Mitotic entry and exit: the rise and fall of cyclin-Cdk-Cks activity

Riele, H.P.J. te [Promotor]Wolthuis, R.M.F. [Copromotor

Effective pair potentials for spherical nanoparticles

An effective description for spherical nanoparticles in a fluid of point particles is presented. The points inside the nanoparticles and the point particles are assumed to interact via spherically symmetric additive pair potentials, while the distribution of points inside the nanoparticles is taken to be spherically symmetric and smooth. The resulting effective pair interactions between a nanoparticle and a point particle, as well as between two nanoparticles, are then given by spherically symmetric potentials. If overlap between particles is allowed, the effective potential generally has non-analytic points, but for each effective potential the expressions for different overlapping cases can be written in terms of one analytic auxiliary potential. Effective potentials for hollow nanoparticles (appropriate e.g. for buckyballs) are also considered, and shown to be related to those for solid nanoparticles. Finally, explicit expressions are given for the effective potentials derived from basic pair potentials of power law and exponential form, as well as from the commonly used London-Van der Waals, Morse, Buckingham, and Lennard-Jones potential. The applicability of the latter is demonstrated by comparison with an atomic description of nanoparticles with an internal face centered cubic structure.Comment: 27 pages, 12 figures. Unified description of overlapping and nonoverlapping particles added, as well as a comparison with an idealized atomic descriptio

Constructing smooth potentials of mean force, radial, distribution functions and probability densities from sampled data

In this paper a method of obtaining smooth analytical estimates of probability densities, radial distribution functions and potentials of mean force from sampled data in a statistically controlled fashion is presented. The approach is general and can be applied to any density of a single random variable. The method outlined here avoids the use of histograms, which require the specification of a physical parameter (bin size) and tend to give noisy results. The technique is an extension of the Berg-Harris method [B.A. Berg and R.C. Harris, Comp. Phys. Comm. 179, 443 (2008)], which is typically inaccurate for radial distribution functions and potentials of mean force due to a non-uniform Jacobian factor. In addition, the standard method often requires a large number of Fourier modes to represent radial distribution functions, which tends to lead to oscillatory fits. It is shown that the issues of poor sampling due to a Jacobian factor can be resolved using a biased resampling scheme, while the requirement of a large number of Fourier modes is mitigated through an automated piecewise construction approach. The method is demonstrated by analyzing the radial distribution functions in an energy-discretized water model. In addition, the fitting procedure is illustrated on three more applications for which the original Berg-Harris method is not suitable, namely, a random variable with a discontinuous probability density, a density with long tails, and the distribution of the first arrival times of a diffusing particle to a sphere, which has both long tails and short-time structure. In all cases, the resampled, piecewise analytical fit outperforms the histogram and the original Berg-Harris method.Comment: 14 pages, 15 figures. To appear in J. Chem. Phy

An Extension of the Fluctuation Theorem

Heat fluctuations are studied in a dissipative system with both mechanical and stochastic components for a simple model: a Brownian particle dragged through water by a moving potential. An extended stationary state fluctuation theorem is derived. For infinite time, this reduces to the conventional fluctuation theorem only for small fluctuations; for large fluctuations, it gives a much larger ratio of the probabilities of the particle to absorb rather than supply heat. This persists for finite times and should be observable in experiments similar to a recent one of Wang et al.Comment: 12 pages, 1 eps figure in color (though intelligible in black and white

Mode-coupling theory for structural and conformational dynamics of polymer melts

A mode-coupling theory for dense polymeric systems is developed which unifyingly incorporates the segmental cage effect relevant for structural slowing down and polymer chain conformational degrees of freedom. An ideal glass transition of polymer melts is predicted which becomes molecular-weight independent for large molecules. The theory provides a microscopic justification for the use of the Rouse theory in polymer melts, and the results for Rouse-mode correlators and mean-squared displacements are in good agreement with computer simulation results.Comment: 4 pages, 3 figures, Phys. Rev. Lett. in pres

Extended Heat-Fluctuation Theorems for a System with Deterministic and Stochastic Forces

