Casimir force between arbitrary objects in equilibrium is related to scattering from individual bodies. We extend this approach to heat transfer and Casimir forces in non-equilibrium cases where each body, and the environment, is at a different temperature. The formalism tracks the radiation from each body and its scatterings by the other objects. We discuss the radiation from a cylinder, emphasizing its polarized nature, and obtain the heat transfer between a sphere and a plate, demonstrating the validity of proximity transfer approximation at close separations and arbitrary temperatures., Comment: 4 pages, 2 figures, published version, minor changes (e.g. typos)

Neurotransmitter receptor molecules, concentrated in postsynaptic domains along with scaffold and a number of other molecules, are key regulators of signal transmission across synapses. Employing experiment and theory, we develop a quantitative description of synaptic receptor domains in terms of a reaction-diffusion model. We show that interactions between only receptor and scaffold molecules, together with the rapid diffusion of receptors on the cell membrane, are sufficient for the formation and stable characteristic size of synaptic receptor domains. Our work reconciles long-term stability of synaptic receptor domains with rapid turnover and diffusion of individual receptors., Comment: 5 pages, 3 figures, Supplementary Material

Casimir forces between conductors at the sub-micron scale cannot be ignored in the design and operation of micro-electromechanical (MEM) devices. However, these forces depend non-trivially on geometry, and existing formulae and approximations cannot deal with realistic micro-machinery components with sharp edges and tips. Here, we employ a novel approach to electromagnetic scattering, appropriate to perfect conductors with sharp edges and tips, specifically to wedges and cones. The interaction of these objects with a metal plate (and among themselves) is then computed systematically by a multiple-scattering series. For the wedge, we obtain analytical expressions for the interaction with a plate, as functions of opening angle and tilt, which should provide a particularly useful tool for the design of MEMs. Our result for the Casimir interactions between conducting cones and plates applies directly to the force on the tip of a scanning tunneling probe; the unexpectedly large temperature dependence of the force in these configurations should attract immediate experimental interest.

We examine whether fluctuation-induced forces can lead to stable levitation. First, we analyze a collection of classical objects at finite temperature that contain fixed and mobile charges, and show that any arrangement in space is unstable to small perturbations in position. This extends Earnshaw's theorem for electrostatics by including thermal fluctuations of internal charges. Quantum fluctuations of the electromagnetic field are responsible for Casimir/van der Waals interactions. Neglecting permeabilities, we find that any equilibrium position of items subject to such forces is also unstable if the permittivities of all objects are higher or lower than that of the enveloping medium; the former being the generic case for ordinary materials in vacuum., Comment: 4 pages, 1 figure

The Casimir force has been computed exactly for only a few simple geometries, such as infinite plates, cylinders, and spheres. We show that a parabolic cylinder, for which analytic solutions to the Helmholtz equation are available, is another case where such a calculation is possible. We compute the interaction energy of a parabolic cylinder and an infinite plate (both perfect mirrors), as a function of their separation and inclination, $H$ and $\theta$, and the cylinder's parabolic radius $R$. As $H/R\to 0$, the proximity force approximation becomes exact. The opposite limit of $R/H\to 0$ corresponds to a semi-infinite plate, where the effects of edge and inclination can be probed., Comment: 5 pages, 3 figures, uses RevTeX; v2: expanded conclusions; v3: fixed missing factor in Eq. (3) and incorrect diagram label (no changes to results); v4: fix similar factor in Eq. (16) (again no changes to results)

We consider a model system in which anomalous diffusion is generated by superposition of underlying linear modes with a broad range of relaxation times. In the language of Gaussian polymers, our model corresponds to Rouse (Fourier) modes whose friction coefficients scale as wavenumber to the power $2-z$. A single (tagged) monomer then executes subdiffusion over a broad range of time scales, and its mean square displacement increases as $t^\alpha$ with $\alpha=1/z$. To demonstrate non-trivial aspects of the model, we numerically study the absorption of the tagged particle in one dimension near an absorbing boundary or in the interval between two such boundaries. We obtain absorption probability densities as a function of time, as well as the position-dependent distribution for unabsorbed particles, at several values of $\alpha$. Each of these properties has features characterized by exponents that depend on $\alpha$. Characteristic distributions found for different values of $\alpha$ have similar qualitative features, but are not simply related quantitatively. Comparison of the motion of translocation coordinate of a polymer moving through a pore in a membrane with the diffusing tagged monomer with identical $\alpha$ also reveals quantitative differences., Comment: LaTeX, 10 pages, 8 eps figures

