arXiv subjects

L. Santen

Publications and source records attributed to L. Santen.

At least 19 recordsLinked to original sources

arXiv2011

Particle interactions and lattice dynamics: Scenarios for efficient bidirectional stochastic transport?

Intracellular transport processes driven by molecular motors can be described by stochastic lattice models of self-driven particles. Here we focus on bidirectional transport models excluding the exchange of particles on the same track. We explore the possibility to have efficient transport in these systems. One possibility would be to have appropriate interactions between the various motors' species, so as to form lanes. However, we show that the lane formation mechanism based on modified attachment/detachment rates as it was proposed previously is not necessarily connected to an efficient transport state and is suppressed when the diffusivity of unbound particles is finite. We propose another interaction mechanism based on obstacle avoidance that allows to have lane formation for limited diffusion. Besides, we had shown in a separate paper that the dynamics of the lattice itself could be a key ingredient for the efficiency of bidirectional transport. Here we show that lattice dynamics and interactions can both contribute in a cooperative way to the efficiency of transport. In particular, lattice dynamics can decrease the interaction threshold beyond which lanes form. Lattice dynamics may also enhance the transport capacity of the system even when lane formation is suppressed.

physics.bio-ph↗

arXiv2010

Bidirectional transport on a dynamic lattice

Bidirectional variants of stochastic many particle models for transport by molecular motors show a strong tendency to form macroscopic clusters on static lattices. Inspired by the fact that the microscopic tracks for molecular motors are dynamical, we study the influence of different types of lattice dynamics on stochastic bidirectional transport. We observe a transition toward efficient transport (corresponding to the dissolution of large clusters) controlled by the lattice dynamics.

physics.bio-ph↗

arXiv2010

Structural evolution of protein-biofilms: Simulations and Experiments

The control of biofilm formation is a challenging goal that has not been reached yet in many aspects. One is the role of van der Waals forces and another the importance of mutual interactions between the adsorbing and the adsorbed biomolecules ('critical crowding'). Here, a combined exeperimental and theoretical approach is presented that fundamentally probes both aspects. On three model proteins, lysozyme, α-amylase and bovine serum albumin (BSA), the adsorption kinetics is studied. Composite substrates are used enabling a separation of the short- and the long-range forces. Though usually neglected, experimental evidence is given for the influence of van der Waals forces on the protein adsorption as revealed by in situ ellipsometry. The three proteins were chosen for their different conformational stability in order to investigate the influence of conformational changes on the adsorption kinetics. Monte Carlo simulations are used to develop a model for these experimental results by assuming an internal degree of freedom to represent conformational changes. The simulations also provide data on the distribution of adsorption sites. By in situ atomic force microscopy we can also test this distribution experimentally which opens the possibility to e.g. investigate the interactions between adsorbed proteins.

cond-mat.soft↗

arXiv2010

Traffic of cytoskeletal motors with disordered attachment rates

Motivated by experimental results on the interplay between molecular motors and tau proteins, we extend lattice-based models of intracellular transport to include a second species of particle which locally influences the motor-filament attachment rate. We consider various exactly solvable limits of a stochastic multi-particle model before focusing on the low-motor-density regime. Here, an approximate treatment based on the random walk behaviour of single motors gives good quantitative agreement with simulation results for the tau-dependence of the motor current. Finally, we discuss the possible physiological implications of our results.

q-bio.SC↗

arXiv2009

Aging of dynamically stabilized microtubules

The microtubule network, an important part of the cytoskeleton, is constantly remodeled by alternating phases of growth and shrinkage of individual filaments. Plus-end tracking proteins (+TIPs) interact with the microtubule and in many cases alter its dynamics. While it is established that the prototypal CLIP-170 enhances microtubule stability by increasing rescues, the plus-end tracking mechanism is still under debate. We present a model for microtubule dynamics in which a rescue factor is dynamically added to the filament while growing. As a consequence, the filament shows aging behavior which should be experimentally accessible and thus allow one to exclude some hypothesized models of the inclusion of rescue factors at the microtubule plus end. Additionally, we show the strong influence of the cell geometry on the quantitative results.

