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It is well known that path probabilities of Brownian motion correspond to the equilibrium configurational probabilities of flexible Gaussian polymers, while those of active Brownian motion correspond to in-extensible semiflexible polymers. Here we investigate the properties of the equilibrium polymer that corresponds to the trajectories of particles acted on simultaneously by both Brownian as well as active noise. Through this mapping we can see interesting crossovers in mechanical properties of the polymer with changing contour length. The polymer end-to-end distribution exhibits Gaussian behaviour for short lengths, which changes to the form of semiflexible filaments at intermediate lengths, to finally go back to a Gaussian form for long contour lengths. By performing a Laplace transform of the governing Fokker-Planck equation of the active Brownian particle, we discuss a direct method to derive exact expressions for all the moments of the relevant dynamical variables, in arbitrary dimensions. These are verified via numerical simulations and used to describe interesting qualitative features such as, for example, dynamical crossovers. Finally we discuss the kurtosis of the ABP's position which we compute exactly and show that it can be used to differentiate between active Brownian particles and active Ornstein-Uhlenbeck process., Comment: 14 pages, 13 figures; modifications for better clarity

We consider a model of an extensible semiflexible filament moving in two dimensions on a motility assay of motor proteins represented explicitly as active harmonic linkers. Their heads bind stochastically to polymer segments within a capture radius, and extend along the filament in a directed fashion before detaching. Both the extension and detachment rates are load-dependent and generate an active drive on the filament. The filament undergoes a first order phase transition from open chain to spiral conformations and shows a reentrant behavior in both the active extension and the turnover, defined as the ratio of attachment-detachment rates. Associated with the phase transition, the size and shape of the polymer changes non-monotonically, and the relevant autocorrelation functions display double-exponential decay. The corresponding correlation times show a maximum signifying the dominance of spirals. The orientational dynamics captures the rotation of spirals, and its correlation time decays with activity as a power law., Comment: 13 pages, 14 figures; version accepted for publication in Soft Matter

We consider an active Brownian particle in a $d$-dimensional harmonic trap, in the presence of translational diffusion. While the Fokker-Planck equation can not in general be solved to obtain a closed form solution of the joint distribution of positions and orientations, as we show, it can be utilized to evaluate the exact time dependence of all moments, using a Laplace transform approach. We present explicit calculation of several such moments at arbitrary times and their evolution to the steady state. In particular we compute the kurtosis of the displacement, a quantity which clearly shows the difference of the active steady state properties from the equilibrium Gaussian form. We find that it increases with activity to asymptotic saturation, but varies non-monotonically with the trap-stiffness, thereby capturing a recently observed active- to- passive re-entrant behavior., Comment: 17 pages, 7 figures; version accepted for publication in Journal of Statistical Mechanics: Theory and Experiment

Stochastic motion of macrospins is similar to driven diffusion of Brownian particles on the surface of a sphere. One crucial difference is in how the micro-states transform under time reversal. This dictates the form of stochastic entropy production (sEP). An excess sEP in the reservoir, in addition to a Clausius term, may appear depending on the interpretation of stochastic trajectory, thereby, precluding such analysis without a detailed knowledge of the governing dynamics. To show this, we derive expressions of sEP using Fokker–Planck equation, and the ratio of probability distributions of time-forward and time-reversed trajectories. We calculate probability distributions of sEP using numerical simulations, and obtain good agreement with the detailed fluctuation theorem. Within adiabatic approximation, analytic form for the distribution function is also derived.

In eukaryotic cells, motor proteins (MP) bind to cytoskeletal filaments and move along them in a directed manner generating active stresses. During cell division a spindle structure of overlapping antiparallel microtubules (MT) form whose stability and dynamics under the influence of MPs has been studied extensively. Although passive cross linkers (PCL) were known to provide structural stability to filamentous network, consequences of the interplay between ATP dependent active forces of MPs and passive entropic forces of PCLs on MT overlap remains largely unexplored. Here, we formulate and characterize a model to study this, using linear stability analysis and numerical integration. In presence of PCLs, we find dynamic phase transitions with changing activity exhibiting regimes of stable partial overlap with or without oscillations, instability towards complete overlap, and stable limit cycle oscillations that emerge via a supercritical Hopf bifurcation characterized by an oscillation frequency determined by the MP and PCL parameters. We show that the overlap dynamics and stability depend crucially on whether both the MTs of overlapping pair are movable or one is immobilized, having potential implications for in vivo and in vitro studies., 13 pages, 9 figures

