From aggressive driving to molecular motor traffic

Motivated by recent experimental results for the step sizes of dynein motor proteins, we develope a cellular automata model for intra-cellular traffic of dynein motors incorporating special features of the hindrance-dependent step size of the individual motors. We begin by investigating the properties of the aggressive driving model (ADM), a simple cellular automata-based model of vehicular traffic, a unique feature of which is that it allows a natural extension to capture the essential features of dynein motor traffic. We first calculate several collective properties of the ADM, under both periodic and open boundary conditions, analytically using two different mean-field approaches as well as by carrying out computer simulations. Then we extend the ADM by incorporating the possibilities of attachment and detachment of motors on the track which is a common feature of a large class of motor proteins that are collectively referred to as cytoskeletal motors. The interplay of the boundary and bulk dynamics of attachment and detachment of the motors to the track gives rise a phase where high and low density phases separated by a stable domain wall coexist. We also compare and contrast our results with the model of Parmeggiani et. al. (Phys. Rev. Lett. {\bf 90}, 086601 (2003)) which can be regarded as a minimal model for traffic of a closely related family of motor proteins called kinesin. Finally, we compare the transportation efficiencies of dynein and kinesin motors over a range of values of the model parameters.Comment: Final Version Accepted for Publication in J. Phys. A (IOP, UK

Evolution of Spatially Inhomogeneous Eco-Systems: An Unified Model Based Approach

Recently we have extended our the "unified" model of evolutionary ecology to incorporate the {\it spatial inhomogeneities} of the eco-system and the {\it migration} of individual organisms from one patch to another within the same eco-system. In this paper an extension of our recent model is investigated so as to describe the {\it migration} and {\it speciation} in a more realistic way.Comment: Latex, 10 pages, 8 figure

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

Competition of coarsening and shredding of clusters in a driven diffusive lattice gas

We investigate a driven diffusive lattice gas model with two oppositely moving species of particles. The model is motivated by bi-directional traffic of ants on a pre-existing trail. A third species, corresponding to pheromones used by the ants for communication, is not conserved and mediates interactions between the particles. Here we study the spatio-temporal organization of the particles. In the uni-directional variant of this model it is known to be determined by the formation and coarsening of ``loose clusters''. For our bi-directional model, we show that the interaction of oppositely moving clusters is essential. In the late stages of evolution the cluster size oscillates because of a competition between their `shredding' during encounters with oppositely moving counterparts and subsequent "coarsening" during collision-free evolution. We also establish a nontrivial dependence of the spatio-temporal organization on the system size

Evolutionary ecology in-silico:evolving foodwebs, migrating population and speciation

We have generalized our ``unified'' model of evolutionary ecology by taking into account the possible movements of the organisms from one ``patch'' to another within the same eco-system. We model the spatial extension of the eco-system (i.e., the geography) by a square lattice where each site corresponds to a distinct ``patch''. A self-organizing hierarchical food web describes the prey-predator relations in the eco-system. The same species at different patches have identical food habits but differ from each other in their reproductive characteristic features. By carrying out computer simulations up to $10^9$ time steps, we found that, depending on the values of the set of parameters, the distribution of the lifetimes of the species can be either exponential or a combination of power laws. Some of the other features of our ``unified'' model turn out to be robust against migration of the organisms.Comment: 12 pages of PS file, including LATEX text and 9 EPS figure

Using Computational modeling to understand in-vitro and in-vivo transport by molecular motors

by Ambarish Kunwa

Alpine snowpit profiles of polar organic compounds from Mt. Tateyama central Japan: Atmospheric transport of organic pollutants with Asian dust

Snowpit samples (n = 10) were collected (19 April 2008) from the snowpit sequences (depth 6.60 m) at the Murodo-Daira site (36.58 degrees N, 137.60 degrees E, elevation of 2450 m a.s.l.) of Mt. Tateyama (3015 m a.s.l.), central Japan. The first time, low molecular weight diacids, omega-oxoacids, pyruvic acid, and alpha-dicarbonyls were measured for this snowpit sequence. Higher concentrations of short-chain diacids (C-2-C-5) are observed in dusty snow than nondusty snow samples. Longer chain diacids (C-7-C-12) are significant in granular and dusty snow samples. Aromatic and aliphatic unsaturated diacids showed higher concentrations in the slightly dusty layer deposited in winter. Except for a clean layer, molecular distributions of diacids are characterized by the predominance of oxalic acid (C-2, ave, 20 +/- 22 ng/g-snow) followed by succinic (C-4, 7.2 +/- 5.9 ng/g-snow), and malonic acids (C-3, 3.3 +/- 2.9 ng/g-snow) for all the snow layers. Lower C-3/C-4 ratios (0.46) suggest that organic aerosols are rather fresh without serious photochemical aging during the long-range transport over central Japan. The higher concentrations of the secondary species in dusty snow than non-dusty samples were mainly attributed to the heterogeneous reaction. The strong correlations of incloud oxidation products of isoprene, aromatic acids, and fatty acids suggest that condensation, oxidation, and photolysis are important reaction mechanisms for the formation of diacids. Chinese Loess (Kosa particles) and Mongolian Gobi desert's dust provided the surface area for polar organic compounds, traveled to several thousand kilometers in the lower troposphere, and snow metamorphism altered the chemical composition of diacids and related compounds

Unification of small and large time scales for biological evolution: deviations from power law

We develop a unified model that describes both "micro" and "macro" evolutions within a single theoretical framework. The ecosystem is described as a dynamic network; the population dynamics at each node of this network describes the "microevolution" over ecological time scales (i.e., birth, ageing, and natural death of individual organisms), while the appearance of new nodes, the slow changes of the links, and the disappearance of existing nodes accounts for the "macroevolution" over geological time scales (i.e., the origination, evolution, and extinction of species). In contrast to several earlier claims in the literature, we observe strong deviations from power law in the regime of long lifetimes