arXiv subjects
Publications and source records attributed to J. M. J. van Leeuwen.
The equations governing the radiation balance are discussed and exactly solved for the model of the semi-gray atmosphere, i.e. an atmosphere that has regions of transparant frequencies and regions with the same absorption coefficient.
The analogy between the quantum evolution and that of the master equation is explored. By stressing the stochastic nature of quantum evolution a number of conceptual difficulties in the interpretation of quantum mechanics are avoided.
The Uhlenbeck-Ford model for soft repulsion, which has only a repulsive interaction, is extended by inclusion of an attraction. This extension still allows an analytical evaluation of the virial coefficients. The integrals over the graph contributions are reduced to a combinatorial problem. We have calculated the virial coefficients to order 6 in the density. A link is made between this model and more common interactions, like the 12-6 Lennard-Jones potential.
The friction felt by a speed skater is calculated as function of the velocity and tilt angle of the skate. This calculation is an extension of the more common theory of friction of upright skates. Not only in rounding a curve the skate has to be tilted, but also in straightforward skating small tilt angles occur, which turn out to be of noticeable influence on the friction. As for the upright skate the friction remains fairly insensitive of the velocities occurring in speed skating.
The pressure distribution is calculated underneath a skate which is pushed in the ice by the weight of a skater at rest. Due to the sharp edges of the skate the deformation is partly elastic and partly plastic. The ratio of the plastic and elastic contribution to the reaction force is determined. Using this ratio the deformation in ice with a finite hardness can be mapped on the problem of the deformation in a purely elastic medium with infinite hardness. Both the upright skate and the tilted position are exactly calculated.
The friction of a stationary moving skate on smooth ice is investigated, in particular in relation to the formation of a thin layer of water between skate and ice. It is found that the combination of ploughing and sliding gives a friction force that is rather insensitive for parameters such as velocity and temperature. The weak dependence originates from the pressure adjustment inside the water layer. For instance, high velocities, which would give rise to high friction, also lead to large pressures, which, in turn, decrease the contact zone and so lower the friction. The theory is a combination and completion of two existing but conflicting theories on the formation of the water layer.
We study the dynamics of a double-stranded DNA (dsDNA) segment, as a semiflexible polymer, in a shear flow, the strength of which is customarily expressed in terms of the dimensionless Weissenberg number Wi. Polymer chains in shear flows are well-known to undergo tumbling motion. When the chain lengths are much smaller than the persistence length, one expects a (semiflexible) chain to tumble as a rigid rod. At low Wi, a polymer segment shorter than the persistence length does indeed tumble as a rigid rod. However, for higher Wi the chain does not tumble as a rigid rod, even if the polymer segment is shorter than the persistence length. In particular, from time to time the polymer segment may assume a buckled form, a phenomenon commonly known as Euler buckling. Using a bead-spring Hamiltonian model for extensible dsDNA fragments, we first analyze Euler buckling in terms of the oriented deterministic state (ODS), which is obtained as the steady-state solution of the dynamical equations by turning off the stochastic (thermal) forces at a fixed orientation of the chain. The ODS exhibits symmetry breaking at a critical Weissenberg number Wi$_{\text c}$, analogous to a pitchfork bifurcation in dynamical systems. We then follow up the analysis with simulations and demonstrate symmetry breaking in computer experiments, characterized by a unimodal to bimodal transformation of the probability distribution of the second Rouse mode with increasing Wi. Our simulations reveal that shear can cause strong deformation for a chain that is shorter than its persistence length, similar to recent experimental observations.