We study polymers attached to spherical (circular) or paraboloidal (parabolic) probes in three (two) dimensions. Both self-avoiding and random walks are examined numerically. The behavior of a polymer of size $R_0$ attached to the tip of a probe with radius of curvature $R$, differs qualitatively for large and small values of the ratio $s=R_0/R$. We demonstrate that the scaled compliance (inverse force constant) $S/R_0^2$, and scaled mean position of the polymer end-point $/R$ can be expressed as a function of $s$. Scaled compliance is anisotropic, and quite large in the direction parallel to the surface when $R_0\sim R$. The exponent $\gamma$, characterizing the number of polymer configurations, crosses over from a value of $\gamma_1$ - characteristic of a planar boundary - at small $s$ to one reflecting the overall shape of the probe at large $s$. For a spherical probe the crossover is to an unencumbered polymer, while for a parabolic probe we cannot rule out a new exponent., Comment: LaTeX, 6 pages, 4 figures

We study thermodynamics properties of a one dimensional gas of hard elongated particles. The particle centers are restricted to a line, while they can rotate in two-dimensional space. Correlations between orientations of the objects are studied (by transfer matrix method) as a function of density and aspect ratio. The behavior in the extreme high-density (jamming) limit is described by a few universality classes depending on the object's shape. In particular, there is a diverging correlation length when the contact point of adjacent objects is far from the line along which their centers move, as for needles and rectangles., Comment: LaTeX, 6 pages, 4 figures

We give a comprehensive presentation of methods for calculating the Casimir force to arbitrary accuracy, for any number of objects, arbitrary shapes, susceptibility functions, and separations. The technique is applicable to objects immersed in media other than vacuum, nonzero temperatures, and spatial arrangements in which one object is enclosed in another. Our method combines each object's classical electromagnetic scattering amplitude with universal translation matrices, which convert between the bases used to calculate scattering for each object, but are otherwise independent of the details of the individual objects. The method is illustrated by re-deriving the Lifshitz formula for infinite half spaces, by demonstrating the Casimir-Polder to van der Waals cross-over, and by computing the Casimir interaction energy of two infinite, parallel, perfect metal cylinders either inside or outside one another. Furthermore, it is used to obtain new results, namely the Casimir energies of a sphere or a cylinder opposite a plate, all with finite permittivity and permeability, to leading order at large separation., Comment: 43 pages, 10 figures

T lymphocytes (T cells) orchestrate adaptive immune responses upon activation. T cell activation requires sufficiently strong binding of T cell receptors (TCRs) on their surface to short peptides (p) derived from foreign proteins, which are bound to major histocompatibility (MHC) gene products (displayed on antigen presenting cells). A diverse and self-tolerant T cell repertoire is selected in the thymus. We map thymic selection processes to an extreme value problem and provide an analytic expression for the amino acid compositions of selected TCRs (which enable its recognition functions)., Comment: 4 pages, 3 figures, accepted for publication in PRL

Positive feedback regulation is ubiquitous in cell signaling networks, often leading to binary outcomes in response to graded stimuli. However, the role of such feedbacks in clustering, and in spatial spreading of activated molecules, has come to be appreciated only recently. We focus on the latter, using a simple model developed in the context of Ras activation with competing negative and positive feedback mechanisms. We find that positive feedback, in the presence of slow diffusion, results in clustering of activated molecules on the plasma membrane, and rapid spatial spreading as the front of the cluster propagates with a constant velocity (dependent on the feedback strength). The advancing fronts of the clusters of the activated species are rough, with scaling consistent with the Kardar-Parisi-Zhang (KPZ) equation in one dimension. Our minimal model is general enough to describe signal transduction in a wide variety of biological networks where activity in the membrane-proximal region is subject to feedback regulation., Comment: 37 pages, 8 figures. Journal of Chemical Physics (in press)

We study a one dimensional gas of needle-like objects as a testing ground for a formalism that relates the thermodynamic properties of "hard" potentials to the probabilities for contacts between particles. Specifically, we use Monte Carlo methods to calculate the pressure and elasticity coefficient of the hard-needle gas as a function of its density. The results are then compared to the same quantities obtained analytically from a transfer matrix approach., Comment: Revtex4, 4 eps figures

