arXiv subjects

Mir Abbas Jalali

Publications and source records attributed to Mir Abbas Jalali.

At least 19 recordsLinked to original sources

arXiv2019

Propulsion and Mixing Generated by the Digitized Gait of Caenorhabditis elegans

Nematodes have evolved to swim in highly viscous environments. Artificial mechanisms that mimic the locomotory functions of nematodes can be efficient viscous pumps. We experimentally simulate the motion of the head segment of Caenorhabditis elegans by introducing a reciprocating and rocking blade. We show that the bio-inspired blade's motion not only induces a flow structure similar to that of the worm, but also mixes the surrounding fluid by generating a circulatory flow. When confined between two parallel walls, the blade causes a steady Poiseuille flow through closed circuits. The pumping efficiency is comparable with the swimming efficiency of the worm. If implanted in a sealed chamber and actuated remotely, the blade can provide pumping and mixing functions for microprocessors cooled by polymeric flows and microfluidic devices.

physics.flu-dyn↗

arXiv2015

Rigidity of transmembrane proteins determines their cluster shape

Protein aggregation in cell membrane is vital for the majority of biological functions. Recent experimental results suggest that transmembrane domains of proteins such as $α$-helices and $β$-sheets have different structural rigidities. We use molecular dynamics simulation of a coarse-grained model of protein-embedded lipid membranes to investigate the mechanisms of protein clustering. For a variety of protein concentrations, our simulations under thermal equilibrium conditions reveal that the structural rigidity of transmembrane domains dramatically affects interactions and changes the shape of the cluster. We have observed stable large aggregates even in the absence of hydrophobic mismatch which has been previously proposed as the mechanism of protein aggregation. According to our results, semi-flexible proteins aggregate to form two-dimensional clusters while rigid proteins, by contrast, form one-dimensional string-like structures. By assuming two probable scenarios for the formation of a two-dimensional triangular structure, we calculate the lipid density around protein clusters and find that the difference in lipid distribution around rigid and semiflexible proteins determines the one- or two-dimensional nature of aggregates. It is found that lipids move faster around semiflexible proteins than rigid ones. The aggregation mechanism suggested in this paper can be tested by current state-of-the-art experimental facilities.

physics.bio-ph↗

arXiv2015

Terminal retrograde turn of rolling rings

We report an unexpected reverse spiral turn in the final stage of the motion of rolling rings. It is well known that spinning disks rotate in the same direction of their initial spin until they stop. While a spinning ring starts its motion with a kinematics similar to disks, i.e. moving along a cycloidal path prograde with the direction of its rigid body rotation, the mean trajectory of its center of mass later develops an inflection point so that the ring makes a spiral turn and revolves in a retrograde direction around a new center. Using high speed imaging and numerical simulations of models featuring a rolling rigid body, we show that the hollow geometry of a ring tunes the rotational air drag resistance so that the frictional force at the contact point with the ground changes its direction at the inflection point and puts the ring on a retrograde spiral trajectory. Our findings have potential applications in designing topologically new surface-effect flying objects capable of performing complex reorientation and translational maneuvers.

physics.class-ph↗

arXiv2014

Versatile low-Reynolds-number swimmer with three-dimensional maneuverability

We design and simulate the motion of a new swimmer, the {\it Quadroar}, with three dimensional translation and reorientation capabilities in low Reynolds number conditions. The Quadroar is composed of an $\texttt{I}$-shaped frame whose body link is a simple linear actuator, and four disks that can rotate about the axes of flange links. The time symmetry is broken by a combination of disk rotations and the one-dimensional expansion/contraction of the body link. The Quadroar propels on forward and transverse straight lines and performs full three dimensional reorientation maneuvers, which enable it to swim along arbitrary trajectories. We find continuous operation modes that propel the swimmer on planar and three dimensional periodic and quasi-periodic orbits. Precessing quasi-periodic orbits consist of slow lingering phases with cardioid or multiloop turns followed by directional propulsive phases. Quasi-periodic orbits allow the swimmer to access large parts of its neighboring space without using complex control strategies. We also discuss the feasibility of fabricating a nano-scale Quadroar by photoactive molecular rotors.

