Diffusion in an elastic medium: A model for macromolecule transport across the nuclear pore complex

Nuclear pore complexes (NPCs) are very selective filters that sit on the membrane of the nucleus and monitor the transport between the cytoplasm and the nucleoplasm. For the central plug of NPC two models have been suggested in the literature. The first suggests that the plug is a reversible hydrogel while the other suggests that it is a polymer brush. Here we propose a model for the transport of a protein through the plug, which is general enough to cover both the models. The protein stretches the plug and creates a local deformation, which together with the protein, we refer to as the bubble. We start with the free energy for creation of the bubble and consider its motion within the plug. The relevant coordinate is the center of the bubble which executes random walk. We find that for faster relaxation of the gel, the diffusion of the bubble is greater. (C) 2014 Elsevier-B.V. All rights reserved.

Healing time for the growth of thin films on patterned substrates

The healing times for the growth of thin films on patterned substrates are studied using simulations of two discrete models of surface growth: the Family model and the Das Sarma-Tamborenea (DT) model. The healing time, defined as the time at which the characteristics of the growing interface are ``healed'' to those obtained in growth on a flat substrate, is determined via the study of the nearest-neighbor height difference correlation function. Two different initial patterns are considered in this work: a relatively smooth tent-shaped triangular substrate and an atomically rough substrate with singlesite pillars or grooves. We find that the healing time of the Family and DT models on aL x L triangular substrate is proportional to L-z, where z is the dynamical exponent of the models. For the Family model, we also analyze theoretically, using a continuum description based on the linear Edwards-Wilkinson equation, the time evolution of the nearest-neighbor height difference correlation function in this system. The correlation functions obtained from continuum theory and simulation are found to be consistent with each other for the relatively smooth triangular substrate. For substrates with periodic and random distributions of pillars or grooves of varying size, the healing time is found to increase linearly with the height (depth) of pillars (grooves). We show explicitly that the simulation data for the Family model grown on a substrate with pillars or grooves do not agree with results of a calculation based on the continuum Edwards-Wilkinson equation. This result implies that a continuum description does not work when the initial pattern is atomically rough. The observed dependence of the healing time on the substrate size and the initial height (depth) of pillars (grooves) can be understood from the details of the diffusion rule of the atomistic model. The healing time of both models for pillars is larger than that for grooves with depth equal to the height of the pillars. The calculated healing time for both Family and DT models is found to depend on how the pillars and grooves are distributed over the substrate. (C) 2014 Elsevier B.V. All rights reserved.

Transition from dissipative to conservative dynamics in equations of hydrodynamics

We show, by using direct numerical simulations and theory, how, by increasing the order of dissipativity (alpha) in equations of hydrodynamics, there is a transition from a dissipative to a conservative system. This remarkable result, already conjectured for the asymptotic case alpha -> infinity U. Frisch et al., Phys. Rev. Lett. 101, 144501 (2008)], is now shown to be true for any large, but finite, value of alpha greater than a crossover value alpha(crossover). We thus provide a self-consistent picture of how dissipative systems, under certain conditions, start behaving like conservative systems and hence elucidate the subtle connection between equilibrium statistical mechanics and out-of-equilibrium turbulent flows.

An integral fluctuation theorem for systems with unidirectional transitions

The fluctuations of a Markovian jump process with one or more unidirectional transitions, where R-ij > 0 but R-ji = 0, are studied. We find that such systems satisfy an integral fluctuation theorem. The fluctuating quantity satisfying the theorem is a sum of the entropy produced in the bidirectional transitions and a dynamical contribution, which depends on the residence times in the states connected by the unidirectional transitions. The convergence of the integral fluctuation theorem is studied numerically and found to show the same qualitative features as systems exhibiting microreversibility.