The binding of a transcription factor (TF) to a DNA operator site can initiate or repress the expression of a gene. Computational prediction of sites recognized by a TF has traditionally relied upon knowledge of several cognate sites, rather than an ab initio approach. Here, we examine the possibility of using structure-based energy calculations that require no knowledge of bound sites but rather start with the structure of a protein-DNA complex. We study the PurR E. coli TF, and explore to which extent atomistic models of protein-DNA complexes can be used to distinguish between cognate and non-cognate DNA sites. Particular emphasis is placed on systematic evaluation of this approach by comparing its performance with bioinformatic methods, by testing it against random decoys and sites of homologous TFs. We also examine a set of experimental mutations in both DNA and the protein. Using our explicit estimates of energy, we show that the specificity for PurR is dominated by direct protein-DNA interactions, and weakly influenced by bending of DNA., Comment: 26 pages, 3 figures

Motivated by recent DNA-pulling experiments, we revisit the Poland-Scheraga model of melting a double-stranded polymer. We include distinct bending rigidities for both the double-stranded segments, and the single-stranded segments forming a bubble. There is also bending stiffness at the branch points between the two segment types. The transfer matrix technique for single persistent chains is generalized to describe the branching bubbles. Properties of spherical harmonics are then exploited in truncating and numerically solving the resulting transfer matrix. This allows efficient computation of phase diagrams and force-extension curves (isotherms). While the main focus is on exposition of the transfer matrix technique, we provide general arguments for a reentrant melting transition in stiff double strands. Our theoretical approach can also be extended to study polymers with bubbles of any number of strands, with potential applications to molecules such as collagen., Comment: 9 pages, 7 figures

We study the passage (translocation) of a self-avoiding polymer through a membrane pore in two dimensions. In particular, we numerically measure the probability distribution Q(T) of the translocation time T, and the distribution P(s,t) of the translocation coordinate s at various times t. When scaled with the mean translocation time , Q(T) becomes independent of polymer length, and decays exponentially for large T. The probability P(s,t) is well described by a Gaussian at short times, with a variance that grows sub-diffusively as t^{\alpha} with \alpha~0.8. For times exceeding , P(s,t) of the polymers that have not yet finished their translocation has a non-trivial stable shape., Comment: 5 pages, 4 figures

We study collective interaction effects that result from the change of free quantum electrodynamic field fluctuations by one- and two-dimensional perfect metal structures. The Casimir interactions in geometries containing plates and cylinders is explicitly computed using partial wave expansions of constrained path integrals. We generalize previously obtained results and provide a more detailed description of the technical aspects of the approach \cite{Emig06}. We find that the interactions involving cylinders have a weak logarithmic dependence on the cylinder radius, reflecting that one-dimensional perturbations are marginally relevant in 4D space-time. For geometries containing two cylinders and one or two plates, we confirm a previously found non-monotonic dependence of the interaction on the object's separations which does not follow from pair-wise summation of two-body forces. Qualitatively, this effect is explained in terms of fluctuating charges and currents and their mirror images.

We present an exact solution of percolation in a generalized class of Watts-Strogatz graphs defined on a 1-dimensional underlying lattice. We find a non-classical critical point in the limit of the number of long-range bonds in the system going to zero, with a discontinuity in the percolation probability and a divergence in the mean finite-cluster size. We show that the critical behavior falls into one of three regimes depending on the proportion of occupied long-range to unoccupied nearest-neighbor bonds, with each regime being characterized by different critical exponents. The three regimes can be united by a single scaling function around the critical point. These results can be used to identify the number of long-range links necessary to secure connectivity in a communication or transportation chain. As an example, we can resolve the communication problem in a game of "telephone"., Comment: 10 pages, 4 figures, revtex4

We analyze the Casimir force between two parallel infinite metal cylinders, with nearby metal plates (sidewalls), using complementary methods for mutual confirmation. The attractive force between cylinders is shown to have a nonmonotonic dependence on the separation to the plates. This intrinsically multi-body phenomenon, which occurs with either one or two sidewalls (generalizing an earlier result for squares between two sidewalls), does not follow from any simple two-body force description. We can, however, explain the nonmonotonicity by considering the screening (enhancement) of the interactions by the fluctuating charges (currents) on the two cylinders, and their images on the nearby plate(s). Furthermore, we show that this effect also implies a nonmonotonic dependence of the cylinder-plate force on the cylinder-cylinder separation., Comment: 5 pages, 4 figures

