Correlation and cross-linking effects in imprinting sites for divalent adsorption in gels
This paper has been withdrawn by the author(s), as required by JPC-Journal of Physical Chemistry for reasons of publication.
cond-mat.soft↗
arXiv subjects
Mehran Kardar
Publications and source records attributed to Mehran Kardar.
Apex Exponents for Polymer--Probe Interactions
We consider self-avoiding polymers attached to the tip of an impenetrable probe. The scaling exponents $γ_1$ and $γ_2$, 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 $ε$-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.
cond-mat.stat-mech↗
Symmetry-Breaking Motility
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.
cond-mat.stat-mech↗
Statistics of lines of natural images and implications for visual detection
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.
q-bio.NC↗
Untangling influences of hydrophobicity on protein sequences and structures
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 $α$-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.
q-bio.BM↗
Casimir forces, surface fluctuations, and thinning of superfluid films
Recent experiments on the wetting of $^{4}$He have shown that the film becomes thinner at the $λ$ 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.
cond-mat.stat-mech↗
Symmetry considerations and development of pinwheels in visual maps
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.
cond-mat.stat-mech↗
Non-Linear Stochastic Equations with Calculable Steady States
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.
cond-mat.stat-mech↗
Information Flow through a Chaotic Channel: Prediction and Postdiction at Finite Resolution
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.
nlin.CD↗
Anomalous Dynamics of Forced Translocation
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+ν}, respectively, where νis 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).
cond-mat.soft↗
The long reach of DNA sequence heterogeneity in diffusive processes
Many biological processes involve one dimensional diffusion over a correlated inhomogeneous energy landscape with a correlation length $ξ_c$. Typical examples are specific protein target location on DNA, nucleosome repositioning, or DNA translocation through a nanopore, in all cases with $ξ_c\approx$ 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 $N_c \gg ξ_c$: 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.
q-bio.BM↗
Tight and loose shapes in flat entangled dense polymers
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.
cond-mat.soft↗
Interplay between phase ordering and roughening on growing films
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.
cond-mat.stat-mech↗
Entropic competition between knots and slip-links
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.
cond-mat.soft↗
Knot Probability for Self-Avoiding Loops on a Cubic Lattice
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.
cond-mat.stat-mech↗
An Effective Membrane Model of the Immunological Synapse
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.
cond-mat.soft↗
Normal and Lateral Casimir Forces between Deformed Plates
The Casimir force between macroscopic bodies depends strongly on their shape and orientation. To study this geometry dependence in the case of two deformed metal plates, we use a path integral quantization of the electromagnetic field which properly treats the many-body nature of the interaction, going beyond the commonly used pairwise summation (PWS) of van der Waals forces. For arbitrary deformations we provide an analytical result for the deformation induced change in Casimir energy, which is exact to second order in the deformation amplitude. For the specific case of sinusoidally corrugated plates, we calculate both the normal and the lateral Casimir forces. The deformation induced change in the Casimir interaction of a flat and a corrugated plate shows an interesting crossover as a function of the ratio of the mean platedistance H to the corrugation length λ: For λ\ll H we find a slower decay \sim H^{-4}, compared to the H^{-5} behavior predicted by PWS which we show to be valid only for λ\gg H. The amplitude of the lateral force between two corrugated plates which are out of registry is shown to have a maximum at an optimal wavelength of λ\approx 2.5 H. With increasing H/λ\gtrsim 0.3 the PWS approach becomes a progressively worse description of the lateral force due to many-body effects. These results may be of relevance for the design and operation of novel microelectromechanical systems (MEMS) and other nanoscale devices.
cond-mat.stat-mech↗
Structure Space of Model Proteins --A Principle Component Analysis
We study the space of all compact structures on a two-dimensional square lattice of size $N=6\times6$. Each structure is mapped onto a vector in $N$-dimensions according to a hydrophobic model. Previous work has shown that the designabilities of structures are closely related to the distribution of the structure vectors in the $N$-dimensional space, with highly designable structures predominantly found in low density regions. We use principal component analysis to probe and characterize the distribution of structure vectors, and find a non-uniform density with a single peak. Interestingly, the principal axes of this peak are almost aligned with Fourier eigenvectors, and the corresponding Fourier eigenvalues go to zero continuously at the wave-number for alternating patterns ($q=π$). These observations provide a stepping stone for an analytic description of the distribution of structural points, and open the possibility of estimating designabilities of realistic structures by simply Fourier transforming the hydrophobicities of the corresponding sequences.
physics.bio-ph↗