arXiv subjects

Vahid Rezania

Publications and source records attributed to Vahid Rezania.

At least 19 recordsLinked to original sources

arXiv2019

On the capacitive properties of individual microtubules and their meshworks

Microtubules are hollow cylindrical polymers composed of the highly negatively-charged (~23e), high dipole moment (1750 D) protein a,b-tubulin. While the roles of microtubules in chromosomal segregation, macromolecular transport and cell migration are relatively well-understood, studies on the electrical properties of microtubules have only recently gained strong interest. Here, we show that while microtubules at physiological concentrations increase solution capacitance, free tubulin has no appreciable effect. For a particular microtubule concentration, we were able to quantify these effects by determining the capacitance and resistance of a single 20 um-long microtubule to be 1.86 x 10^(-12) F and 1.07 x 10^12 Ohms respectively. Further, we observed a decrease in electrical resistance of solution, with charge transport peaking between 20-60 Hz in the presence of microtubules, consistent with recent findings that microtubules exhibit electric oscillations at such low frequencies. Our results show that in addition to macromolecular transport, microtubules also act as charge-storage devices through counterionic condensation across a broad frequency spectrum. We conclude with a hypothesis of an electrically-tunable cytoskeleton where the dielectric properties of tubulin are polymerization-state dependent.

physics.bio-ph↗

arXiv2015

On the Classical Vibrational Coherence of Carbonyl Groups in the Selectivity Filter Backbone of KcsA Ion Channel

It has been suggested that quantum coherence in the selectivity filter of ion channel may play a key role in fast conduction and selectivity of ions. However, it has not been clearly elucidated yet why classical coherence is not sufficient for this purpose. In this paper, we investigate the classical vibrational coherence between carbonyl groups oscillations in the selectivity filter of KcsA ion channels based on the data obtained from molecular dynamics simulations. Our results show that classical coherence plays no effective role in fast ionic conduction.

q-bio.BM↗

arXiv2011

A Physiologically-Based Flow Network Model for Hepatic Drug Elimination I: Regular Lattice Lobule Model

We develop a physiologically-based lattice model for the transport and metabolism of drugs in the functional unit of the liver, called the lobule. In contrast to earlier studies, we have emphasized the dominant role of convection in well-vascularized tissue with a given structure. Estimates of convective, diffusive and reaction contributions are given. We have compared drug concentration levels observed exiting the lobule with their predicted detailed distribution inside the lobule, assuming that most often the former is accessible information while the latter is not.

physics.bio-ph↗

arXiv2011

Modeling the Effects of Drug Binding on the Dynamic Instability of Microtubules

We propose a stochastic model that accounts for the growth, catastrophe and rescue processes of steady state microtubules assembled from MAP-free tubulin. Both experimentally and theoretically we study the perturbation of microtubule dynamic instability by S-methyl-D-DM1, a synthetic derivative of the microtubule-targeted agent maytansine and a potential anticancer agent. We find that to be an effective suppressor of microtubule dynamics a drug must primarily suppress the loss of GDP tubulin from the microtubule tip.

physics.bio-ph↗

arXiv2009

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.

q-bio.SC↗

arXiv2009

A continuous model for microtubule dynamics with catastrophe, rescue and nucleation processes

Microtubules are a major component of the cytoskeleton distinguished by highly dynamic behavior both in vitro and in vivo. We propose a general mathematical model that accounts for the growth, catastrophe, rescue and nucleation processes in the polymerization of microtubules from tubulin dimers. Our model is an extension of various mathematical models developed earlier formulated in order to capture and unify the various aspects of tubulin polymerization including the dynamic instability, growth of microtubules to saturation, time-localized periods of nucleation and depolymerization as well as synchronized oscillations exhibited by microtubules under various experimental conditions. Our model, while attempting to use a minimal number of adjustable parameters, covers a broad range of behaviors and has predictive features discussed in the paper. We have analyzed the resultant behaviors of the microtubules changing each of the parameter values at a time and observing the emergence of various dynamical regimes.