In a very long Gaussian polymer on time scales shorter that the maximal relaxation time, the mean squared distance travelled by a tagged monomer grows as ~t^{1/2}. We analyze such sub-diffusive behavior in the presence of one or two absorbing boundaries and demonstrate the differences between this process and the sub-diffusion described by the fractional Fokker-Planck equation. In particular, we show that the mean absorption time of diffuser between two absorbing boundaries is finite. Our results restrict the form of the effective dispersion equation that may describe such sub-diffusive processes., Comment: 8 pages, 8 figures, RevTex4

A nematic membrane is a sheet with embedded orientational order, which can occur in biological cells, liquid crystal films, manufactured materials, and other soft matter systems. By formulating the free energy of nematic films using tensor contractions from differential geometry, we elucidate the elastic terms allowed by symmetry, and indicate differences from hexatic membranes. We find that topological defects in the orientation field can cause the membrane to buckle over a size set by the competition between surface tension and in-plane elasticity. In the absence of bending rigidity the resulting shape is universal, known as a parabolic pseudosphere or a revolved tractrix. Bending costs oppose such buckling and modify the shape in a predictable manner. In particular, the anisotropic rigidities of nematic membranes lead to different shapes for aster and vortex defects, in principle enabling measurement of couplings specific to nematic membranes., Comment: 9 pages, 3 figures

A number of recently discovered protein structures incorporate a rather unexpected structural feature: a knot in the polypeptide backbone. These knots are extremely rare, but their occurrence is likely connected to protein function in as yet unexplored fashion. Our analysis of the complete Protein Data Bank reveals several new knots which, along with previously discovered ones, can shed light on such connections. In particular, we identify the most complex knot discovered to date in human ubiquitin hydrolase, and suggest that its entangled topology protects it against unfolding and degradation by the proteasome. Knots in proteins are typically preserved across species and sometimes even across kingdoms. However, we also identify a knot which only appears in some transcarbamylases while being absent in homologous proteins of similar structure. The emergence of the knot is accompanied by a shift in the enzymatic function of the protein. We suggest that the simple insertion of a short DNA fragment into the gene may suffice to turn an unknotted into a knotted structure in this protein., Comment: 6 pages, 2 figures, 1 table

Experiments on $^4$He films reveal an attractive Casimir-like force at the bulk $\lambda$-point, and in the superfluid regime. Previous work has explained the magnitude of this force at the $\lambda$ transition and deep in the superfluid region but not the substantial attractive force immediately below the $\lambda$-point. Utilizing a simple mean-field calculation renormalized by critical fluctuations we obtain an effective Casimir force that is qualitatively consistent with the scaling function $\vartheta$ obtained by collapse of experimental data., Comment: 4 pages

We consider self-avoiding polymers attached to the tip of an impenetrable probe. The scaling exponents $\gamma_1$ and $\gamma_2$, characterizing the number of configurations for the attachment of the polymer by one end, or at its midpoint, vary continuously with the tip's angle. These apex exponents are calculated analytically by $\epsilon$-expansion, and numerically by simulations in three dimensions. We find that when the polymer can move through the attachment point, it typically slides to one end; the apex exponents quantify the entropic barrier to threading the eye of the probe.

Locomotion of bacteria by actin polymerization, and in vitro motion of spherical beads coated with a protein catalyzing polymerization, are examples of active motility. Starting from a simple model of forces locally normal to the surface of a bead, we construct a phenomenological equation for its motion. The singularities at a continuous transition between moving and stationary beads are shown to be related to the symmetries of its shape. Universal features of the phase behavior are calculated analytically and confirmed by simulations. Fluctuations in velocity are shown to be generically non-Maxwellian and correlated to the shape of the bead., Comment: 4 pages, 2 figures, REVTeX; formatting of references corrected

As borders between different regions, lines are an important element of natural images. Already at the level of the mammalian primary visual cortex (V1), neurons respond best to lines of a given orientation. We reduce a set of images to linear segments and analyze their statistical properties. In particular, appropriately defined Fourier spectra show more power in their transverse component than in the longitudinal one. We then characterize filters that are best suited for extracting information from such images, and find some qualitative consistency with neural connections in V1. We also demonstrate that such filters are efficient in reconstructing missing lines in an image.

