27 research outputs found
Nonlinear Dynamics of Dipoles in Microtubules: Pseudo-Spin Model
We perform a theoretical study of the dynamics of the electric field
excitations in a microtubule by taking into consideration the realistic
cylindrical geometry, dipole-dipole interactions of the tubulin-based protein
heterodimers, the radial electric field produced by the solvent, and a possible
degeneracy of energy states of individual heterodimers. The consideration is
done in the frames of the classical pseudo-spin model. We derive the system of
nonlinear dynamical ordinary differential equations of motion for interacting
dipoles, and the continuum version of these equations. We obtain the solutions
of these equations in the form of snoidal waves, solitons, kinks, and localized
spikes. Our results will help to a better understanding of the functional
properties of microtubules including the motor protein dynamics and the
information transfer processes. Our considerations are based on classical
dynamics. Some speculations on the role of possible quantum effects are also
made.Comment: 14 pages, 15 figures. The high resolution figure files are available
by reques
Kink solitons in DNA
We here examine the nonlinear dynamics of artificial homogeneous DNA chain
relying on the plain-base rotator model. It is shown that such dynamics can
exhibit kink and antikink solitons of sine-Gordon type. In that respect we
propose possible experimental assays based on single molecule micromanipulation
techniques. The aim of these experiments is to excite the rotational waves and
to determine their speeds along excited DNA. We propose that these experiments
should be conducted either for the case of double stranded (DS) or single
stranded (SS) DNA. A key question is to compare the corresponding velocities of
the rotational waves indicating which one is bigger. The ratio of these
velocities appears to be related with the sign of the model parameter
representing ratio of the hydrogen-bonding and the covalent-bonding interaction
within the considered DNA chain.Comment: 15 pages, 5 figure
The importance of quantum decoherence in brain processes
Based on a calculation of neural decoherence rates, we argue that that the
degrees of freedom of the human brain that relate to cognitive processes should
be thought of as a classical rather than quantum system, i.e., that there is
nothing fundamentally wrong with the current classical approach to neural
network simulations. We find that the decoherence timescales ~10^{-13}-10^{-20}
seconds are typically much shorter than the relevant dynamical timescales
(~0.001-0.1 seconds), both for regular neuron firing and for kink-like
polarization excitations in microtubules. This conclusion disagrees with
suggestions by Penrose and others that the brain acts as a quantum computer,
and that quantum coherence is related to consciousness in a fundamental way.Comment: Minor changes to match accepted PRE version. 15 pages with 5 figs
included. Color figures and links at
http://www.physics.upenn.edu/~max/brain.html or from [email protected].
Physical Review E, in pres
Neural cytoskeleton capabilities for learning and memory
This paper proposes a physical model involving the key structures within the neural cytoskeleton as major players in molecular-level processing of information required for learning and memory storage. In particular, actin filaments and microtubules are macromolecules having highly charged surfaces that enable them to conduct electric signals. The biophysical properties of these filaments relevant to the conduction of ionic current include a condensation of counterions on the filament surface and a nonlinear complex physical structure conducive to the generation of modulated waves. Cytoskeletal filaments are often directly connected with both ionotropic and metabotropic types of membrane-embedded receptors, thereby linking synaptic inputs to intracellular functions. Possible roles for cable-like, conductive filaments in neurons include intracellular information processing, regulating developmental plasticity, and mediating transport. The cytoskeletal proteins form a complex network capable of emergent information processing, and they stand to intervene between inputs to and outputs from neurons. In this manner, the cytoskeletal matrix is proposed to work with neuronal membrane and its intrinsic components (e.g., ion channels, scaffolding proteins, and adaptor proteins), especially at sites of synaptic contacts and spines. An information processing model based on cytoskeletal networks is proposed that may underlie certain types of learning and memory
Spectroscopic evidence for Davydov-like solitons in acetanilide
Detailed measurements of infrared absorption and Raman scattering on crystalline acetanilide [(CH3CONHC6H5)x] at low temperature show a new band close to the conventional amide I band. Equilibrium properties and spectroscopic data rule out explanations based on a conventional assignment, crystal defects, Fermi resonance, and upon frozen kinetics between two different subsystems. Thus we cannot account for this band using the concepts of conventional molecular spectroscopy, but a soliton model, similar to that proposed by Davydov for -helix in protein, is in satisfactory agreement with the experimental data. Ā© 1984 The American Physical Society
Calcium signaling modulates the dynamics of cilia and flagella
To adapt to changing environments cells must signal and signaling requires messengers whose concentration varies with time in space. We here consider the messenger role of calcium ions implicated in regulation of the wave-like bending dynamics of cilia and flagella. The emphasis is on microtubules as polyelectrolytes serving as transmission lines for the flow of Ca2+ signals in the axoneme. This signaling is superimposed with a geometric clutch mechanism for the regulation of flagella bending dynamics and our modeling produces results in agreement with experimental data
Resonance mode in DNA dynamics
In this article we use Peyrard-Bishop-Dauxois model (PBD) to study the nonlinear oscillations of DNA nucleotides of extremely
high amplitude (EHA) leading to unzipping of DNA chain in the context of the
process of replication. We give arguments that the EHA mode is nothing but
the resonance mode (RM). We launched an idea about how molecular mechano-chemical energy transduction can be the origin of the RM. We
compared some parameters of the solitonic wave in DNA in resonant and non-resonant regime
Role of nonlinear localized Ca2+ pulses along microtubules in tuning the mechano-sensitivity of hair cells
This paper aims to provide an overview of the polyelectrolyte model and the current understanding of the creation and propagation of localized pulses of positive ions flowing along cellular microtubules. In that context, Ca2+ ions may move freely on the surface of microtubule along the protofilament axis, thus leading to signal transport. Special emphasis in this paper is placed on the possible role of this mechanism in the function of microtubule based kinocilium, a component of vestibular hair cells of the inner ear. We discuss how localized pulses of Ca2+ ions play a crucial role in tuning the activity of dynein motors, which are involved in mechano sensitivity of the kinocilium. A prevailing notion holds that the concentration of Ca2+ ions around the microtubules within the kinocilium represents the control parameter for Hopf bifurcation. Therefore, a key feature of this mechanism is that the velocities of these Ca2+ pulses be sufficiently high to exert control at acoustic frequencies. (C) 2015 Elsevier Ltd. All rights reserved
High amplitude mode and DNA opening
In this article, we define and analyse an extremely high amplitude (EHA) mode in DNA dynamics. The dynamics of a DNA chain is described by the Peyrard-Bishop-Dauxois model. We show that a local opening of the DNA chain in a process of m-RNA transcription is the EHA behaviour. Also, we point out that the helicoidal structure brings about the possibility for the EHA mode to occur