Phase space path integral approach to harmonic oscillator with a time-dependent force constant

The quantum statistical mechanical propagator for a harmonic oscillator with a time-dependent force constant, m omega(2)(t), has been investigated in the past and was found to have only a formal solution in terms of the solutions of certain ordinary differential equations. Such path integrals are frequently encountered in semiclassical path integral evaluations and having exact analytical expressions for such path integrals is of great interest. In a previous work, we had obtained the exact propagator for motion in an arbitrary time-dependent harmonic potential in the overdamped limit of friction using phase space path integrals in the context of Levy flights - a result that can be easily extended to Brownian motion. In this paper, we make a connection between the overdamped Brownian motion and the imaginary time propagator of quantum mechanics and thereby get yet another way to evaluate the latter exactly. We find that explicit analytic solution for the quantum statistical mechanical propagator can be written when the time-dependent force constant has the form omega(2)(t) = lambda(2)(t) - d lambda(t)/dt where lambda(t) is any arbitrary function of t and use it to evaluate path integrals which have not been evaluated previously. We also employ this method to arrive at a formal solution of the propagator for both Levy flights and Brownian subjected to a time-dependent harmonic potential in the underdamped limit of friction. (C) 2015 Elsevier B.V. All rights reserved.

Estimation of nonlinearities from pseudodynamic and dynamic responses of bridge structures using the Delay Vector Variance method

Analysis of the variability in the responses of large structural systems and quantification of their linearity or nonlinearity as a potential non-invasive means of structural system assessment from output-only condition remains a challenging problem. In this study, the Delay Vector Variance (DVV) method is used for full scale testing of both pseudo-dynamic and dynamic responses of two bridges, in order to study the degree of nonlinearity of their measured response signals. The DVV detects the presence of determinism and nonlinearity in a time series and is based upon the examination of local predictability of a signal. The pseudo-dynamic data is obtained from a concrete bridge during repair while the dynamic data is obtained from a steel railway bridge traversed by a train. We show that DVV is promising as a marker in establishing the degree to which a change in the signal nonlinearity reflects the change in the real behaviour of a structure. It is also useful in establishing the sensitivity of instruments or sensors deployed to monitor such changes. (C) 2015 Elsevier B.V. All rights reserved.

Anomalous lifetime statistics of ligand-receptor binding in a tethered polymer system

In this paper, motivated by observations of non-exponential decay times in the stochastic binding and release of ligand-receptor systems, exemplified by the work of Rogers et al on optically trapped DNA-coated colloids (Rogers et al 2013 Soft Matter 9 6412), we explore the general problem of polymer-mediated surface adhesion using a simplified model of the phenomenon in which a single polymer molecule, fixed at one end, binds through a ligand at its opposite end to a flat surface a fixed distance L away and uniformly covered with receptor sites. Working within the Wilemski-Fixman approximation to diffusion-controlled reactions, we show that for a flexible Gaussian chain, the predicted distribution of times f(t) for which the ligand and receptor are bound is given, for times much shorter than the longest relaxation time of the polymer, by a power law of the form t(-1/4). We also show when the effects of chain stiffness are incorporated into this model (approximately), the structure of f(t) is altered to t(-1/2). These results broadly mirror the experimental trends in the work cited above.

Autoregressive cascades on random networks

A network cascade model that captures many real-life correlated node failures in large networks via load redistribution is studied. The considered model is well suited for networks where physical quantities are transmitted, e.g., studying large scale outages in electrical power grids, gridlocks in road networks, and connectivity breakdown in communication networks, etc. For this model, a phase transition is established, i.e., existence of critical thresholds above or below which a small number of node failures lead to a global cascade of network failures or not. Theoretical bounds are obtained for the phase transition on the critical capacity parameter that determines the threshold above and below which cascade appears or disappears, respectively, that are shown to closely follow numerical simulation results. (C) 2015 Elsevier B.V. All rights reserved.

Autoregressive cascades on random networks

A network cascade model that captures many real-life correlated node failures in large networks via load redistribution is studied. The considered model is well suited for networks where physical quantities are transmitted, e.g., studying large scale outages in electrical power grids, gridlocks in road networks, and connectivity breakdown in communication networks, etc. For this model, a phase transition is established, i.e., existence of critical thresholds above or below which a small number of node failures lead to a global cascade of network failures or not. Theoretical bounds are obtained for the phase transition on the critical capacity parameter that determines the threshold above and below which cascade appears or disappears, respectively, that are shown to closely follow numerical simulation results. (C) 2015 Elsevier B.V. All rights reserved.