physics.bio-ph↗

arXiv2009

A model for bidirectional traffic of cytoskeletal motors

We introduce a stochastic lattice gas model including two particle species and two parallel lanes. One lane with exclusion interaction and directed motion and the other lane without exclusion and unbiased diffusion, mimicking a micotubule filament and the surrounding solution. For a high binding affinity to the filament, jam-like situations dominate the system's behaviour. The fundamental process of position exchange of two particles is approximated. In the case of a many-particle system, we were able to identify a regime in which the system is rather homogenous presenting only small accumulations of particles and a regime in which an important fraction of all particles accumulates in the same cluster. Numerical data proposes that this cluster formation will occur at all densities for large system sizes. Coupling of several filaments leads to an enhanced cluster formation compared to the uncoupled system, suggesting that efficient bidirectional transport on one-dimensional filaments relies on long-ranged interactions and track formation.

cond-mat.stat-mech↗

arXiv2005

Partially asymmetric exclusion models with quenched disorder

We consider the one-dimensional partially asymmetric exclusion process with random hopping rates, in which a fraction of particles (or sites) have a preferential jumping direction against the global drift. In this case the accumulated distance traveled by the particles, x, scales with the time, t, as x ~ t^{1/z}, with a dynamical exponent z > 0. Using extreme value statistics and an asymptotically exact strong disorder renormalization group method we analytically calculate, z_{pt}, for particlewise (pt) disorder, which is argued to be related to the dynamical exponent for sitewise (st) disorder as z_{st}=z_{pt}/2. In the symmetric situation with zero mean drift the particle diffusion is ultra-slow, logarithmic in time.

cond-mat.dis-nn↗

arXiv2003

Shock formation in an exclusion process with creation and annihilation

We investigate shock formation in an asymmetric exclusion process with creation and annihilation of particles in the bulk. We show how the continuum mean-field equations can be studied analytically and hence derive the phase diagrams of the model. In the large system-size limit direct simulations of the model show that the stationary state is correctly described by the mean-field equations, thus the predicted mean field phase diagrams are expected to be exact. The emergence of shocks and the structure of the phase diagram are discussed. We also analyse the fluctuations of the shock position by using a phenomenological random walk picture of the shock dynamics. The stationary distribution of shock positions is calculated, by virtue of which the numerically determined finite-size scaling behaviour of the shock width is explained.

cond-mat.stat-mech↗

arXiv2002

A realistic two-lane traffic model for highway traffic

A two-lane extension of a recently proposed cellular automaton model for traffic flow is discussed. The analysis focuses on the reproduction of the lane usage inversion and the density dependence of the number of lane changes. It is shown that the single-lane dynamics can be extended to the two-lane case without changing the basic properties of the model which are known to be in good agreement with empirical single-vehicle data. Therefore it is possible to reproduce various empirically observed two-lane phenomena, like the synchronization of the lanes, without fine-tuning of the model parameters.

cond-mat.stat-mech↗

arXiv2000

Boundary-induced phase transitions in traffic flow

Boundary-induced phase transitions are one of the surprising phenomena appearing in nonequilibrium systems. These transitions have been found in driven systems, especially the asymmetric simple exclusion process. However, so far no direct observations of this phenomenon in real systems exists. Here we present evidence for the appearance of such a nonequilibrium phase transition in traffic flow occurring on highways in the vicinity of on- and off-ramps. Measurements on a German motorway close to Cologne show a first-order nonequilibrium phase transition between a free-flow phase and a congested phase. It is induced by the interplay of density waves (caused by an on-ramp) and a shock wave moving on the motorway. The full phase diagram, including the effect of off-ramps, is explored using computer simulations and suggests means to optimize the capacity of a traffic network.

cond-mat.stat-mech↗

arXiv2000

CA Models for Traffic Flow: Comparison with Empirical Single-Vehicle Data

Although traffic simulations with cellular-automata models give meaningful results compared with empirical data, highway traffic requires a more detailed description of the elementary dynamics. Based on recent empirical results we present a modified Nagel-Schreckenberg cellular automaton model which incorporates both a slow-to-start and an anticipation rule, which takes into account especially brake lights. The focus in this article lies on the comparison with empirical single-vehicle data.

