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Register a new userDiffusion of two molecular species in a crowded environment: theory and experiments
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Diffusion of a two component fluid is studied in the framework of differential equations, but where these equations are systematically derived from a well-defined microscopic model. The model has a finite carrying capacity imposed upon it at the mesoscopic level and this is shown to lead to non-linear cross diffusion terms that modify the conventional Fickean picture. After reviewing the derivation of the model, the experiments carried out to test the model are described. It is found that it can adequately explain the dynamics of two dense ink drops simultaneously evolving in a container filled with water. The experiment shows that molecular crowding results in the formation of a dynamical barrier that prevents the mixing of the drops. This phenomenon is successfully captured by the model. This suggests that the proposed model can be justifiably viewed as a generalization of standard diffusion to a multispecies setting, where crowding and steric interferences are taken into account.
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We summarise different results on the diffusion of a tracer particle in lattice gases of hard-core particles with stochastic dynamics, which are confined to narrow channels -- single-files, comb-like structures and quasi-one-dimensional channels with the width equal to several particle diameters. We show that in such geometries a surprisingly rich, sometimes even counter-intuitive, behaviour emerges, which is absent in unbounded systems. We also present a survey of different results obtained for a tracer particle diffusion in unbounded systems, which will permit a reader to have an exhaustively broad picture of the tracer diffusion in crowded environments.
We report the study of a new experimental granular Brownian motor, inspired to the one published in [Phys. Rev. Lett. 104, 248001 (2010)], but different in some ingredients. As in that previous work, the motor is constituted by a rotating pawl whose surfaces break the rotation-inversion symmetry through alternated patches of different inelasticity, immersed in a gas of granular particles. The main novelty of our experimental setup is in the orientation of the main axis, which is parallel to the (vertical) direction of shaking of the granular fluid, guaranteeing an isotropic distribution for the velocities of colliding grains, characterized by a variance $v_0^2$. We also keep the granular system diluted, in order to compare with Boltzmann-equation-based kinetic theory. In agreement with theory, we observe for the first time the crucial role of Coulomb friction which induces two main regimes: (i) rare collisions (RC), with an average drift $ < omega > sim v_0^3$, and (ii) frequent collisions (FC), with $ < omega > sim v_0$. We also study the fluctuations of the angle spanned in a large time interval, $Delta theta$, which in the FC regime is proportional to the work done upon the motor. We observe that the Fluctuation Relation is satisfied with a slope which weakly depends on the relative collision frequency.
Brownian dynamics simulations are an increasingly popular tool for understanding spatially-distributed biochemical reaction systems. Recent improvements in our understanding of the cellular environment show that volume exclusion effects are fundamental to reaction networks inside cells. These systems are frequently studied by incorporating inert hard spheres (crowders) into three-dimensional Brownian dynamics simulations, however these methods are extremely slow owing to the sheer number of possible collisions between particles. Here we propose a rigorous crowder-free method to dramatically increase simulation speed for crowded biochemical reaction systems by eliminating the need to explicitly simulate the crowders. We consider both the case where the reactive particles are point particles, and where they themselves occupy a volume. We use simulations of simple chemical reaction networks to confirm that our simplification is just as accurate as the original algorithm, and that it corresponds to a large speed increase.
Following the work of Leutheusser [Physica A 127, 667 (1984)], the solution to the Percus-Yevick equation for a seven-dimensional hard-sphere fluid is explicitly found. This allows the derivation of the equation of state for the fluid taking both the virial and the compressibility routes. An analysis of the virial coefficients and the determination of the radius of convergence of the virial series are carried out. Molecular dynamics simulations of the same system are also performed and a comparison between the simulation results for the compressibility factor and theoretical expressions for the same quantity is presented.
We determine the rate of escape from a potential well, and the diffusion coefficient in a periodic potential, of a random walker that moves under the influence of the potential in between successive collisions with the heat bath. In the overdamped limit, both the escape rate and the diffusion coefficient coincide with those of a Langevin particle. Conversely, in the underdamped limit the two dynamics have a different temperature dependence. In particular, at low temperature the random walk has a smaller escape rate, but a larger diffusion coefficient.
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