Microtubules are cylindrically shaped cytoskeletal biopolymers that are essential for cell motility, cell division and intracellular trafficking. Here, we investigate their polyelectrolyte character that plays a very important role in ionic transport throughout the intra-cellular environment. The model we propose demonstrates an essentially nonlinear behavior of ionic currents which are guided by microtubules. These features are primarily due to the dynamics of tubulin C-terminal tails which are extended out of the surface of the microtubule cylinder. We also demonstrate that the origin of nonlinearity stems from the nonlinear capacitance of each tubulin dimer. This brings about conditions required for the creation and propagation of solitonic ionic waves along the microtubule axis. We conclude that a microtubule plays the role of a biological nonlinear transmission line for ionic currents. These currents might be of particular significance in cell division and possibly also in cognitive processes taking place in nerve cells.

We present hybrid OpenMP/MPI (Open Multi-Processing/Message Passing Interface) parallelized versions of earlier published C programs (D. Vudragović et al. (2012) [1]) for calculating both stationary and nonstationary solutions of the time-dependent Gross-Pitaevskii (GP) equation in three spatial dimensions. The GP equation describes the properties of dilute Bose-Einstein condensates at ultra-cold temperatures. Hybrid versions of programs use the same algorithms as the C ones, involving real-and imaginary-time propagation based on a split-step Crank-Nicolson method, but consider only a fully-anisotropic three-dimensional GP equation, where algorithmic complexity for large grid sizes necessitates parallelization in order to reduce execution time and/or memory requirements per node. Since distributed memory approach is required to address the latter, we combine MPI programing paradigm with existing OpenMP codes, thus creating fully flexible parallelism within a combined distributed/shared memory model, suitable for different modern computer architectures. The two presented C/OpenMP/MPI programs for real-and imaginary-time propagation are optimized and accompanied by a customizable makefile. We present typical scalability results for the provided OpenMP/MPI codes and demonstrate almost linear speedup until inter-process communication time starts to dominate over calculation time per iteration. Such a scalability study is necessary for large grid sizes in order to determine optimal number of MPI nodes and OpenMP threads per node. Nature of problem: These programs are designed to solve the time-dependent Gross-Pitaevskii (GP) nonlinear partial differential equation in three spatial dimensions in a fully anisotropic trap using a hybrid OpenMP/MPI parallelization approach. The GP equation describes the properties of a dilute trapped Bose-Einstein condensate. Keywords Solution method:The time-dependent GP equation is solved by the split-step Crank-Nicolson method using discretization in space and time. The discretized equation is then solved by propagation, in either imaginary or real time, over small time steps. The method yields solutions of stationary and/or non-stationary problems. Reasons for the new version: Previous C [1] and Fortran [2]programs are widely used within the ultracold atoms and nonlinear optics communities, as well as in various other fields [3]. This new version represents extension of the two previously OpenMP-parallelized programs (imagtime3d-th and realtime3d-th) for propagation in imaginary and real time in three spatial dimensions to a hybrid, fully distributed OpenMP/MPI programs (imagtime3d-hyb and realtime3d-hyb). Hybrid extensions of previous OpenMP codes enable interested researchers to numerically study Bose-Einstein condensates in much greater detail (i.e., with much finer resolution) than with OpenMP codes. In OpenMP (threaded) versions of programs, numbers of discretization points in X, Y, and Z directions are bound by the total amount of available memory on a single computing ...

We elucidate the model introduced by Tuszynski et al.1 in order to obtain more biophysically tractable results regarding the role of actin filaments in ionic transport throughout living cells.

Calcium ions (Ca) tune and control numerous diverse aspects of cochlear and vestibular physiological processes. This paper is focused on the Ca control of mechanotransduction in sensory hair cells in the context of polyelectrolyte properties of actin filaments within the hair-bundles of inner ear. These actin filaments appear to serve as efficient pathways for the flow of Ca ions inside stereocilia. We showed how this can be utilized for tuning of force-generating myosin motors. In an established model, we unified the Ca nonlinear dynamics involved in the control of myosin adaptation motors with mechanical displacements of hair-bundles. The model shows that the characteristic time scales fit reasonably well with the available experimental data for spontaneous oscillations in the inner ear. This scenario promises to fill a gap in our understanding of the role of Ca ions in the regulation of processes in the auditory cells of the inner ear.

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