Cost effective campaigning in social networks

Campaigners are increasingly using online social networking platforms for promoting products, ideas and information. A popular method of promoting a product or even an idea is incentivizing individuals to evangelize the idea vigorously by providing them with referral rewards in the form of discounts, cash backs, or social recognition. Due to budget constraints on scarce resources such as money and manpower, it may not be possible to provide incentives for the entire population, and hence incentives need to be allocated judiciously to appropriate individuals for ensuring the highest possible outreach size. We aim to do the same by formulating and solving an optimization problem using percolation theory. In particular, we compute the set of individuals that are provided incentives for minimizing the expected cost while ensuring a given outreach size. We also solve the problem of computing the set of individuals to be incentivized for maximizing the outreach size for given cost budget. The optimization problem turns out to be non trivial; it involves quantities that need to be computed by numerically solving a fixed point equation. Our primary contribution is, that for a fairly general cost structure, we show that the optimization problems can be solved by solving a simple linear program. We believe that our approach of using percolation theory to formulate an optimization problem is the first of its kind. (C) 2016 Elsevier B.V. All rights reserved.

Multiscale Coupling in Complex Mechanical Systems

Multiscale coupling attracts broad interests from mechanics, physics and chemistry to biology. The diversity and coupling of physics at different scales are two essential features of multiscale problems in far-from-equilibrium systems. The two features present fundamental difficulties and are great challenges to multiscale modeling and simulation. The theory of dynamical system and statistical mechanics provide fundamental tools for the multiscale coupling problems. The paper presents some closed multiscale formulations, e.g., the mapping closure approximation, multiscale large-eddy simulation and statistical mesoscopic damage mechanics, for two typical multiscale coupling problems in mechanics, that is, turbulence in fluids and failure in solids. It is pointed that developing a tractable, closed nonequilibrium statistical theory may be an effective approach to deal with the multiscale coupling problems. Some common characteristics of the statistical theory are discussed.

Multiscale Coupling: Challenges and Opportunities

Multiscale coupling is ubiquitous in nature and attracts broad interests of scientists from mathematicians, physicists, machinists, chemists to biologists. However, much less attention has been paid to its intrinsic implication. In this paper, multiscale coupling is introduced by studying two typical examples in classic mechanics: fluid turbulence and solid failure. The nature of multiscale coupling in the two examples lies in their physical diversities and strong coupling over wide-range scales. The theories of dynamical system and statistical mechanics provide fundamental methods for the multiscale coupling problems. The diverse multiscale couplings call for unified approaches and might expedite new concepts, theories and disciplines.

Turbulent passive scalar field of a small prandtl number

The statistical-mechanics theory of the passive scalar field convected by turbulence, developed in an earlier paper [Phys. Fluids 28, 1299 (1985)], is extended to the case of a small molecular Prandtl number. The set of governing integral equations is solved by the equation-error method. The resultant scalar-variance spectrum for the inertial range is F(k)~x−5/3/[1+1.21x1.67(1+0.353x2.32)], where x is the wavenumber scaled by Corrsin's dissipation wavenumber. This result reduces to the − (5)/(3) law in the inertial-convective range. It also approximately reduces to the − (17)/(3) law in the inertial-diffusive range, but the proportionality constant differs from Batchelor's by a factor of 3.6.

A passive scalar field convected by turbulence

Classical statistical mechanics is applied to the study of a passive scalar field convected by isotropic turbulence. A complete set of independent real parameters and dynamic equations are worked out to describe the dynamic state of the passive scalar field. The corresponding Liouville equation is solved by a perturbation method based upon a Langevin–Fokker–Planck model. The closure problem is treated by a variational approach reported in earlier papers. Two integral equations are obtained for two unknown functions: the scalar variance spectrum F(k) and the effective damping coefficient (k). The appearance of the energy spectrum of the velocity field in the two integral equations represents the coupling of the scalar field with the velocity field. As an application of the theory, the two integral equations are solved to derive the inertial-convective-range spectrum, obtaining F(k)=0.61 −1/3 k−5/3. Here is the dissipation rate of the scalar variance and is the dissipation rate of the energy of the velocity field. This theoretical value of the scalar Kolmogorov constant, 0.61, is in good agreement with experiments.

Universal equilibrium range of turbulence

An attempt is made to determine the form of F(x), the dimensionless function of universal nature which occurs in the energy spectrum for the universal equilibrium range of fully developed turbulence, by the method of statistical mechanics without introducing any parameter of semiempirical nature. Then, the validity of the variational approach to the closure problem of turbulence theory is tested by applying it to the study of the universal equilbrium range of turbulence.