Counter Chemotactic Flow in Quasi-One-Dimensional Path

Quasi-one-dimensional bidirectional particle flow including the effect of chemotaxis is investigated through a modification of the John-Schadschneider-Chowdhury-Nishinari model. Specifically, we permit multiple lanes to be shared by both directionally traveling particles. The relation between particle density and flux is studied for several evaporation rates of pheromone, and the following results are obtained: i) in the low-particle-density range, the flux is enlarged by pheromone if the pheromone evaporation rate is sufficiently low, ii) in the high particle-density range, the flux is largest at a reasonably high evaporation rate and, iii) if the evaporation rate is at the level intermediate between the above two cases, the flux is kept small in the entire range of particle densities. The mechanism of these behaviors is investigated by observing the spatial-temporal evolution of particles and the average cluster size in the system.Comment: 4 pages, 9 figure

Effects of non-universal large scales on conditional structure functions in turbulence

We report measurements of conditional Eulerian and Lagrangian structure functions in order to assess the effects of non-universal properties of the large scales on the small scales in turbulence. We study a 1m $\times$ 1m $\times$ 1.5m flow between oscillating grids which produces $R_\lambda=285$ while containing regions of nearly homogeneous and highly inhomogeneous turbulence. Large data sets of three-dimensional tracer particle velocities have been collected using stereoscopic high speed cameras with real-time image compression technology. Eulerian and Lagrangian structure functions are measured in both homogeneous and inhomogeneous regions of the flow. We condition the structure functions on the instantaneous large scale velocity or on the grid phase. At all scales, the structure functions depend strongly on the large scale velocity, but are independent of the grid phase. We see clear signatures of inhomogeneity near the oscillating grids, but even in the homogeneous region in the center we see a surprisingly strong dependence on the large scale velocity that remains at all scales. Previous work has shown that similar correlations extend to very high Reynolds numbers. Comprehensive measurements of these effects in a laboratory flow provide a powerful tool for assessing the effects of shear, inhomogeneity and intermittency of the large scales on the small scales in turbulence

Dynamic instability of microtubules: effect of catastrophe-suppressing drugs

Microtubules are stiff filamentary proteins that constitute an important component of the cytoskeleton of cells. These are known to exhibit a dynamic instability. A steadily growing microtubule can suddenly start depolymerizing very rapidly; this phenomenon is known as ``catastrophe''. However, often a shrinking microtubule is ``rescued'' and starts polymerizing again. Here we develope a model for the polymerization-depolymerization dynamics of microtubules in the presence of {\it catastrophe-suppressing drugs}. Solving the dynamical equations in the steady-state, we derive exact analytical expressions for the length distributions of the microtubules tipped with drug-bound tubulin subunits as well as those of the microtubules, in the growing and shrinking phases, tipped with drug-free pure tubulin subunits. We also examine the stability of the steady-state solutions.Comment: Minor corrections; final published versio

Stochastic modeling of cargo transport by teams of molecular motors

Many different types of cellular cargos are transported bidirectionally along microtubules by teams of molecular motors. The motion of this cargo-motors system has been experimentally characterized in vivo as processive with rather persistent directionality. Different theoretical approaches have been suggested in order to explore the origin of this kind of motion. An effective theoretical approach, introduced by M\"uller et al., describes the cargo dynamics as a tug-of-war between different kinds of motors. An alternative approach has been suggested recently by Kunwar et al., who considered the coupling between motor and cargo in more detail. Based on this framework we introduce a model considering single motor positions which we propagate in continuous time. Furthermore, we analyze the possible influence of the discrete time update schemes used in previous publications on the system's dynamic.Comment: Cenference proceedings - Traffic and Granular Flow 1

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.Comment: 20 pages, 9 figure

From the cell membrane to the nucleus: unearthing transport mechanisms for Dynein

Mutations in the motor protein cytoplasmic dynein have been found to cause Charcot-Marie-Tooth disease, spinal muscular atrophy, and severe intellectual disabilities in humans. In mouse models, neurodegeneration is observed. We sought to develop a novel model which could incorporate the effects of mutations on distance travelled and velocity. A mechanical model for the dynein mediated transport of endosomes is derived from first principles and solved numerically. The effects of variations in model parameter values are analysed to find those that have a significant impact on velocity and distance travelled. The model successfully describes the processivity of dynein and matches qualitatively the velocity profiles observed in experiments

Stimulus-specific hypothalamic encoding of a persistent defensive state

Persistent neural activity in cortical, hippocampal, and motor networks has been described as mediating working memory for transiently encountered stimuli. Internal emotional states, such as fear, also persist following exposure to an inciting stimulus, but it is unclear whether slow neural dynamics are involved in this process. Neurons in the dorsomedial and central subdivisions of the ventromedial hypothalamus (VMHdm/c) that express the nuclear receptor protein NR5A1 (also known as SF1) are necessary for defensive responses to predators in mice. Optogenetic activation of these neurons, referred to here as VMHdm^(SF1) neurons, elicits defensive behaviours that outlast stimulation, which suggests the induction of a persistent internal state of fear or anxiety. Here we show that in response to naturalistic threatening stimuli, VMHdm^(SF1) neurons in mice exhibit activity that lasts for many tens of seconds. This persistent activity was correlated with, and required for, persistent defensive behaviour in an open-field assay, and depended on neurotransmitter release from VMHdm^(SF1) neurons. Stimulation and calcium imaging in acute slices showed that there is local excitatory connectivity between VMHdm^(SF1) neurons. Microendoscopic calcium imaging of VMHdm^(SF1) neurons revealed that persistent activity at the population level reflects heterogeneous dynamics among individual cells. Unexpectedly, distinct but overlapping VMHdm^(SF1) subpopulations were persistently activated by different modalities of threatening stimulus. Computational modelling suggests that neither recurrent excitation nor slow-acting neuromodulators alone can account for persistent activity that maintains stimulus identity. Our results show that stimulus-specific slow neural dynamics in the hypothalamus, on a time scale orders of magnitude longer than that of working memory in the cortex, contribute to a persistent emotional state

Hydrodynamic modeling of traffic jams in intracellular transport in axons

Irregularities in intracellular traffic in axons caused by mutations of molecular motors may lead to “traffic jams”, which often result in swelling of axons causing such neurodegenerative diseases as Alzheimer’s disease and Down syndrome. Hence, it is of particular interest to mathematically model the formation of traffic jams in axons. This paper adopts the hydrodynamic continuity equations for intracellular transport of organelles as developed by Smith and Simmons [1] whereas the Kerner and Konhäuser [2] model for traffic jams in highway traffic is applied to predict the velocity field. It is observed that combination of the two sets of equations can comprehensively predict the traffic jams in axons without the need to any additional assumption or modification