physics.flu-dyn↗

arXiv2014

Collective Dynamics of Interacting Particles in Unsteady Flows

We use the Fokker-Planck equation and its moment equations to study the collective behavior of interacting particles in unsteady one-dimensional flows. Particles interact according to a long-range attractive and a short-range repulsive potential field known as Morse potential. We assume Stokesian drag force between particles and their carrier fluid, and find analytic single-peaked traveling solutions for the spatial density of particles in the catastrophic phase. In steady flow conditions the streaming velocity of particles is identical to their carrier fluid, but we show that particle streaming is asynchronous with an unsteady carrier fluid. Using linear perturbation analysis, the stability of traveling solutions is investigated in unsteady conditions. It is shown that the resulting dispersion relation is an integral equation of the Fredholm type, and yields two general families of stable modes: singular modes whose eigenvalues form a continuous spectrum, and a finite number of discrete global modes. Depending on the value of drag coefficient, stable modes can be over-damped, critically damped, or decaying oscillatory waves. The results of linear perturbation analysis are confirmed through the numerical solution of the fully nonlinear Fokker-Planck equation.

physics.flu-dyn↗

arXiv2013

Anomalous diffusion of proteins in sheared lipid membranes

We use coarse grained molecular dynamics simulations to investigate diffusion properties of sheared lipid membranes with embedded transmembrane proteins. In membranes without proteins, we find normal in-plane diffusion of lipids in all flow conditions. Protein embedded membranes behave quite differently: by imposing a simple shear flow and sliding the monolayers of the membrane over each other, the motion of protein clusters becomes strongly superdiffusive in the shear direction. In such a circumstance, subdiffusion regime is predominant perpendicular to the flow. We show that superdiffusion is a result of accelerated chaotic motions of protein--lipid complexes within the membrane voids, which are generated by hydrophobic mismatch or the transport of lipids by proteins.

physics.bio-ph↗

arXiv2013

Global drag-induced instabilities in protoplanetary disks

We use the Fokker-Planck equation and model the dispersive dynamics of solid particles in annular protoplanetary disks whose gas component is more massive than the particle phase. We model particle--gas interactions as hard sphere collisions, determine the functional form of diffusion coefficients, and show the existence of two global unstable modes in the particle phase. These modes have spiral patterns with the azimuthal wavenumber $m=1$ and rotate slowly. We show that in ring-shaped disks, the phase space density of solid particles increases linearly in time towards an accumulation point near the location of pressure maximum, while instabilities grow exponentially. Therefore, planetesimals and planetary cores can be efficiently produced near the peaks of unstable density waves. In this mechanism, particles migrating towards the accumulation point will not participate in the formation of planets, and should eventually form a debris ring like the main asteroid belt or classical Kuiper belt objects. We present the implications of global instabilities to the formation of ice giants and terrestrial planets in the solar system.

astro-ph.EP↗

arXiv2012

Long-lived and unstable modes of Brownian suspensions in microchannels

We investigate the stability of the pressure-driven, low-Reynolds flow of Brownian suspensions with spherical particles in microchannels. We find two general families of stable/unstable modes: (i) degenerate modes with symmetric and anti-symmetric patterns; (ii) single modes that are either symmetric or anti-symmetric. The concentration profiles of degenerate modes have strong peaks near the channel walls, while single modes diminish there. Once excited, both families would be detectable through high-speed imaging. We find that unstable modes occur in concentrated suspensions whose velocity profiles are sufficiently flattened near the channel centreline. The patterns of growing unstable modes suggest that they are triggered due to Brownian migration of particles between the central bulk that moves with an almost constant velocity, and highly-sheared low-velocity region near the wall. Modes are amplified because shear-induced diffusion cannot efficiently disperse particles from the cavities of the perturbed velocity field.

