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Register a new userEffects of hydrodynamic noise on the diffusion of polymers in dilute solutions
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The Rouse-Zimm equation for the position vectors of beads mapping the polymer is generalized by taking into account the viscous aftereffect and the hydrodynamic noise. For the noise, the random fluctuations of the hydrodynamic tensor of stresses are responsible. The preaveraging of the Oseen tensor for the nonstationary Navier-Stokes equation allowed us to relate the time correlation functions of the Fourier components of the bead position to the correlation functions of the hydrodynamic field created by the noise. The velocity autocorrelation function of the center of inertia of the polymer coil is considered in detail for both the short and long times when it behaves according to the t^(-3/2) law and does not depend on any polymer parameters. The diffusion coefficient of the polymer is close to that from the Zimm theory, with corrections depending on the ratio between the size of the bead and the size of the whole coil.
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In this work we study the noise induced effects on the dynamics of short polymers crossing a potential barrier, in the presence of a metastable state. An improved version of the Rouse model for a flexible polymer has been adopted to mimic the molecular dynamics by taking into account both the interactions between adjacent monomers and introducing a Lennard-Jones potential between all beads. A bending recoil torque has also been included in our model. The polymer dynamics is simulated in a two-dimensional domain by numerically solving the Langevin equations of motion with a Gaussian uncorrelated noise. We find a nonmonotonic behaviour of the mean first passage time and the most probable translocation time, of the polymer centre of inertia, as a function of the polymer length at low noise intensity. We show how thermal fluctuations influence the motion of short polymers, by inducing two different regimes of translocation in the molecule transport dynamics. In this context, the role played by the length of the molecule in the translocation time is investigated.
Starting from our recent chemical master equation derivation of the model of an autocatalytic reaction-diffusion chemical system with reactions $U+2V {stackrel {lambda_0}{rightarrow}}~ 3 V;$ and $V {stackrel {mu}{rightarrow}}~P$, $U {stackrel { u}{rightarrow}}~ Q$, we determine the effects of intrinsic noise on the momentum-space behavior of its kinetic parameters and chemical concentrations. We demonstrate that the intrinsic noise induces $n rightarrow n$ molecular interaction processes with $n geq 4$, where $n$ is the number of molecules participating of type $U$ or $V$. The momentum dependences of the reaction rates are driven by the fact that the autocatalytic reaction (inelastic scattering) is renormalized through the existence of an arbitrary number of intermediate elastic scatterings, which can also be interpreted as the creation and subsequent decay of a three body composite state $sigma = phi_u phi_v^2$, where $phi_i$ corresponds to the fields representing the densities of $U$ and $V$. Finally, we discuss the difference between representing $sigma$ as a composite or an elementary particle (molecule) with its own kinetic parameters. In one dimension we find that while they show markedly different behavior in the short spatio-temporal scale, high momentum (UV) limit, they are formally equivalent in the large spatio-temporal scale, low momentum (IR) regime. On the other hand in two dimensions and greater, due to the effects of fluctuations, there is no way to experimentally distinguish between a fundamental and composite $sigma$. Thus in this regime $sigma$ behave as an entity unto itself suggesting that it can be effectively treated as an independent chemical species.
Single-file diffusion (SFD) of an infinite one-dimensional chain of interacting particles has a long-time mean-square displacement (MSD) ~t^1/2, independent of the type of inter-particle repulsive interaction. This behavior is also observed in finite-size chains, although only for certain intervals of time t depending on the chain length L, followed by the ~t for t->infinity, as we demonstrate for a closed circular chain of diffusing interacting particles. Here we show that spatial correlation of noise slows down SFD and can result, depending on the amount of correlated noise, in either subdiffusive behavior ~t^alpha, where 0<alpha<1/2, or even in a total suppression of diffusion (in the limit N-> infinity). Spatial correlation can explain the subdiffusive behavior in recent SFD experiments in circular channels.
Patients at high risk for sudden death often exhibit complex heart rhythms in which abnormal heartbeats are interspersed with normal heartbeats. We analyze such a complex rhythm in a single patient over a 12-hour period and show that the rhythm can be described by a theoretical model consisting of two interacting oscillators with stochastic elements. By varying the magnitude of the noise, we show that for an intermediate level of noise, the model gives best agreement with key statistical features of the dynamics.
We give two different, statistically consistent definitions of the length l of a prime knot tied into a polymer ring. In the good solvent regime the polymer is modelled by a self avoiding polygon of N steps on cubic lattice and l is the number of steps over which the knot ``spreads in a given configuration. An analysis of extensive Monte Carlo data in equilibrium shows that the probability distribution of l as a function of N obeys a scaling of the form p(l,N) ~ l^(-c) f(l/N^D), with c ~ 1.25 and D ~ 1. Both D and c could be independent of knot type. As a consequence, the knot is weakly localized, i.e. <l> ~ N^t, with t=2-c ~ 0.75. For a ring with fixed knot type, weak localization implies the existence of a peculiar characteristic length l^(nu) ~ N^(t nu). In the scaling ~ N^(nu) (nu ~0.58) of the radius of gyration of the whole ring, this length determines a leading power law correction which is much stronger than that found in the case of unrestricted topology. The existence of such correction is confirmed by an analysis of extensive Monte Carlo data for the radius of gyration. The collapsed regime is studied by introducing in the model sufficiently strong attractive interactions for nearest neighbor sites visited by the self-avoiding polygon. In this regime knot length determinations can be based on the entropic competition between two knotted loops separated by a slip link. These measurements enable us to conclude that each knot is delocalized (t ~ 1).
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