Heat fluctuations over a time \tau in a non-equilibrium stationary state and in a transient state are studied for a simple system with deterministic and stochastic components: a Brownian particle dragged through a fluid by a harmonic potential which is moved with constant velocity. Using a Langevin equation, we find the exact Fourier transform of the distribution of these fluctuations for all \tau. By a saddle-point method we obtain analytical results for the inverse Fourier transform, which, for not too small \tau, agree very well with numerical results from a sampling method as well as from the fast Fourier transform algorithm. Due to the interaction of the deterministic part of the motion of the particle in the mechanical potential with the stochastic part of the motion caused by the fluid, the conventional heat fluctuation theorem is, for infinite and for finite \tau, replaced by an extended fluctuation theorem that differs noticeably and measurably from it. In particular, for large fluctuations, the ratio of the probability for absorption of heat (by the particle from the fluid) to the probability to supply heat (by the particle to the fluid) is much larger here than in the conventional fluctuation theorem.Comment: 23 pages, 6 figures. Figures are now in color, Eq. (67) was corrected and a footnote was added on the d-dimensional cas

Fronts with a Growth Cutoff but Speed Higher than v∗v^*

Fronts, propagating into an unstable state $\phi=0$, whose asymptotic speed $v_{\text{as}}$ is equal to the linear spreading speed $v^*$ of infinitesimal perturbations about that state (so-called pulled fronts) are very sensitive to changes in the growth rate $f(\phi)$ for $\phi \ll 1$. It was recently found that with a small cutoff, $f(\phi)=0$ for $\phi < \epsilon$, $v_{\text{as}}$ converges to $v^*$ very slowly from below, as $\ln^{-2} \epsilon$. Here we show that with such a cutoff {\em and} a small enhancement of the growth rate for small $\phi$ behind it, one can have $v_{\text{as}} > v^*$, {\em even} in the limit $\epsilon \to 0$. The effect is confirmed in a stochastic lattice model simulation where the growth rules for a few particles per site are accordingly modified.Comment: 4 pages, 4 figures, to appear in Rapid Comm., Phys. Rev.

Velocity distributions in dissipative granular gases

Motivated by recent experiments reporting non-Gaussian velocity distributions in driven dilute granular materials, we study by numerical simulation the properties of 2D inelastic gases. We find theoretically that the form of the observed velocity distribution is governed primarily by the coefficient of restitution $\eta$ and $q=N_H/N_C$, the ratio between the average number of heatings and the average number of collisions in the gas. The differences in distributions we find between uniform and boundary heating can then be understood as different limits of $q$, for $q \gg 1$ and $q \lesssim 1$ respectively.Comment: 5 figure

The Weakly Pushed Nature of "Pulled" Fronts with a Cutoff

The concept of pulled fronts with a cutoff $\epsilon$ has been introduced to model the effects of discrete nature of the constituent particles on the asymptotic front speed in models with continuum variables (Pulled fronts are the fronts which propagate into an unstable state, and have an asymptotic front speed equal to the linear spreading speed $v^*$ of small linear perturbations around the unstable state). In this paper, we demonstrate that the introduction of a cutoff actually makes such pulled fronts weakly pushed. For the nonlinear diffusion equation with a cutoff, we show that the longest relaxation times $\tau_m$ that govern the convergence to the asymptotic front speed and profile, are given by $\tau_m^{-1} \simeq [(m+1)^2-1] \pi^2 / \ln^2 \epsilon$, for $m=1,2,...$.Comment: 4 pages, 2 figures, submitted to Brief Reports, Phys. Rev.

Event-Driven Dynamics of Rigid Bodies Interacting via Discretized Potentials

A framework for performing event-driven, adaptive time step simulations of systems of rigid bodies interacting under stepped or terraced potentials in which the potential energy is only allowed to have discrete values is outlined. The scheme is based on a discretization of an underlying continuous potential that effectively determines the times at which interaction energies change. As in most event-driven approaches, the method consists of specifying a means of computing the free motion, evaluating the times at which interactions occur, and determining the consequences of interactions on subsequent motion for the terraced-potential. The latter two aspects are shown to be simply expressible in terms of the underlying smooth potential. Within this context, algorithms for computing the times of interaction events and carrying out efficient event-driven simulations are discussed. The method is illustrated on system composed of rigid rods in which the constituents interact via a terraced potential that depends on the relative orientations of the rods.Comment: 9 pages, 5 figure