cond-mat.stat-mech↗

arXiv2000

Effect of on- and off-ramps in cellular automata models for traffic flow

We present results on the modeling of on- and off-ramps in cellular automata for traffic flow, especially the Nagel-Schreckenberg model. We study two different types of on-ramps that cause qualitatively the same effects. In a certain density regime one observes plateau formation in the fundamental diagram. The plateau value depends on the input-rate of cars at the on-ramp. The on-ramp acts as a local perturbation that separates the system into two regimes: A regime of free flow and another one where only jammed states exist. This phase separation is the reason for the plateau formation and implies a behaviour analogous to that of stationary defects. This analogy allows to perform very fast simulations of complex traffic networks with a large number of on- and off-ramps because one can parametrise on-ramps in an exceedingly easy way.

cond-mat.stat-mech↗

arXiv1999

Statistical Analysis of Freeway Traffic

Single-vehicle data of freeway traffic as well as selected Floating-Car (FC) data are analyzed in great detail. Traffic states are distinguished by means of aggregated data. We propose a method for a quantitative classification of these states. The data of individual vehicles allows for insights into the interaction of vehicles. The time-headway distribution reveals a characteristic structure dominated by peaks and controlled by the underlying traffic states. The tendency to reach a pleasant level of ``driving comfort'' gives rise to new $v(Δx)$-diagrams, known as Optimal-Velocity (OV) curves. The insights found at locally fixed detectors can be confirmed by FC data. In fundamental diagrams derived from local measurements interesting high-flow states can be observed.

cond-mat.stat-mech↗

arXiv1999

A new cellular automata model for city traffic

We present a new cellular automata model of vehicular traffic in cities by combining ideas borrowed from the Biham-Middleton-Levine (BML) model of city traffic and the Nagel-Schreckenberg (NaSch) model of highway traffic. The model exhibits a dynamical phase transition to a completely jammed phase at a critical density which depends on the time periods of the synchronized signals.

cond-mat.stat-mech↗

arXiv1999

Single-vehicle data of highway traffic - a statistical analysis

In the present paper single-vehicle data of highway traffic are analyzed in great detail. By using the single-vehicle data directly empirical time-headway distributions and speed-distance relations can be established. Both quantities yield relevant information about the microscopic states. Several fundamental diagrams are also presented, which are based on time-averaged quantities and compared with earlier empirical investigations. In the remaining part time-series analyses of the averaged as well as the single-vehicle data are carried out. The results will be used in order to propose objective criteria for an identification of the different traffic states, e.g. synchronized traffic.

cond-mat↗

arXiv1998

Metastable States in Cellular Automata for Traffic Flow

Measurements on real traffic have revealed the existence of metastable states with very high flow. Such states have not been observed in the Nagel-Schreckenberg (NaSch) model which is the basic cellular automaton for the description of traffic. Here we propose a simple generalization of the NaSch model by introducing a velocity-dependent randomization. We investigate a special case which belongs to the so-called slow-to-start rules. It is shown that this model exhibits metastable states, thus sheding some light on the prerequisites for the occurance of hysteresis effects in the flow-density relation.

cond-mat.stat-mech↗

arXiv1997

Disorder Effects in CA-Models for Traffic Flow

We investigate the effect of quenched disorder in the Nagel-Schreckenberg model of traffic flow. Spatial inhomogenities, i.e. lattice sites where the braking probability is enlarged, are considered as well as particle disorder, i.e. cars of a different maximum velocity. Both types of disorder lead to segregated states.

cond-mat.stat-mech↗

arXiv1997

Metastable States in CA models for Traffic Flow

Measurements of traffic flow show the existence of metastable states of very high throughput. These observations cannot be reproduced by the CA model of Nagel and Schreckenberg (NaSch model), not even qualitatively. Here we present two variants on the NaSch model with modified acceleration rules ('slow-to-start' rules). Although these models are still discrete in time and space, different types of metastable states can be observed.

cond-mat.stat-mech↗