Inspired by recent experiments on the effects of cytosolic crowders on the organization of bacterial chromosomes, we consider a "feather-boa" type model chromosome in the presence of non-additive crowders, encapsulated within a cylindrical cell. We observe spontaneous emergence of complementary helicity of the confined polymer and crowders. This feature is reproduced within a simplified effective model of the chromosome. This latter model further establishes the occurrence of longitudinal and transverse spatial segregation transitions between the chromosome and crowders upon increasing crowder size., 7 pages, 5 figures; minor modifications; version accepted for publication in Europhysics Letters

Motivated by recent experiments probing shape, size and dynamics of bacterial chromosomes in growing cells, we consider a polymer model consisting of a circular backbone to which side-loops are attached, confined to a cylindrical cell. Such a model chromosome spontaneously adopts a helical shape, which is further compacted by molecular crowders to occupy a nucleoid-like subvolume of the cell. With increasing cell length, the longitudinal size of the chromosome increases in a non-linear fashion to finally saturate, its morphology gradually opening up while displaying a changing number of helical turns. For shorter cells, the chromosome extension varies non-monotonically with cell size, which we show is associated with a radial to longitudinal spatial reordering of the crowders. Confinement and crowders constrain chain dynamics leading to anomalous diffusion. While the scaling exponent for the mean squared displacement of center of mass grows and saturates with cell length, that of individual loci displays broad distribution with a sharp maximum., Comment: 12 pages, 12 figures

SummaryWhile the spatiotemporal structure of the genome is crucial to its biological function, many basic questions remain unanswered on the morphology and segregation of chromosomes. Here, we experimentally show inEscherichia colithat spatial confinement plays a dominant role in determining both the chromosome size and position. In non-dividing cells with lengths up to 10 times normal, single chromosomes are observed to expand more than 4 fold in size, an effect only modestly influenced by deletions of various nucleoid-associated proteins. Chromosomes show pronounced internal dynamics but exhibit a robust positioning where single nucleoids reside strictly at mid-cell, while two nucleoids self-organize at ¼ and ¾ cell positions. Molecular dynamics simulations of model chromosomes recapitulate these phenomena and indicate that these observations can be attributed to depletion effects induced by cytosolic crowders. These findings highlight boundary confinement as a key causal factor that needs to be considered for understanding chromosome organization.

We consider an explicit model of a semiflexible filament moving in two dimensions on a gliding assay of motor proteins, which attach to and detach from filament segments stochastically, with a detachment rate that depends on the local load experienced. Attached motor proteins move along the filament to one of its ends with a velocity that varies non-linearly with the motor protein extension. The resultant force on the filament drives it out of equilibrium. The distance from equilibrium is reflected in the end-to-end distribution, modified bending stiffness, and a transition to spiral morphology of the polymer. The local stress dependence of activity results in correlated fluctuations in the speed and direction of the center of mass leading to a series of ballistic-diffusive crossovers in its dynamics., Comment: 11 pages, 11 figures; version accepted for publication in Physical Review E

We present and compare different versions of a simple particle pump-model that describes average directed current of repulsively interacting particles in a narrow channel, due to time-varying local potentials. We analyze the model on discrete lattice with particle exclusion, using three choices of potential-dependent hopping rates that obey microscopic reversibility. Treating the strength of the external potential as a small parameter with respect to thermal energy, we present a perturbative calculation to obtain the expression for average directed current. This depends on driving frequency, phase, and particle density. The directed current vanishes as density goes to zero or close packing. For two choices of hopping rates, it reaches maximum at intermediate densities, while for a third choice, it shows a curious current reversal with increasing density. This can be interpreted in terms of a particle-hole symmetry. Stochastic simulations of the model show good agreement with our analytic predictions., Comment: 9 pages, 1 figure: Based on invited talk delivered by the author at StatPhys-Kolkata VIII, Kolkata (India), December, 2014

The nature of the melting transition for a system of hard discs with translational degrees of freedom in two spatial dimensions has been analysed by a combination of computer simulation methods and a finite size scaling technique. The behaviour of the system is consistent with the predictions of the Kosterlitz–Thouless–Halperin–Nelson–Young (KTHNY) theory. The structural and elastic properties of binary colloidal mixtures in two and three spatial dimensions are discussed as well as those of colloidal systems with quenched point impurities. Hard and soft discs in external periodic (light-) fields show rich phase diagrams including freezing and melting transitions when the density of the system is varied. Monte Carlo simulations for detailed finite size scaling analysis of various thermodynamic quantities like the order parameter, its cumulants, etc, have been used in order to map the phase diagram of the system for various values of the density and the amplitude of the external potential. For hard discs we find clear indication of a reentrant liquid phase over a significant region of the parameter space. The simulations therefore show that the system of hard discs behaves in a fashion similar to charge stabilized colloids which are known to undergo an initial freezing, followed by a remelting transition as the amplitude of the imposed modulating field produced by crossed laser beams is steadily increased. Detailed analysis of the simulation data shows several features consistent with a recent dislocation unbinding theory of laser induced melting. The differences and similarities of systems with soft potentials (DLVO, 1/r12, 1/r6) and the relation to experimental data is analysed.

