arXiv subjects

Mehran Kardar

Publications and source records attributed to Mehran Kardar.

At least 91 records · Page 5Linked to original sources

arXiv2010

First Passage Distributions in a Collective Model of Anomalous Diffusion with Tunable Exponent

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 $t^α$ with $α=1/z$. 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 $α$. Each of these properties has features characterized by exponents that depend on $α$. Characteristic distributions found for different values of $α$ 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 $α$ also reveals quantitative differences.

cond-mat.stat-mech↗

arXiv2009

Constraints on stable equilibria with fluctuation-induced forces

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.

quant-ph↗

arXiv2009

Configurations of polymers attached to probes

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 $γ$, characterizing the number of polymer configurations, crosses over from a value of $γ_1$ - 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.

cond-mat.stat-mech↗

arXiv2009

Universality in the jamming limit for elongated hard particles in one dimension

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.

cond-mat.stat-mech↗

arXiv2009

Scattering Theory Approach to Electrodynamic Casimir Forces

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.

quant-ph↗

arXiv2009

Thymic selection of T-cell receptors as an extreme value problem

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).

physics.bio-ph↗

arXiv2009

Positive Feedback Regulation Results in Spatial Clustering and Fast Spreading of Active Signaling Molecules on a Cell Membrane

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.

cond-mat.soft↗

arXiv2009

One-dimensional gas of hard needles

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.

cond-mat.stat-mech↗

arXiv2008

Predicting Transcription Factor Specificity with All-Atom Models

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.

q-bio.BM↗

arXiv2008

Melting of persistent double-stranded polymers

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.

cond-mat.soft↗

arXiv2008

Casimir forces between cylinders and plates

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.

cond-mat.stat-mech↗

arXiv2008

Probability distributions for polymer translocation

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^α with α~0.8. For times exceeding , P(s,t) of the polymers that have not yet finished their translocation has a non-trivial stable shape.

cond-mat.stat-mech↗

arXiv2008

Unusual percolation in simple small-world networks

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".

cond-mat.dis-nn↗

arXiv2007

Nonmonotonic effects of parallel sidewalls on Casimir forces between cylinders

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.

cond-mat.stat-mech↗

arXiv2007

Anomalous Diffusion with Absorbing Boundary

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.

cond-mat.stat-mech↗

arXiv2007

Defects in nematic membranes can buckle into pseudospheres

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.

cond-mat.soft↗

arXiv2007

Intricate Knots in Proteins: Function and Evolution

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.

physics.bio-ph↗

arXiv2007

Thinning of superfluid films below the critical point

Experiments on $^4$He films reveal an attractive Casimir-like force at the bulk $λ$-point, and in the superfluid regime. Previous work has explained the magnitude of this force at the $λ$ transition and deep in the superfluid region but not the substantial attractive force immediately below the $λ$-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.

cond-mat.stat-mech↗