2,278 research outputs found
Model of ionic currents through microtubule nanopores and the lumen
It has been suggested that microtubules and other cytoskeletal filaments may
act as electrical transmission lines. An electrical circuit model of the
microtubule is constructed incorporating features of its cylindrical structure
with nanopores in its walls. This model is used to study how ionic conductance
along the lumen is affected by flux through the nanopores when an external
potential is applied across its two ends. Based on the results of Brownian
dynamics simulations, the nanopores were found to have asymmetric inner and
outer conductances, manifested as nonlinear IV curves. Our simulations indicate
that a combination of this asymmetry and an internal voltage source arising
from the motion of the C-terminal tails causes a net current to be pumped
across the microtubule wall and propagate down the microtubule through the
lumen. This effect is demonstrated to enhance and add directly to the
longitudinal current through the lumen resulting from an external voltage
source, and could be significant in amplifying low-intensity endogenous
currents within the cellular environment or as a nano-bioelectronic device.Comment: 43 pages, 6 figures, revised versio
Algebraic and Topological Indices of Molecular Pathway Networks in Human Cancers
Protein-protein interaction networks associated with diseases have gained
prominence as an area of research. We investigate algebraic and topological
indices for protein-protein interaction networks of 11 human cancers derived
from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. We find a
strong correlation between relative automorphism group sizes and topological
network complexities on the one hand and five year survival probabilities on
the other hand. Moreover, we identify several protein families (e.g. PIK, ITG,
AKT families) that are repeated motifs in many of the cancer pathways.
Interestingly, these sources of symmetry are often central rather than
peripheral. Our results can aide in identification of promising targets for
anti-cancer drugs. Beyond that, we provide a unifying framework to study
protein-protein interaction networks of families of related diseases (e.g.
neurodegenerative diseases, viral diseases, substance abuse disorders).Comment: 15 pages, 4 figure
Are there optical communication channels in the brain?
Despite great progress in neuroscience, there are still fundamental
unanswered questions about the brain, including the origin of subjective
experience and consciousness. Some answers might rely on new physical
mechanisms. Given that biophotons have been discovered in the brain, it is
interesting to explore if neurons use photonic communication in addition to the
well-studied electro-chemical signals. Such photonic communication in the brain
would require waveguides. Here we review recent work [S. Kumar, K. Boone, J.
Tuszynski, P. Barclay, and C. Simon, Scientific Reports 6, 36508 (2016)]
suggesting that myelinated axons could serve as photonic waveguides. The light
transmission in the myelinated axon was modeled, taking into account its
realistic imperfections, and experiments were proposed both in-vivo and
in-vitro to test this hypothesis. Potential implications for quantum biology
are discussed.Comment: 13 pages, 5 figures, review of arXiv:1607.02969 for Frontiers in
Bioscience, updated figures, new references on existence of opsins in the
brain and experimental effects of light on neuron
A Bio-Polymer Transistor: Electrical Amplification by Microtubules
Microtubules (MTs) are important cytoskeletal structures, engaged in a number
of specific cellular activities, including vesicular traffic, cell
cyto-architecture and motility, cell division, and information processing
within neuronal processes. MTs have also been implicated in higher neuronal
functions, including memory, and the emergence of "consciousness". How MTs
handle and process electrical information, however, is heretofore unknown. Here
we show new electrodynamic properties of MTs. Isolated, taxol-stabilized
microtubules behave as bio-molecular transistors capable of amplifying
electrical information. Electrical amplification by MTs can lead to the
enhancement of dynamic information, and processivity in neurons can be
conceptualized as an "ionic-based" transistor, which may impact among other
known functions, neuronal computational capabilities.Comment: This is the final submitted version. The published version should be
downloaded from Biophysical Journa
A first principle (3+1) dimensional model for microtubule polymerization
In this paper we propose a microscopic model to study the polymerization of
microtubules (MTs). Starting from fundamental reactions during MT's assembly
and disassembly processes, we systematically derive a nonlinear system of
equations that determines the dynamics of microtubules in 3D. %coexistence with
tubulin dimers in a solution. We found that the dynamics of a MT is
mathematically expressed via a cubic-quintic nonlinear Schrodinger (NLS)
equation. Interestingly, the generic 3D solution of the NLS equation exhibits
linear growing and shortening in time as well as temporal fluctuations about a
mean value which are qualitatively similar to the dynamic instability of MTs
observed experimentally. By solving equations numerically, we have found
spatio-temporal patterns consistent with experimental observations.Comment: 12 pages, 2 figures. Accepted in Physics Letters
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