physics.flu-dyn↗

arXiv2012

Density waves in debris discs and galactic nuclei

We study the linear perturbations of collisionless near-Keplerian discs. Such systems are models for debris discs around stars and the stellar discs surrounding supermassive black holes at the centres of galaxies. Using a finite-element method, we solve the linearized collisionless Boltzmann equation and Poisson's equation for a wide range of disc masses and rms orbital eccentricities to obtain the eigenfrequencies and shapes of normal modes. We find that these discs can support large-scale `slow' modes, in which the frequency is proportional to the disc mass. Slow modes are present for arbitrarily small disc mass so long as the self-gravity of the disc is the dominant source of apsidal precession. We find that slow modes are of two general types: parent modes and hybrid child modes, the latter arising from resonant interactions between parent modes and singular van Kampen modes. The most prominent slow modes have azimuthal wavenumbers $m=1$ and $m=2$. We illustrate how slow modes in debris discs are excited during a fly-by of a neighbouring star. Many of the non-axisymmetric features seen in debris discs (clumps, eccentricity, spiral waves) that are commonly attributed to planets could instead arise from slow modes; the two hypotheses can be distinguished by long-term measurements of the pattern speed of the features.

astro-ph.EP↗

arXiv2011

Vesicle deformations by clusters of transmembrane proteins

We carry out a coarse-grained molecular dynamics simulation of phospholipid vesicles with transmembrane proteins. We measure the mean and Gaussian curvatures of our protein-embedded vesicles and quantitatively show how protein clusters change the shapes of their host vesicles. The effects of depletion force and vesiculation on protein clustering are also investigated. By increasing the protein concentration, clusters are fragmented to smaller bundles, which are then redistributed to form more symmetric structures corresponding to lower bending energies. Big clusters and highly aspherical vesicles cannot be formed when the fraction of protein to lipid molecules is large.

cond-mat.soft↗

arXiv2010

Generalized Schwarzschild's method

We describe a new finite element method (FEM) to construct continuous equilibrium distribution functions of stellar systems. The method is a generalization of Schwarzschild's orbit superposition method from the space of discrete functions to continuous ones. In contrast to Schwarzschild's method, FEM produces a continuous distribution function (DF) and satisfies the intra element continuity and Jeans equations. The method employs two finite-element meshes, one in configuration space and one in action space. The DF is represented by its values at the nodes of the action-space mesh and by interpolating functions inside the elements. The Galerkin projection of all equations that involve the DF leads to a linear system of equations, which can be solved for the nodal values of the DF using linear or quadratic programming, or other optimization methods. We illustrate the superior performance of FEM by constructing ergodic and anisotropic equilibrium DFs for spherical stellar systems (Hernquist models). We also show that explicitly constraining the DF by the Jeans equations leads to smoother and/or more accurate solutions with both Schwarzschild's method and FEM.

astro-ph.IM↗

arXiv2010

Finite element modelling of perturbed stellar systems

I formulate a general finite element method (FEM) for self-gravitating stellar systems. I split the configuration space to finite elements, and express the potential and density functions over each element in terms of their nodal values and suitable interpolating functions. General expressions are then introduced for the Hamiltonian and phase space distribution functions of the stars that visit a given element. Using the weighted residual form of Poisson's equation, I derive the Galerkin projection of the perturbed collisionless Boltzmann equation, and assemble the global evolutionary equations of nodal distribution functions. The FEM is highly adaptable to all kinds of potential and density profiles, and it can deal with density clumps and initially non-axisymmetric systems. I use ring elements of non-uniform widths, choose linear and quadratic interpolation functions in the radial direction, and apply the FEM to the stability analysis of the cutout Mestel disc. I also integrate the forced evolutionary equations and investigate the disturbances of a stable stellar disc due to the gravitational field of a distant satellite galaxy. The performance of the FEM and its prospects are discussed.

astro-ph.IM↗

arXiv2009

Nanoscopic spontaneous motion of liquid trains: non-equilibrium molecular dynamics simulation