Using a recently developed bead-spring model for semiflexible polymers that takes into account their natural extensibility, we report an efficient algorithm to simulate the dynamics for polymers like double-stranded DNA (dsDNA) in the absence of hydrodynamic interactions. The dsDNA is modelled with one bead-spring element per basepair, and the polymer dynamics is described by the Langevin equation. The key to efficiency is that we describe the equations of motion for the polymer in terms of the amplitudes of the polymer's fluctuation modes, as opposed to the use of the physical positions of the beads. We show that, within an accuracy tolerance level of $5\%$ of several key observables, the model allows for single Langevin time steps of $\approx1.6$, 8, 16 and 16 ps for a dsDNA model-chain consisting of 64, 128, 256 and 512 basepairs (i.e., chains of 0.55, 1.11, 2.24 and 4.48 persistence lengths) respectively. Correspondingly, in one hour, a standard desktop computer can simulate 0.23, 0.56, 0.56 and 0.26 ms of these dsDNA chains respectively. We compare our results to those obtained from other methods, in particular, the (inextensible discretised) WLC model. Importantly, we demonstrate that at the same level of discretisation, i.e., when each discretisation element is one basepair long, our algorithm gains about 5-6 orders of magnitude in the size of time steps over the inextensible WLC model. Further, we show that our model can be mapped one-on-one to a discretised version of the extensible WLC model; implying that the speed-up we achieve in our model must hold equally well for the latter. We also demonstrate the use of the method by simulating efficiently the tumbling behaviour of a dsDNA segment in a shear flow.
We study the dynamical properties of semiflexible polymers with a recently introduced bead-spring model. We focus on double-stranded DNA. The two parameters of the model, $T^*$ and $ν$, are chosen to match its experimental force-extension curve. The bead-spring Hamiltonian is approximated in the first order by the Hessian that is quadratic in the bead positions. The eigenmodels of the Hessian provide the longitudinal (stretching) and transverse (bending) eigenmodes of the polymer, and the corresponding eigenvalues match well with the established phenomenology of semiflexible polymers. Using the longitudinal and transverse eigenmodes, we obtain analytical expressions of (i) the autocorrelation function of the end-to-end vector, (ii) the autocorrelation function of a bond (i.e., a spring, or a tangent) vector at the middle of the chain, and (iii) the mean-square displacement of a tagged bead in the middle of the chain, as sum over the contributions from the modes. We also perform simulations with the full dynamics of the model. The simulations yield numerical values of the correlation functions (i-iii) that agree very well with the analytical expressions for the linearized dynamics. We also study the mean-square displacement of the longitudinal component of the end-to-end vector that showcases strong nonlinear effects in the polymer dynamics, and we identify at least an effective $t^{7/8}$ power-law regime in its time-dependence. Nevertheless, in comparison to the full mean-square displacement of the end-to-end vector the nonlinear effects remain small at all times --- it is in this sense we state that our results demonstrate that the linearized dynamics suffices for dsDNA fragments that are shorter than or comparable to the persistence length. Our results are consistent with those of the wormlike chain (WLC) model, the commonly used descriptive tool of semiflexible polymers.
The tumbling of a rigid rod in a shear flow is analyzed in the high viscosity limit. Following Burgers, the Master Equation is derived for the probability distribution of the orientation of the rod. The equation contains one dimensionless number, the Weissenberg number, which is the ratio of the shear rate and the orientational diffusion constant. The equation is solved for the stationary state distribution for arbitrary Weissenberg numbers, in particular for the limit of high Weissenberg numbers. The stationary state gives an interesting flow pattern for the orientation of the rod, showing the interplay between flow due to the driving shear force and diffusion due to the random thermal forces of the fluid. The average tumbling time and tumbling frequency are calculated as a function of the Weissenberg number. A simple cross-over function is proposed which covers the whole regime from small to large Weissenberg numbers.
The conditions are investigated under which a row of increasing dominoes is able to keep tumbling over. The analysis is restricted to the simplest case of frictionless dominoes that only can topple not slide. The model is scale invariant, i.e. dominoes and distance grow in size at a fixed rate, while keeping the aspect ratios of the dominoes constant. The maximal growth rate for which a domino effect exist is determined as a function of the mutual separation.