physics.bio-ph↗

arXiv2008

Modeling polymerization of microtubules: a quantum mechanical approach

In this paper a quantum mechanical description of the assembly/disassembly process for microtubules is proposed. We introduce creation and annihilation operators that raise or lower the microtubule length by a tubulin layer. Following that, the Hamiltonian and corresponding equations of motion for the quantum fields are derived that describe the dynamics of microtubules. These Heisenberg-type equations are then transformed to semi-classical equations using the method of coherent structures. We find that the dynamics of a microtubule can be mathematically expressed via a cubic-quintic nonlinear Schrödinger (NLS) equation. We show that a vortex filament, a generic solution of the NLS equation, exhibits linear growth/shrinkage in time as well as temporal fluctuations about some mean value which is qualitatively similar to the dynamic instability of microtubules.

q-bio.BM↗

arXiv2008

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.

q-bio.QM↗

arXiv2007

Modeling transcription factor binding events to DNA using a random walker/jumper representation on a 1D/2D lattice with different affinity sites

Surviving in a diverse environment requires corresponding organism responses. At the cellular level, such adjustment relies on the transcription factors (TFs) which must rapidly find their target sequences amidst a vast amount of non-relevant sequences on DNA molecules. Whether these transcription factors locate their target sites through a 1D or 3D pathway is still a matter of speculation. It has been suggested that the optimum search time is when the protein equally shares its search time between 1D and 3D diffusions. In this paper, we study the above problem using a Monte Carlo simulation by considering a very simple physical model. A 1D strip, representing a DNA, with a number of low affinity sites, corresponding to non-target sites, and high affinity sites, corresponding to target sites, is considered and later extended to a 2D strip. We study the 1D and 3D exploration pathways, and combinations of the two modes by considering three different types of molecules: a walker that randomly walks along the strip with no dissociation; a jumper that represents dissociation and then re-association of a TF with the strip at later time at a distant site; and a hopper that is similar to the jumper but it dissociates and then re-associates at a faster rate than the jumper. We analyze the final probability distribution of molecules for each case and find that TFs can locate their targets fast enough even if they spend 15% of their search time diffusing freely in the solution. This indeed agrees with recent experimental results obtained by Elf et al. 2007 and is in contrast with theoretical expectation.

q-bio.QM↗

arXiv2007

From a quantum mechanical description of the assembly processes in microtubules to their semiclassical nonlinear dynamics

In this paper a quantum mechanical description of the assembly/disassembly process for microtubules is proposed. We introduce creation and annihilation operators that raise or lower the microtubule length by a tubulin layer. Following that, the Hamiltonian and corresponding equations of motion are derived that describe the dynamics of microtubules. These Heisenberg-type equations are then transformed to semi-classical equations using the method of coherent structures. The latter equations are very similar to the phenomenological equations that describe dynamic instability of microtubules in a tubulin solution.

q-bio.CB↗

arXiv2005

QPOs and firehose instabilities in neutron star magnetospheres in accreting systems

We show that the interaction of an accretion disk with the magnetosphere of a neutron star can excite resonant shear Alfven waves with Hz-kHz frequencies in a region of enhanced density gradients. This is the the region where accretion material flows along the magnetic field lines in the magnetosphere. We argue that due to the pressure anisotropy produced by the plasma flow, firehose instabilities are likely to occur. Furthermore, for a dipolar field topology, we show that a new instability develops due to both magnetic field curvature and the plasma flow.

astro-ph↗

arXiv2005

Quasi-periodic oscillations: Resonant shear Alfv`en waves in neutron star magnetospheres

In this paper we propose a new model for quasi-periodic oscillations (QPOs) based on oscillating magnetohydrodynamic modes in neutron star magnetospheres. We argue that the interaction of the accretion disk with the magnetosphere can excite resonant shear Alfv`en waves in a region of enhanced density gradients, the region where accretion material flows along the magnetic field lines in the magnetosphere. We demonstrate that depending on the distance of this region from the star and the magnetic field strength, the frequency of the field line resonance can range from several Hz (weaker field, farther from star), to approximately kHz frequencies (stronger field, ~ 2-10 stellar radii from the star). We show that such oscillations are able to significantly modulate inflow of matter from the high density region toward the star's surface, and possibly produce the observed X-ray spectrum. In addition, we show that the observed 2:3 frequency ratio of QPOs is a natural result of our model.

