Multipolar Reactive DPD: A Novel Tool for Spatially Resolved Systems Biology

This article reports about a novel extension of dissipative particle dynamics (DPD) that allows the study of the collective dynamics of complex chemical and structural systems in a spatially resolved manner with a combinatorially complex variety of different system constituents. We show that introducing multipolar interactions between particles leads to extended membrane structures emerging in a self-organized manner and exhibiting both the necessary mechanical stability for transport and fluidity so as to provide a two-dimensional self-organizing dynamic reaction environment for kinetic studies in the context of cell biology. We further show that the emergent dynamics of extended membrane bound objects is in accordance with scaling laws imposed by physics.Comment: submitted to CMSB 0

Aster formation and rupture transition in semi-flexible fiber networks with mobile cross-linkers

Fibrous active network structures whose properties are regulated by motor proteins, or simply motors, are fundamental to life. Here, a full elastic and three dimensional model for such networks and motors is presented. The effects of surface anchoring are accounted for and we demonstrate that for unidirectional motors two basic contractile phases emerge in these systems. The transition is governed by a single parameter (tb/tc) which is the ratio of the breaking strain (tb) and the motility limiting strain (tc) of the motors. For tb/tc [less, similar] 2 and clamped boundaries, the network ruptures and formation of local asters occurs with a high density of motors at the centre and the fibers radially spanning out. This phase displays contraction strain during the formation of asters but the network stress is relaxed once the asters have emerged, demonstrating that the formation of aster-like structures provides a mechanism for stress relaxation. For 2.7 [less, similar] tb/tc the network remains intact, but reaches a force equilibrium with a high contraction strain in the case of clamped boundaries. Between these two limits the network is partly ruptured. Experimental measurements (e.g. J. T. Nishizaka, H. Miyata, H. Yoshikawa, S. Ishiwata and K. Kinosita Jr., Nature, 1995, 377, 251 and J. F. Finer, R. M. Simmons, J. A. Spudich, Nature, 1994, 368, 113) indicate that actin filament and myosin motors interact with tb/tc ˜ 2.7 which is right at the limit of motor induced fracture for a random network, indicating that e.g. a cytoskeleton with active myosin is susceptible to rupture. This is perhaps not a coincidence and may well be an important factor contributing to cellular dynamics. In the case of free boundaries the network collapses onto one single aster. We also show that the distribution of energy on the motors is a power-law, below the motility limit energy, with the exponent -0.5

Myosin motor mediated contraction is enough to produce cytokinesis in the absence of polymerisation

Actin filament networks play an active role in cytokinesis of eukaryotic cells. These networks, linked mainly by myosin, are concentrated below the cell membrane forming a spherical supporting shell. During cytokinesis, this network is modified such that a contractile ring is formed along the diameter of the shell. We present a realistic three-dimensional simulation model to study the dynamics of this spherical shell of elastic actin filaments and myosin motors. The results show compelling evidence that this fibre-spring model, with the motors activated in a narrow region around the division plane, is sufficient to reproduce most of the essential mechanics of cytokinesis: A spontaneous formation of a contractile ring, a characteristic filament orientation structure, and realistic cleavage furrow dynamics. These results demonstrate that, though cytokinesis is a highly complex process with large variation in intricate details, the fundamental dynamics are largely generic. In particular, motor mediated contraction of an unstructured filament mesh is sufficient to undergo division without concentrated and directed polymerization in the cleavage zone

Nonlinear 3D flow of Casson-Carreau fluids with homogeneous–heterogeneous reactions: A comparative study

Nonlinear convective flow of magneto-Carreau-Casson liquids past a deformable surface under the aspects of heterogeneous and homogeneous reactions is investigated. The present phenomenon also included the interaction of nonlinear radiation, Ohmic and Joule dissipations. At moderate to high temperature, the nonlinear convection and radiation are significant. The governed nonlinear system is illustrated numerically via Runge-Kutta based shooting scheme in the domain [0,∞). Role of significant parameters on flow fields as well as on the fiction factor, heat and mass transportation rates are determined and discussed in depth. Comparison is done for distinct flow fields of Carreau and Casson fluids. It is evaluated that the velocities of Casson liquid are higher in comparison to Carreau fluid model. However, liquid temperature for Casson fluid model is weaker in comparison to Carreau fluid. Keywords: Carreau fluid, Casson fluid, Nonlinear thermal radiation: Nonlinear convection, Homogeneous–heterogeneous reactio