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Y. Kafri

Publications and source records attributed to Y. Kafri.

At least 19 recordsLinked to original sources
arXiv2015

Pressure is not a state function for generic active fluids

Pressure is the mechanical force per unit area that a confined system exerts on its container. In thermal equilibrium, it depends only on bulk properties (density, temperature, etc.) through an equation of state. Here we show that in a wide class of active systems the pressure depends on the precise interactions between the active particles and the confining walls. In general, therefore, active fluids have no equation of state, their mechanical pressures exhibit anomalous properties that defy the familiar thermodynamic reasoning that holds in equilibrium. The pressure remains a function of state, however, in some specific and well-studied active models that tacitly restrict the character of the particle-wall and/or particle-particle interactions.

cond-mat.stat-mech↗
arXiv2015

Multilane driven diffusive systems

We consider networks made of parallel lanes along which particles hop according to driven diffusive dynamics. The particles also hop transversely from lane to lane, hence indirectly coupling their longitudinal dynamics. We present a general method for constructing the phase diagram of these systems which reveals that in many cases their physics reduce to that of single-lane systems. The reduction to an effective single-lane description legitimizes, for instance, the use of a single TASEP to model the hopping of molecular motors along the many tracks of a single microtubule. Then, we show how, in quasi-2D settings, new phenomena emerge due to the presence of non-zero transverse currents, leading, for instance, to strong `shear localisation' along the network.

cond-mat.stat-mech↗
arXiv2015

Pressure and Phase Equilibria in Interacting Active Brownian Spheres

We derive from first principles the mechanical pressure $P$, defined as the force per unit area on a bounding wall, in a system of spherical, overdamped, active Brownian particles at density $ρ$. Our exact result relates $P$, in closed form, to bulk correlators and shows that (i) $P(ρ)$ is a state function, independent of the particle-wall interaction; (ii) interactions contribute two terms to $P$, one encoding the slow-down that drives motility-induced phase separation, and the other a direct contribution well known for passive systems; (iii) $P(ρ)$ is equal in coexisting phases. We discuss the consequences of these results for the motility-induced phase separation of active Brownian particles, and show that the densities at coexistence do not satisfy a Maxwell construction on $P$.

cond-mat.soft↗
arXiv2014

Disorder induced power-law response of a superconducting vortex on a plane

We report drive-response experiments on individual superconducting vortices on a plane, a realization for a 1+1-dimensional directed polymer in random media. For this we use magnetic force microscopy (MFM) to image and manipulate individual vortices trapped on a twin boundary in YBCO near optimal doping. We find that when we drag a vortex with the magnetic tip it moves in a series of jumps. As theory suggests the jump-size distribution does not depend on the applied force and is consistent with power-law behavior. The measured power is much larger than widely accepted theoretical calculations.

cond-mat.supr-con↗
arXiv2011

How the DNA sequence affects the Hill curve of transcriptional response

The Hill coefficient is often used as a direct measure of the cooperativity of binding processes. It is an essential tool for probing properties of reactions in many biochemical systems. Here we analyze existing experimental data and demonstrate that the Hill coefficient characterizing the binding of transcription factors to their cognate sites can in fact be larger than one -- the standard indication of cooperativity -- even in the absence of any standard cooperative binding mechanism. By studying the problem analytically, we demonstrate that this effect occurs due to the disordered binding energy of the transcription factor to the DNA molecule and the steric interactions between the different copies of the transcription factor. We show that the enhanced Hill coefficient implies a significant reduction in the number of copies of the transcription factors which is needed to occupy a cognate site and, in many cases, can explain existing estimates for numbers of the transcription factors in cells. The mechanism is general and should be applicable to other biological recognition processes.

physics.bio-ph↗
arXiv2011

Classes of fast and specific search mechanisms for proteins on DNA

Problems of search and recognition appear over different scales in biological systems. In this review we focus on the challenges posed by interactions between proteins, in particular transcription factors, and DNA and possible mechanisms which allow for a fast and selective target location. Initially we argue that DNA-binding proteins can be classified, broadly, into three distinct classes which we illustrate using experimental data. Each class calls for a different search process and we discuss the possible application of different search mechanisms proposed over the years to each class. The main thrust of this review is a new mechanism which is based on barrier discrimination. We introduce the model and analyze in detail its consequences. It is shown that this mechanism applies to all classes of transcription factors and can lead to a fast and specific search. Moreover, it is shown that the mechanism has interesting transient features which allow for stability at the target despite rapid binding and unbinding of the transcription factor from the target.

q-bio.BM↗
arXiv2011

Phase diagram of two-lane driven diffusive systems

We consider a large class of two-lane driven diffusive systems in contact with reservoirs at their boundaries and develop a stability analysis as a method to derive the phase diagrams of such systems. We illustrate the method by deriving phase diagrams for the asymmetric exclusion process coupled to various second lanes: a diffusive lane; an asymmetric exclusion process with advection in the same direction as the first lane, and an asymmetric exclusion process with advection in the opposite direction. The competing currents on the two lanes naturally lead to a very rich phenomenology and we find a variety of phase diagrams. It is shown that the stability analysis is equivalent to an `extremal current principle' for the total current in the two lanes. We also point to classes of models where both the stability analysis and the extremal current principle fail.

cond-mat.stat-mech↗
arXiv2009

Non-equilibrium phase transitions in tubulation by molecular motors

The extraction of membrane tubes by molecular motors is known to play an important role for the transport properties of eukaryotic cells. By studying a generic class of models for the tube extraction, we discover a rich phase diagram. In particular we show that the density of motors along the tube can exhibit shocks, inverse shocks and plateaux, depending on parameters which could in principle be probed experimentally. In addition the phase diagram exhibits interesting reentrant behavior.

