Movements of molecular motors: Ratchets, random walks and traffic phenomena

Processive molecular motors which drive the traffic of organelles in cells move in a directed way along cytoskeletal filaments. On large time scales, they perform motor walks, i.e., peculiar random walks which arise from the repeated unbinding from and rebinding to filaments. Unbound motors perform Brownian motion in the surrounding fluid. In addition, the traffic of molecular motors exhibits many cooperative phenomena. In particular, it faces similar problems as the traffic on streets such as the occurrence of traffic jams and the coordination of (two-way) traffic. These issues are studied here theoretically using lattice models.Comment: latex, uses elsart.cls and phyeauth.cls (included), 10 pages, 6 figures, to appear in the proceedings of FQMT'04, Pragu

Phase transitions in systems with two species of molecular motors

Systems with two species of active molecular motors moving on (cytoskeletal) filaments into opposite directions are studied theoretically using driven lattice gas models. The motors can unbind from and rebind to the filaments. Two motors are more likely to bind on adjacent filament sites if they belong to the same species. These systems exhibit (i) Continuous phase transitions towards states with spontaneously broken symmetry, where one motor species is largely excluded from the filament, (ii) Hysteresis of the total current upon varying the relative concentrations of the two motor species, and (iii) Coexistence of traffic lanes with opposite directionality in multi-filament systems. These theoretical predictions should be experimentally accessible.Comment: 7 pages, 4 figures, epl style (.cls-file included), to appear in Europhys. Lett. (http://www.edpsciences.org/epl

The Preference for Round Number Prices

This study determines if a preference for round prices exists in the wheat market and how wheat sales react to price movements around whole dollar amounts. The results show round prices are slightly more prevalent than non-round prices and that transactions increase when price moves above a whole dollar amount.Demand and Price Analysis,

Transport by molecular motors in the presence of static defects

The transport by molecular motors along cytoskeletal filaments is studied theoretically in the presence of static defects. The movements of single motors are described as biased random walks along the filament as well as binding to and unbinding from the filament. Three basic types of defects are distinguished, which differ from normal filament sites only in one of the motors' transition probabilities. Both stepping defects with a reduced probability for forward steps and unbinding defects with an increased probability for motor unbinding strongly reduce the velocities and the run lengths of the motors with increasing defect density. For transport by single motors, binding defects with a reduced probability for motor binding have a relatively small effect on the transport properties. For cargo transport by motors teams, binding defects also change the effective unbinding rate of the cargo particles and are expected to have a stronger effect.Comment: 20 pages, latex, 7 figures, 1 tabl

Deterministic and stochastic descriptions of gene expression dynamics

A key goal of systems biology is the predictive mathematical description of gene regulatory circuits. Different approaches are used such as deterministic and stochastic models, models that describe cell growth and division explicitly or implicitly etc. Here we consider simple systems of unregulated (constitutive) gene expression and compare different mathematical descriptions systematically to obtain insight into the errors that are introduced by various common approximations such as describing cell growth and division by an effective protein degradation term. In particular, we show that the population average of protein content of a cell exhibits a subtle dependence on the dynamics of growth and division, the specific model for volume growth and the age structure of the population. Nevertheless, the error made by models with implicit cell growth and division is quite small. Furthermore, we compare various models that are partially stochastic to investigate the impact of different sources of (intrinsic) noise. This comparison indicates that different sources of noise (protein synthesis, partitioning in cell division) contribute comparable amounts of noise if protein synthesis is not or only weakly bursty. If protein synthesis is very bursty, the burstiness is the dominant noise source, independent of other details of the model. Finally, we discuss two sources of extrinsic noise: cell-to-cell variations in protein content due to cells being at different stages in the division cycles, which we show to be small (for the protein concentration and, surprisingly, also for the protein copy number per cell) and fluctuations in the growth rate, which can have a significant impact.Comment: 23 pages, 5 figures; Journal of Statistical physics (2012

Determining Returns to Storage: USDA Data versus Micro Level Data

USDA data are commonly used to determine producers' returns to storage. Aggregating data may result in a loss of information, leading to underestimated returns. This study compares USDA and elevator data from Oklahoma to determine how much USDA data underestimates returns. Results indicate USDA data only slightly underestimate returns to storage.Research Methods/ Statistical Methods,

3D System Integration for high density Interconnects

3D-Integration is a promising technology towards higher interconnect densities and shorter wiring lengths between multiple chip stacks, thus achieving a very high performance level combined with low power consumption. This technology also offers the possibility to build up systems with high complexity by combining devices of different technologies. The fundamental processing steps will be described, as well as appropriate handling concepts and first electrical results of realized 3D-integrated stacks

Traffic by multiple species of molecular motors

We study the traffic of two types of molecular motors using the two-species symmetric simple exclusion process (ASEP) with periodic boundary conditions and with attachment and detachment of particles. We determine characteristic properties such as motor densities and currents by simulations and analytical calculations. For motors with different unbinding probabilities, mean field theory gives the correct bound density and total current of the motors, as shown by numerical simulations. For motors differing in their stepping probabilities, the particle-hole symmetry of the current-density relationship is broken and mean field theory fails drastically. The total motor current exhibits exponential finite-size scaling, which we use to extrapolate the total current to the thermodynamic limit. Finally, we also study the motion of a single motor in the background of many non-moving motors.Comment: 23 pages, 6 figures, late

Traffic of Molecular Motors

Molecular motors perform active movements along cytoskeletal filaments and drive the traffic of organelles and other cargo particles in cells. In contrast to the macroscopic traffic of cars, however, the traffic of molecular motors is characterized by a finite walking distance (or run length) after which a motor unbinds from the filament along which it moves. Unbound motors perform Brownian motion in the surrounding aqueous solution until they rebind to a filament. We use variants of driven lattice gas models to describe the interplay of their active movements, the unbound diffusion, and the binding/unbinding dynamics. If the motor concentration is large, motor-motor interactions become important and lead to a variety of cooperative traffic phenomena such as traffic jams on the filaments, boundary-induced phase transitions, and spontaneous symmetry breaking in systems with two species of motors. If the filament is surrounded by a large reservoir of motors, the jam length, i.e., the extension of the traffic jams is of the order of the walking distance. Much longer jams can be found in confined geometries such as tube-like compartments.Comment: 10 pages, latex, uses Springer styles (included), to appear in the Proceedings of "Traffic and Granular Flow 2005

Walks of molecular motors in two and three dimensions

Molecular motors interacting with cytoskeletal filaments undergo peculiar random walks consisting of alternating sequences of directed movements along the filaments and diffusive motion in the surrounding solution. An ensemble of motors is studied which interacts with a single filament in two and three dimensions. The time evolution of the probability distribution for the bound and unbound motors is determined analytically. The diffusion of the motors is strongly enhanced parallel to the filament. The analytical expressions are in excellent agreement with the results of Monte Carlo simulations.Comment: 7 pages, 2 figures, to be published in Europhys. Let