We fit the Fourier transforms of solvent accessibility and hydrophobicity profiles of a representative set of proteins to a joint multi-variable Gaussian. This allows us to separate the intrinsic tendencies of sequence and structure profiles from the interactions that correlate them; for example, the $\alpha$-helix periodicity in sequence hydrophobicity is dictated by the solvent accessibility of structures. The distinct intrinsic tendencies of sequence and structure profiles are most pronounced at long periods, where sequence hydrophobicity fluctuates more, while solvent accessibility fluctuations are less than average. Interestingly, correlations between the two profiles can be interpreted as the Boltzmann weight of the solvation energy at room temperature., Comment: 4 pages, 3 figures, 7 eps files

Recent experiments on the wetting of $^{4}$He have shown that the film becomes thinner at the $\lambda$ transition, and in the superfluid phase. The difference in thickness above and below the transition has been attributed to a Casimir interaction which is a consequence of a broken continuous symmetry in the bulk superfluid. However, the observed thinning of the film is larger than can be accounted by this Casimir force. We show that surface fluctuations give rise to an additional force, similar in form but larger in magnitude, which may explain the observations., Comment: 4 pages, 1 figure

Neurons in the visual cortex respond best to rod-like stimuli of given orientation. While the preferred orientation varies continuously across most of the cortex, there are prominent pinwheel centers around which all orientations a re present. Oriented segments abound in natural images, and tend to be collinear}; neurons are also more likely to be connected if their preferred orientations are aligned to their topographic separation. These are indications of a reduced symmetry requiring joint rotations of both orientation preference and the underl ying topography. We verify that this requirement extends to cortical maps of mo nkey and cat by direct statistical analysis. Furthermore, analytical arguments and numerical studies indicate that pinwheels are generically stable in evolving field models which couple orientation and topography.

We reconsider the persistence of information under the dynamics of the logistic map in order to discuss communication through a nonlinear channel where the sender can set the initial state of the system with finite resolution, and the recipient measures it with the same accuracy. We separate out the contributions of global phase space shrinkage and local phase space contraction and expansion to the uncertainty in predicting and postdicting the state of the system. Thus, we determine how the amplification parameter, the time lag, and the resolution influence the possibility for communication. A novel representation for real numbers is introduced that allows for a visualization of the flow of information between scales., Comment: 14 pages, 13 figures

We consider the passage of long polymers of length N through a hole in a membrane. If the process is slow, it is in principle possible to focus on the dynamics of the number of monomers s on one side of the membrane, assuming that the two segments are in equilibrium. The dynamics of s(t) in such a limit would be diffusive, with a mean translocation time scaling as N^2 in the absence of a force, and proportional to N when a force is applied. We demonstrate that the assumption of equilibrium must break down for sufficiently long polymers (more easily when forced), and provide lower bounds for the translocation time by comparison to unimpeded motion of the polymer. These lower bounds exceed the time scales calculated on the basis of equilibrium, and point to anomalous (sub-diffusive) character of translocation dynamics. This is explicitly verified by numerical simulations of the unforced translocation of a self-avoiding polymer. Forced translocation times are shown to strongly depend on the method by which the force is applied. In particular, pulling the polymer by the end leads to much longer times than when a chemical potential difference is applied across the membrane. The bounds in these cases grow as N^2 and N^{1+\nu}, respectively, where \nu is the exponent that relates the scaling of the radius of gyration to N. Our simulations demonstrate that the actual translocation times scale in the same manner as the bounds, although influenced by strong finite size effects which persist even for the longest polymers that we considered (N=512)., Comment: 13 pages, RevTeX4, 16 eps figures

Many biological processes involve one dimensional diffusion over a correlated inhomogeneous energy landscape with a correlation length $\xi_c$. Typical examples are specific protein target location on DNA, nucleosome repositioning, or DNA translocation through a nanopore, in all cases with $\xi_c\approx$ 10 nm. We investigate such transport processes by the mean first passage time (MFPT) formalism, and find diffusion times which exhibit strong sample to sample fluctuations. For a a displacement $N$, the average MFPT is diffusive, while its standard deviation over the ensemble of energy profiles scales as $N^{3/2}$ with a large prefactor. Fluctuations are thus dominant for displacements smaller than a characteristic $N_c \gg \xi_c$: typical values are much less than the mean, and governed by an anomalous diffusion rule. Potential biological consequences of such random walks, composed of rapid scans in the vicinity of favorable energy valleys and occasional jumps to further valleys, is discussed.