astro-ph↗

arXiv2004

X-ray aurora in neutron star magnetospheres

In this study we propose a new generic model for QPOs based on oscillation modes of neutron star magnetospheres. We argue that the interaction of the accretion disk with the magnetosphere can excite resonant shear Alfven waves in a region of enhanced density gradients. We demonstrate that depending on the distance of this enhanced density region from the star and the magnetic field strength, the frequency of the field line resonance can range from several Hz (weaker field, farther from star), to approximately kHz frequencies (stronger field, ~ 2-10 star radii from the star). We show that such oscillations are able to significantly modulate inflow of matter from the high density region toward the star surface, and possibly produce the observed X-ray spectrum. In addition, we show that the observed 2:3 frequency ratio of QPOs is a natural result of our model.

astro-ph↗

arXiv2003

Large frequency drifts during Type I X-ray bursts

We study the spin-down of a neutron star atmosphere during the Type I X-ray burst in low mass X-ray binaries. Using polar cap acceleration models, we show that the resulting stellar ``wind'' torque on the burning shell due to the flowing charged particles (electrons, protons and ions) from the star's polar caps may change the shell's angular momentum during the burst. We conclude that the net change in the angular momentum of the star's atmosphere can account for rather large frequency drifts observed during Type I X-ray burst.

astro-ph↗

arXiv2002

Radiation pattern of the isolated pulsar PSR B1828-11

Based on the free precession model of the isolated pulsar PSR B1828-11, Link & Epstein 2001) showed that the observed pulse durations require the radio beam to have a non-standard shape: the beam duration is larger for beam sweeps farthest from the dipole axis. In their analysis they assumed that the actual precession period is ~ 500 d. Recent theoretical studies suggested that the actual precession period might be ~ 1000 d as seen in observations (Rezania 2002, Wasserman 2002). In this paper, in a good agreement with the observed data (Stairs et al. 2000), we model the changes of the pulse shape in a precession cycle with period ~ 1000 d and find that the variation of the pulse duration follows from a {\it standard} beam pattern in each cycle.

astro-ph↗

arXiv2002

On the precession of the isolated pulsar PSR B1828-11

Analysis of both pulse timing and pulse shape variations of the isolated pulsar PSR B1828-11 shows highly correlated and strong Fourier power at periods \~ 1000, 500, and 250 d (Stairs et al. 2000). The only description based on a free precession of star's rigid crust coupled to the magnetic dipole torque, explains the 500-component, as the fundamental Fourier frequency, with its harmonic 250-component (Link & Epstein 2001). In this paper, we show that if the dipole moment vector varies with time with a period nearly equal to the longest (probably fundamental) observed period (~ 1000 d), the dipole torque may produce the all other harmonics. We also find the second and fourth harmonics at periods ~ 500 and 250 d are dominant for small wobble angle ~ 3^o and large field's inclination angle 89^o.

astro-ph↗

arXiv2002

Normal Modes of Rotating Magnetic Stars

We investigate the effect of a magnetic field on the global oscillation modes of a rotating fluid star in the magnetohydrodynamic approximation. We present general equations for the modification of any type of fluid mode due to a general magnetic field which is not aligned with the star's spin axis. In the case of any internal dipole magnetic field we derive the equations for the frequency corrections to the r-modes. We solve for the frequency correction explicitly for the case when the internal dipole field is force-free, including the uniform density case. In the weak-field limit, the spatial form of the r-mode velocity perturbation is unchanged, but the magnitude of the frequency in the rotating frame increases.

astro-ph↗

arXiv2002

R-modes in the ocean of a magnetic neutron star

We study the dynamics of r-modes in the ocean of a magnetic neutron star. We modeled the star's ocean with a spherical rotating thin shell and assumed that the magnetic field symmetry axis is not aligned to the shell's spin axis. In the magnetohydrodynamic approximation, we calculate the frequency of $\ell=m$ r-modes in the shell of an incompressible fluid. Different r-modes with $\ell$ and $\ell\pm2$ are coupled by the {\it inclined} magnetic field. Kinematical secular effects for the motion of a fluid element in the shell undergoing $\ell=m=2$ r-mode are studied. The magnetic corrected drift velocity of a given fluid element undergoing the $\ell=m$ r-mode oscillations is obtained. The magnetic field increases the magnitude of the fluid drift produced by the r-mode drift velocity, the high-$\ell$ modes in the ocean fluid will damp faster than the low-$\ell$ ones.

astro-ph↗