We consider stochastic rotational dynamics of a macrospin at a constant temperature, in presence of an external magnetic field. Starting from the appropriate Langevin equation which contains multiplicative noise, we calculate entropy production (EP) along stochastic trajectories, and obtain fluctuation theorems. The system remains inherently out of equilibrium due to a spin torque supporting azimuthal current, leading to an excess EP apart from the EP due to heat dissipation. The anomaly may be removed using a redefinition of dissipated heat and stochastic work done. Using numerical simulations, we obtain distribution functions for entropy production along stochastic trajectories to find good agreement with the detailed fluctuation theorem., 8 pages, 4 figures; version accepted for publication in JStat

We consider the single-file motion of colloidal particles interacting via short-ranged repulsion and placed in a traveling wave potential, that varies periodically in time and space. Under suitable driving conditions, a directed time-averaged flow of colloids is generated. We obtain analytic results for the model using a perturbative approach to solve the Fokker-Planck equations. The predictions show good agreement with numerical simulations. We find peaks in the time-averaged directed current as a function of driving frequency, wavelength and particle density and discuss possible experimental realizations. Surprisingly, unlike a closely related exclusion dynamics on a lattice, the directed current in the present model does not show current reversal with density. A linear response formula relating current response to equilibrium correlations is also proposed., published version

We present results of molecular dynamics simulations for two-dimensional repulsively interacting colloids driven by a one dimensional asymmetric and commensurate ratchet potential, switching on and off stochastically. This drives a time-averaged directed current of colloids, exhibiting resonance with change in ratcheting frequency, where the resonance frequency itself depends non-monotonically on density. Using scaling arguments, we obtain analytic results that show good agreement with numerical simulations. With increasing ratcheting frequency, we find non-equilibrium re-entrant transitions between solid and modulated liquid phases., Comment: paper and supplementary; published version

Within the Rayleigh-Helmholtz model of active Brownian particles activity is due to a non-linear velocity dependent force. In the presence of an external trapping potential or a constant force, the steady state of the system breaks detailed balance producing a net entropy. Using molecular dynamics simulations, we obtain the probability distributions of entropy production in these steady states. The distribution functions obey detailed fluctuation theorem for entropy production. Using simulation results, we further show that the steady state response function obeys a modified fluctuation-dissipation relation., Comment: 8 pages, 6 figures; version accepted for publication in Phys. Rev. E

Examples of self propulsion in strongly fluctuating environment is abound in nature, e.g., molecular motors and pumps operating in living cells. Starting from Langevin equation of motion, we develop a fluctuating thermodynamic description of self propelled particles using simple models of velocity dependent forces. We derive fluctuation theorems for entropy production and a modified fluctuation dissipation relation, characterizing the linear response at non-equilibrium steady states. We study these notions in a simple model of molecular motors, and in the Rayleigh-Helmholtz and energy-depot model of self propelled particles., 8 pages, version accepted in Phys. Rev. E

Inspired by recent experiments on the spatial organization of bacterial chromosomes, we consider a type of "bottle brush" polymer consisting of a flexible backbone chain, to which flexible side loops are connected. We show that such a model with an open linear backbone spontaneously adopts a helical structure with a well-defined pitch when confined to small cylindrical volume. This helicity persists over a range of sizes and aspect-ratios of the cylinder, provided the packing fraction of the chain is suitably large. We analyze this results in terms of the interplay between the effective stiffness and actual intra-chain packing effects caused by the side-loops in response to the confinement. For the case of a circular backbone, mimicking e.g. the E. coli chromosome, the polymer adopts a linearized configuration of two parallel helices connected at the cylinder poles., Comment: paper and supplementary; 7 pages, 8 figures

We study the response of one dimensional diffusive systems, consisting of particles interacting via symmetric or asymmetric exclusion, to time-periodic driving from two reservoirs coupled to the ends. The dynamical response of the system can be characterized in terms of the structure factor. We find an interesting frequency dependent response -- the current carrying majority excitons cyclically crosses over from a short wavelength mode to a long wavelength mode with an intermediate regime of coexistence. This effect being boundary driven, decays inversely with system size. Analytic calculations show that this behavior is common to diffusive systems, both in absence and presence of correlations., Comment: 6 pages, 4 eps figures