Macroscale experiments show that a train of two immiscible liquid drops, a bislug, can spontaneously move in a capillary tube because of surface tension asymmetries. We use molecular dynamics simulation of Lennard-Jones fluids to demonstrate this phenomenon for NVT ensembles in sub-micron tubes. We deliberately tune the strength of intermolecular forces and control the velocity of bislug in different wetting and viscosity conditions. We compute the velocity profile of particles across the tube, and explain the origin of deviations from the classical parabolae. We show that the self-generated molecular flow resembles the Poiseuille law when the ratio of the tube radius to its length is less than a critical value.

physics.flu-dyn↗

arXiv2008

New biorthogonal potential--density basis functions

We use the weighted integral form of spherical Bessel functions, and introduce a new analytical set of complete and biorthogonal potential--density basis functions. The potential and density functions of the new set have finite central values and they fall off, respectively, similar to $r^{-(1+l)}$ and $r^{-(4+l)}$ at large radii where $l$ is the latitudinal quantum number of spherical harmonics. The lowest order term associated with $l=0$ is the perfect sphere of de Zeeuw. Our basis functions are intrinsically suitable for the modeling of three dimensional, soft-centred stellar systems and they complement the basis sets of Clutton-Brock, Hernquist & Ostriker and Zhao. We test the performance of our functions by expanding the density and potential profiles of some spherical and oblate galaxy models.

astro-ph↗

arXiv2008

Unstable Disk Galaxies. II. the Origin of Growing and Stationary Modes

I decompose the unstable growing modes of stellar disks to their Fourier components and present the physical mechanism of instabilities in the context of resonances. When the equilibrium distribution function is a non-uniform function of the orbital angular momentum, the capture of stars into the corotation resonance imbalances the disk angular momentum and triggers growing bar and spiral modes. The stellar disk can then recover its angular momentum balance through the response of non-resonant stars. I carry out a complete analysis of orbital structure corresponding to each Fourier component in the radial angle, and present a mathematical condition for the occurrence of van Kampen modes, which constitute a continuous family. I discuss on the discreteness and allowable pattern speeds of unstable modes and argue that the mode growth is saturated due to the resonance overlapping mechanism. An individually growing mode can also be suppressed if the corotation and inner Lindblad resonances coexist and compete to capture a group of stars. Based on this mechanism, I show that self-consistent scale-free disks with a sufficient distribution of non-circular orbits should be stable under perturbations of angular wavenumber $m>1$. I also derive a criterion for the stability of stellar disks against non-axisymmetric excitations.

astro-ph↗

arXiv2007

A New 3D Potential-Density Basis Set

A set of bi-orthogonal potential-density basis functions is introduced to model the density and its associated gravitational field of three dimensional stellar systems. Radial components of our basis functions are weighted integral forms of spherical Bessel functions. We discuss the properties of our basis functions and demonstrate their shapes for the latitudinal Fourier number $l=2$.

astro-ph↗

arXiv2007

Unstable Disk Galaxies. I. Modal Properties

I utilize the Petrov-Galerkin formulation and develop a new method for solving the unsteady collisionless Boltzmann equation in both the linear and nonlinear regimes. In the first order approximation, the method reduces to a linear eigenvalue problem which is solved using standard numerical methods. I apply the method to the dynamics of a model stellar disk which is embedded in the field of a soft-centered logarithmic potential. The outcome is the full spectrum of eigenfrequencies and their conjugate normal modes for prescribed azimuthal wavenumbers. The results show that the fundamental bar mode is isolated in the frequency space while spiral modes belong to discrete families that bifurcate from the continuous family of van Kampen modes. The population of spiral modes in the bifurcating family increases by cooling the disk and declines by increasing the fraction of dark to luminous matter. It is shown that the variety of unstable modes is controlled by the shape of the dark matter density profile.

astro-ph↗

arXiv2007

On the existence of chaotic circumferential waves in spinning disks

We use a third-order perturbation theory and Melnikov's method to prove the existence of chaos in spinning circular disks subject to a lateral point load. We show that the emergence of transverse homoclinic and heteroclinic points respectively lead to a random reversal in the traveling direction of circumferential waves and a random phase shift of magnitude $π$ for both forward and backward wave components. These long-term phenomena occur in imperfect low-speed disks sufficiently far from fundamental resonances.

nlin.CD↗