cond-mat.stat-mech↗
arXiv2009

Searching fast for a target on a DNA without falling to traps

Genomic expression depends critically both on the ability of regulatory proteins to locate specific target sites on a DNA within seconds and on the formation of long lived (many minutes) complexes between these proteins and the DNA. Equilibrium experiments show that indeed regulatory proteins bind tightly to their target site. However, they also find strong binding to other non-specific sites which act as traps that can dramatically increase the time needed to locate the target. This gives rise to a conflict between the speed and stability requirements. Here we suggest a simple mechanism which can resolve this long-standing paradox by allowing the target sites to be located by proteins within short time scales even in the presence of traps. Our theoretical analysis shows that the mechanism is robust in the presence of generic disorder in the DNA sequence and does not require a specially designed target site.

cond-mat.soft↗
arXiv2007

Dynamics of RNA Translocation through a Nanopore

We present a simplified model of the dynamics of translocation of RNA through a nanopore which only allows the passage of unbound nucleotides. In particular, we consider the disorder averaged translocation dynamics of random, two-component, single-stranded nucleotides, by reducing the dynamics to the motion of a random walker on a one-dimensional free energy landscape of translocation. These translocation landscapes are calculated from the folds of the RNA sequences and the voltage bias applied across the nanopore. We compute these landscapes for 1500 randomly drawn two-letter sequences of length 4000. Simulations of the dynamics on these landscapes display anomalous characteristics, similar to random forcing energy landscapes, where the translocation process proceeds slower than linearly in time for sufficiently small voltage biases across the nanopore, but moves linearly in time at large voltage biases. We argue that our simplified model provides an upper bound to the more realistic translocation dynamics, and thus we expect that all RNA translocation models will exhibit anomalous regimes.

q-bio.BM↗
arXiv2006

Loop Dynamics in DNA Denaturation

The dynamics of a loop in DNA molecules at the denaturation transition is studied by scaling arguments and numerical simulations. The autocorrelation function of the state of complementary bases (either closed or open) is calculated. The long-time decay of the autocorrelation function is expressed in terms of the loop exponent c both for homopolymers and heteropolymers. This suggests an experimental method for measuring the exponent c using florescence correlation spectroscopy.

cond-mat.stat-mech↗
arXiv2005

Collective dynamics of molecular motors pulling on fluid membranes

The collective dynamics of $N$ weakly coupled processive molecular motors are considered theoretically. We show, using a discrete lattice model, that the velocity-force curves strongly depend on the effective dynamic interactions between motors and differ significantly from a simple mean field prediction. They become essentially independent of $N$ if it is large enough. For strongly biased motors such as kinesin this occurs if $N\gtrsim 5$. The study of a two-state model shows that the existence of internal states can induce effective interactions.

q-bio.SC↗
arXiv2004

Pause Point Spectra in DNA Constant-Force Unzipping

Under constant applied force, the separation of double-stranded DNA into two single strands is known to proceed through a series of pauses and jumps. Given experimental traces of constant-force unzipping, we present a method whereby the locations of pause points can be extracted in the form of a pause point spectrum. A simple theoretical model of DNA constant-force unzipping is demonstrated to produce good agreement with the experimental pause point spectrum of lambda phage DNA. The locations of peaks in the experimental and theoretical pause point spectra are found to be nearly coincident below 6000 bp. The model only requires the sequence, temperature and a set of empirical base pair binding and stacking energy parameters, and the good agreement with experiment suggests that pause points are primarily determined by the DNA sequence. The model is also used to predict pause point spectra for the BacterioPhage PhiX174 genome. The algorithm for extracting the pause point spectrum might also be useful for studying related systems which exhibit pausing behavior such as molecular motors.

cond-mat.soft↗
arXiv2004

Disorder and non-conservation in a driven diffusive system

We consider a disordered asymmetric exclusion process in which randomly chosen sites do not conserve particle number. The model is motivated by features of many interacting molecular motors such as RNA polymerases. We solve the steady state exactly in the two limits of infinite and vanishing non-conserving rates. The first limit is used as an approximation to large but finite rates and allows the study of Griffiths singularities in a nonequilibrium steady state despite the absence of any transition in the pure model. The disorder is also shown to induce a stretched exponential decay of system density with stretching exponent ϕ= 2/5.

cond-mat.stat-mech↗
arXiv2003

Measurement of the Phase Diagram of DNA Unzipping in the Temperature- Force Plane

We separate double stranded lambda phage DNA by applying a fixed force at a constant temperature ranging from 15C to 50C, and measure the minimum force required to separate the two strands, providing the first experimental determination of the phase boundary between single stranded DNA and double stranded DNA in the temperature- force plane. The measurements also offer information on the free energy of dsDNA at temperatures where dsDNA does not thermally denature in the absence of force. While parts of the phase diagram can be explained using existing models and free energy parameters, others deviate significantly. Possible reasons for the deviations between theory and experiment are considered.

cond-mat.soft↗
arXiv2002

Griffiths singularities in unbinding of strongly disordered polymers

Griffiths singularities occurring in the unbinding of strongly disordered heteropolymers are studied. A model with two randomly distributed binding energies -1 and -v, is introduced and studied analytically by analyzing the Lee-Yang zeros of the partition sum. It is demonstrated that in the limit v -> infinity the model exhibits a Griffiths type singularity at a temperature T_G =O(1) corresponding to melting of long homogeneous domains of the low binding energy. For finite v >> 1 the model is expected to exhibit an additional, unbinding, transition at a high temperature T_M=O(v).

cond-mat.stat-mech↗