We investigate the slow time scales that arise from aging of the paths during the process of path aggregation. This is studied using Monte-Carlo simulations of a model aiming to describe the formation of fascicles of axons mediated by contact axon-axon interactions. The growing axons are represented as interacting directed random walks in two spatial dimensions. To mimic axonal turnover, random walkers are injected and whole paths of individual walkers are removed at specified rates. We identify several distinct time scales that emerge from the system dynamics and can exceed the average axonal lifetime by orders of magnitude. In the dynamical steady state, the position-dependent distribution of fascicle sizes obeys a scaling law. We discuss our findings in terms of an analytically tractable, effective model of fascicle dynamics., 6 pages, 5 figures; changed the order of presentation, rewritten the abstract and introduction, changed the title, expanded discussions; the main results remain the same

We compare two phenomenological models of dephasing that are in use recently. We show that the stochastic absorption model leads to reasonable dephasing in series (double barrier) and parallel (ring) quantum resistors in presence and absence of magnetic flux. For large enough dephasing it leads to Ohm's law. On the other hand a random phase based statistical model that uses averaging over Gaussian random-phases, picked up by the propagators, leads to several inconsistencies. This can be attributed to the failure of this model to dephase interference between complementary electron waves each following time-reversed path of the other., 7 pages, 9 figures

We investigate by direct numerical solution of appropriate renormalization flow equations, the validity of a recent dislocation unbinding theory for laser induced freezing/melting in two dimensions. The bare elastic moduli and dislocation fugacities which are inputs to the flow equations are obtained for three different 2-d systems (hard disk, inverse $12^{th}$ power and the Derjaguin-Landau-Verwey-Overbeek potentials) from a restricted Monte Carlo simulation sampling only configurations {\em without} dislocations. We conclude that (a) the flow equations need to be correct at least up to third order in defect fugacity to reproduce meaningful results, (b) there is excellent quantitative agreement between our results and earlier conventional Monte Carlo simulations for the hard disk system and (c) while the qualitative form of the phase diagram is reproduced for systems with soft potentials there is some quantitative discrepancy which we explain., Comment: 11 pages, 14 figures, submitted to Phys. Rev. E

We calculate the electrical conductivity of a thin crystalline strip of atoms confined within a quasi one dimensional channel of fixed width. The conductivity shows anomalous behavior as the strip is deformed under tensile loading. Beyond a critical strain, the solid fails by the nucleation of alternating bands of solid and {\em smectic} like phases accompanied by a jump in the conductivity. Since the failure of the strip in this system is known to be reversible, the onductivity anomaly may have practical use as a sensitive strain transducer., Comment: 8 pages, 3 figures, communicated for publication in EPL

We study the phenomenon of laser induced freezing, within a numerical renormalization scheme which allows explicit comparison with a recent defect mediated melting theory. Precise values for the `bare' dislocation fugacities and elastic moduli of the 2-d hard disk system are obtained from a constrained Monte Carlo simulation sampling only configurations {\em without} dislocations. These are used as inputs to appropriate renormalization flow equations to obtain the equilibrium phase diagram which shows excellent agreement with earlier simulation results. We show that the flow equations need to be correct at least up to third order in defect fugacity to reproduce meaningful results., Minor Corrections; Combined version of Europhys. Lett. 67 (2004) p. 814 and Europhys. Lett. 68 (2004) p. 160

We study the free energy of the worm-like-chain model, in the constant-extension ensemble, as a function of the stiffness for finite chains of length L. We find that the polymer properties obtained in this ensemble are "qualitatively" different from those obtained using constant-force ensembles. In particular we find that as we change the stiffness parameter, the polymer makes a transition from the flexible to the rigid phase and there is an intermediate regime of parameter values where the free energy has three minima and both phases are stable. This leads to interesting features in the force-extension curves., Published version, 4 pages, 5 figures, revtex

We show using computer simulations and mean field theory that a system of particles in two dimensions, when confined laterally by a pair of parallel hard walls within a quasi one dimensional channel, possesses several anomalous structural and mechanical properties not observed in the bulk. Depending on the density $\rho$ and the distance between the walls $L_y$, the system shows structural characteristics analogous to a weakly modulated liquid, a strongly modulated smectic, a triangular solid or a buckled phase. At fixed $\rho$, a change in $L_y$ leads to many reentrant discontinuous transitions involving changes in the number of layers parallel to the confining walls depending crucially on the commensurability of inter-layer spacing with $L_y$. The solid shows resistance to elongation but not to shear. When strained beyond the elastic limit it fails undergoing plastic deformation but surprisingly, as the strain is reversed, the material recovers completely and returns to its original undeformed state. We obtain the phase diagram from mean field theory and finite size simulations and discuss the effect of fluctuations., Comment: 14 pages, 13 figures; revised version, accepted in J. Chem. Phys