The many-body dynamics exhibited by living objects include group formation within a population, and the non-equilibrium process of attrition between two opposing populations due to competition or conflict. We show analytically and numerically that the combination of these two dynamical processes generates an attrition duration T whose nonlinear dependence on population asymmetry x is in stark contrast to standard mass-action theories. A minority population experiences a longer survival time than two equally balanced populations, irrespective of whether the majority population adopts such internal grouping or not. Adding a third population with pre-defined group sizes allows T(x) to be tailored. Our findings compare favorably to real-world observations.
A colloidal system of spheres interacting with both a deep and narrow attractive potential and a shallow long-ranged barrier exhibits a prepeak in the static structure factor. This peak can be related to an additional mesoscopic length scale of clusters and/or voids in the system. Simulation studies of this system have revealed that it vitrifies upon increasing the attraction into a gel-like solid at intermediate densities. The dynamics at the mesoscopic length scale corresponding to the prepeak represents the slowest mode in the system. Using mode coupling theory with all input directly taken from simulations, we reveal the mechanism for glassy arrest in the system at 40% packing fraction. The effects of the low-q peak and of polydispersity are considered in detail. We demonstrate that the local formation of physical bonds is the process whose slowing down causes arrest. It remains largely unaffected by the large-scale heterogeneities, and sets the clock for the slow cluster mode. Results from mode-coupling theory without adjustable parameters agree semi-quantitatively with the local density correlators but overestimate the lifetime of the mesoscopic structure (voids).
As a generic model system of an asymmetric binary fluid mixture, hexadecane dissolved in carbon dioxide is considered, using a coarse-grained bead-spring model for the short polymer, and a simple spherical particle with Lennard-Jones interactions for the carbon dioxide molecules. In previous work, it has been shown that this model reproduces the real phase diagram reasonable well, and also the initial stages of spinodal decomposition in the bulk following a sudden expansion of the system could be studied. Using the parallelized simulation package ESPResSo on a multiprocessor supercomputer, phase separation of thin fluid films confined between parallel walls that are repulsive for both types of molecules are simulated in a rather large system (1356 x 1356 x 67.8 A^3, corresponding to about 3.2 million atoms). Following the sudden system expansion, a complicated interplay between phase separation in the directions perpendicular and parallel to the walls is found: in the early stages the hexadecane molecules accumulate mostly in the center of the slit pore, but as the coarsening of the structure in the parallel direction proceeds, the inhomogeneity in the perpendicular direction gets much reduced. Studying then the structure factors and correlation functions at fixed distances from the wall, the densities are essentially not conserved at these distances, and hence the behavior differs strongly from spinodal decomposition in the bulk. Some of the characteristic lengths show a nonmonotonic variation with time, and simple coarsening described by power-law growth is only observed if the domain sizes are much larger than the film thickness.
Subject of this work are the applications of a field theoretical model, called here generalized nonlinear sigma model or simply GNLSM,to the dynamics of a chain subjected to constraints. Chains with similar properties and constraints have been discussed in a seminal paper of Edwards and Goodyear using an approach based on the Langevin equation. The GNLSM has been proposed in a previous publication in order to describe the dynamics of a two dimensional chain. In this paper the model is extended to d dimensions and a bending energy term is added to its action. As an application, two observables are computed in the case of a very stiff chain. The first observable is the dynamical form factor of a ring shaped chain. The second observable is a straightforward generalization to dynamics of the static form factor. This observable is relevant in order to estimate the average distance between two arbitrary points of the chain. Finally, a variant of the GNLNM is presented, in which the topological conditions which constrain the motion of two linked chains are imposed with the help of the Gauss linking invariant.
One of the most fundamental quantities associated with polymer translocation through a nanopore is the translocation time $tau$ and its dependence on the chain length $N$. Our simulation results based on both the bond fluctuation Monte Carlo and Molecular Dynamics methods confirm the original prediction $tausim N^{2 u+1}$, which scales in the same manner as the Rouse relaxation time of the chain except for a larger prefactor, and invalidates other scaling claims.
Using Langevin dynamics simulations, we investigate the influence of polymer-pore interactions on the dynamics of biopolymer translocation through nanopores. We find that an attractive interaction can significantly change the translocation dynamics. This can be understood by examining the three components of the total translocation time $tau approx tau_1+tau_2+tau_3$ corresponding to the initial filling of the pore, transfer of polymer from the textit{cis} side to the textit{trans} side, and emptying of the pore, respectively. We find that the dynamics for the last process of emptying of the pore changes from non-activated to activated in nature as the strength of the attractive interaction increases, and $tau_3$ becomes the dominant contribution to the total translocation time for strong attraction. This leads to a new dependence of $tau$ as a function of driving force and chain length. Our results are in good agreement with recent experimental findings, and provide a possible explanation for the different scaling behavior observed in solid state nanopores {it vs.} that for the natural $alpha$-hemolysin channel.
Zhenyuan Zhao
,Juan Camilo Bohorquez
,Alex Dixon
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(2009)
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"Anomalously slow attrition times for asymmetric populations with internal group dynamics"
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Neil F. Johnson
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