We investigate the effects of topological constraints (entanglements) on two dimensional polymer loops in the dense phase, and at the collapse transition (Theta point). Previous studies have shown that in the dilute phase the entangled region becomes tight, and is thus localised on a small portion of the polymer. We find that the entropic force favouring tightness is considerably weaker in dense polymers. While the simple figure-eight structure, created by a single crossing in the polymer loop, localises weakly, the trefoil knot and all other prime knots are loosely spread out over the entire chain. In both the dense and Theta conditions, the uncontracted knot configuration is the most likely shape within a scaling analysis. By contrast, a strongly localised figure-eight is the most likely shape for dilute prime knots. Our findings are compared to recent simulations., Comment: 8 pages, 5 figures

We study the interplay between surface roughening and phase separation during the growth of binary films. Renormalization group calculations are performed on a pair of equations coupling the interface height and order parameter fluctuations. We find a larger roughness exponent at the critical point of the order parameter compared to the disordered phase, and an increase in the upper critical dimension for the surface roughening transition from two to four. Numerical simulations performed on a solid-on-solid model with two types of deposited particles corroborate some of these findings. However, for a range of parameters not accessible to perturbative analysis, we find non-universal behavior with a continuously varying dynamic exponent., Comment: 10 pages, 8 figures

Using canonical Monte Carlo simulations, we introduce a new numerical procedure for comparing the entropic exponents of polymers with different constraints and/or topologies. Setting up competitions between polymer segments which can exchange monomers according to their free energies, we obtain the universal exponents of partition functions, independently of any knowledge of the non-universal part. The method is successfully tested for closed polymer loops decorated with sliding rings. We also investigate the entropic exponents of loops with a fixed knot type, in which case we are limited by strong finite--size effects., Comment: 8 pages, 12 figures

We investigate the probability for appearance of knots in self-avoiding loops (SALs) on a cubic lattice. A set of N-step loops is generated by attempting to combine pairs of (N/2)-step self-avoiding walks constructed by a dimerization method. We demonstrate that our method produces unbiased samples of SALs, and study the knot formation probability as a function of loop size. Our results corroborate the conclusions of Yao et. al. with loops generated by a Monte Carlo method., Comment: RevTeX4, 4 pages, 4 eps figures

The immunological synapse is a patterned collection of different types of receptors and ligands that forms in the intercellular junction between T Cells and antigen presenting cells (APCs) during recognition. The synapse is implicated in information transfer between cells, and is characterized by different spatial patterns of receptors at different stages in the life cycle of T cells. We obtain a minimalist model that captures this experimentally observed phenomenology. A functional RG analysis provides further insights., Comment: 6 pages, 3 figures, submitted for publication

We consider generalizations of the Kardar--Parisi--Zhang equation that accomodate spatial anisotropies and the coupled evolution of several fields, and focus on their symmetries and non-perturbative properties. In particular, we derive generalized fluctuation--dissipation conditions on the form of the (non-linear) equations for the realization of a Gaussian probability density of the fields in the steady state. For the amorphous growth of a single height field in one dimension we give a general class of equations with exactly calculable (Gaussian and more complicated) steady states. In two dimensions, we show that any anisotropic system evolves on long time and length scales either to the usual isotropic strong coupling regime or to a linear-like fixed point associated with a hidden symmetry. Similar results are derived for textural growth equations that couple the height field with additional order parameters which fluctuate on the growing surface. In this context, we propose phenomenological equations for the growth of a crystalline material, where the height field interacts with lattice distortions, and identify two special cases that obtain Gaussian steady states. In the first case compression modes influence growth and are advected by height fluctuations, while in the second case it is the density of dislocations that couples with the height., Comment: 9 pages, revtex4

This paper has been withdrawn by the author(s), as required by JPC-Journal of Physical Chemistry for reasons of publication., Comment: This paper has been withdrawn by the author(s), as required by JPC-Journal of Physical Chemistry for reasons of publication