We present a model for semiflexible polymers in Hamiltonian formulation which interpolates between a Rouse chain and worm-like chain. Both models are realized as limits for the parameters. The model parameters can also be chosen to match the experimental force-extension curve for double-stranded DNA. Near the ground state of the Hamiltonian, the eigenvalues for the longitudinal (stretching) and the transversal (bending) modes of a chain with N springs, indexed by p, scale as lambda_lp ~ (p/N)^2 and lambda_tp ~ p^2(p-1)^2/N^4 respectively for small p. We also show that the associated decay times tau_p ~ (N/p)^4 will not be observed if they exceed the orientational time scale tau_r ~ N^3 for an equally-long rigid rod, as the driven decay is then washed out by diffusive motion.
Using extensive computer simulations, the behavior of the structural modes --- more precisely, the eigenmodes of a phantom Rouse polymer --- are characterized for a polymer in the three-dimensional repton model, and are used to study the polymer's dynamics at time scales well before the tube renewal. Although these modes are not the eigenmodes for a polymer in the repton model, we show that numerically the modes maintain a high degree of statistical independence. The correlations in the mode amplitudes decay exponentially with $(p/N)^2A(t)$, in which $p$ is the mode number, $N$ is the polymer length and $A(t)$ is a single function shared by all modes. In time, the quantity $A(t)$ causes an exponential decay for the mode amplitude correlation functions for times $<1$; a stretched exponential with an exponent 1/2 between times 1 and $τ_R\sim N^2$, the time-scale for diffusion of tagged reptons along the contour of the polymer; and again an exponential decay for times $t>τ_R$. Having assumed statistical independence and the validity of a single function $A(t)$ for all modes, we compute the temporal behavior of three structural quantities: the vectorial distance between the positions of the middle monomer and the center-of-mass, the end-to-end vector, and the vector connecting two nearby reptons around the middle of the polymer. Furthermore, we study the mean-squared displacement of the center-of-mass and the middle repton, and their relation with the temporal behavior of the modes.
Linear polymers are represented as chains of hopping reptons and their motion is described as a stochastic process on a lattice. This admittedly crude approximation still catches essential physics of polymer motion, i.e. the universal properties as function of polymer length. More than the static properties, the dynamics depends on the rules of motion. Small changes in the hopping probabilities can result in different universal behavior. In particular the cross-over between Rouse dynamics and reptation is controlled by the types and strength of the hoppings that are allowed. The properties are analyzed using a calculational scheme based on an analogy with one-dimensional spin systems. It leads to accurate data for intermediately long polymers. These are extrapolated to arbitrarily long polymers, by means of finite-size-scaling analysis. Exponents and cross-over functions for the renewal time and the diffusion coefficient are discussed for various types of motion.
We present a scheme to accurately calculate the persistence probabilities on sequences of $n$ heights above a level $h$ from the measured $n+2$ points of the height-height correlation function of a fluctuating interface. The calculated persistence probabilities compare very well with the measured persistence probabilities of a fluctuating phase-separated colloidal interface for the whole experimental range.
Fluctuations of the interface between coexisting colloidal fluid phases have been measured with confocal microscopy. Due to a very low surface tension, the thermal motions of the interface are so slow, that a record can be made of the positions of the interface. The theory of the interfacial height fluctuations is developed. For a host of correlation functions, the experimental data are compared with the theoretical expressions. The agreement between theory and experiment is remarkably good.
The competition between reptation and Rouse Dynamics is incorporated in the Rubinstein-Duke model for polymer motion by extending it with sideways motions, which cross barriers and create or annihilate hernias. Using the Density-Matrix Renormalization-Group Method as solver of the Master Equation, the renewal time and the diffusion coefficient are calculated as function of the length of the chain and the strength of the sideways motion. These new types of moves have a strong and delicate influence on the asymptotic behavior of long polymers. The effects are analyzed as function of the chain length in terms of effective exponents and crossover scaling functions.
The two-dimensional cage model for polymer motion is discussed with an emphasis on the effect of sideways motions, which cross the barriers imposed by the lattice. Using the Density Matrix Method as a solver of the Master Equation, the renewal time and the diffusion coefficient are calculated as a function of the strength of the barrier crossings. A strong crossover influence of the barrier crossings is found and it is analyzed in terms of effective exponents for a given chain length. The crossover scaling functions and the crossover scaling exponents are calculated.