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Ramin Golestanian

Publications and source records attributed to Ramin Golestanian.

At least 163 records · Page 9Linked to original sources
arXiv2013

Run-and-tumble in a crowded environment: persistent exclusion process for swimmers

The effect of crowding on the run-and-tumble dynamics of swimmers such as bacteria is studied using a discrete lattice model of mutually excluding particles that move with constant velocity along a direction that is randomized at a rate $α$. In stationary state, the system is found to break into dense clusters in which particles are trapped or stopped from moving. The characteristic size of these clusters predominantly scales as $α^{-0.5}$ both in 1D and 2D. For a range of densities, due to cooperative effects, the stopping time scales as ${\cal T}_{1d}^{0.85}$ and as ${\cal T}_{2d}^{0.8}$, where ${\cal T}_d$ is the diffusive time associated with the motion of cluster boundaries. Our findings might be helpful in understanding the early stages of biofilm formation.

cond-mat.soft↗
arXiv2013

Instabilities and Topological Defects in Active Nematics

We study a continuum model of an extensile active nematic to show that mesoscale turbulence develops in two stages: (i) ordered regions undergo an intrinsic hydrodynamic instability generating walls, lines of stong bend deformations, (ii) the walls relax by forming oppositely charged pairs of defects. Both creation and annihilation of defect pairs reinstate nematic regions which undergo further instabilities, leading to a dynamic steady state. We compare this with the development of active turbulence in a contractile active nematic.

cond-mat.soft↗
arXiv2013

Quantum Cherenkov Radiation and Non-contact Friction

We present a number of arguments to demonstrate that a quantum analog of Cherenkov effect occurs when two dispersive objects are in relative motion. Specifically we show that two semi-infinite plates experience friction beyond a threshold velocity which, in their center-of-mass frame, is the phase speed of light within their medium. The loss in mechanical energy is radiated away through the plates before getting fully absorbed in the form of heat. By deriving various correlation functions inside and outside the two plates, we explicitly compute the radiation, and discuss its dependence on the reference frame.

quant-ph↗
arXiv2013

Emergent comet-like swarming of optically driven thermally active colloids

We propose a simple system of optically driven colloids that convert light into heat and move in response to self- and collectively- generated thermal gradients. We show that the system exhibits self-organization into a moving comet-like swarm and characterize the structure and response of the swarm to a light intensity dependent external tuning parameter. We observe many interesting features in this nonequilibrium system including circulation and evaporation, intensity-dependent shape, density and temperature fluctuations, and ejection of hot colloids from the swarm tip.

cond-mat.soft↗
arXiv2013

Velocity Correlations in an Active Nematic

The flow properties of a continuum model for an active nematic is studied and compared with recent experiments on suspensions of microtubule bundles and molecular motors. The velocity correlation length is found to be independent of the strength of the activity while the characteristic velocity scale increases monotonically as the activity is increased, both in agreement with the experimental observations. We interpret our results in terms of the creation and annihilation dynamics of a gas of topological defects.

cond-mat.soft↗
arXiv2013

Phase Dependent Forcing and Synchronization in the three-sphere model of Chlamydomonas

The green alga {\it Chlamydomonas} swims with synchronized beating of its two flagella, and is experimentally observed to exhibit run-and-tumble behaviour similar to bacteria. Recently we studied a simple hydrodynamic three-sphere model of {\it Chlamydomonas} with a phase dependent driving force which can produce run-and-tumble behaviour when intrinsic noise is added, due to the non-linear mechanics of the system. Here, we consider the noiseless case and explore numerically the parameter space in the driving force profiles, which determine whether or not the synchronized state evolves from a given initial condition, as well as the stability of the synchronized state. We find that phase dependent forcing, or a beat pattern, is necessary for stable synchronization in the geometry we work with.

cond-mat.soft↗
arXiv2013

A Scattering Approach to the Dynamical Casimir Effect

We develop a unified scattering approach to dynamical Casimir problems which can be applied to both accelerating boundaries, as well as dispersive objects in relative motion. A general (trace) formula is derived for the radiation from accelerating boundaries. Applications are provided for objects with different shapes in various dimensions, and undergoing rotational or linear motion. Within this framework, photon generation is discussed in the context of a modulated optical mirror. For dispersive objects, we find general results solely in terms of the scattering matrix. Specifically, we discuss the vacuum friction on a rotating object, and the friction on an atom moving parallel to a surface.

quant-ph↗
arXiv2012

Translocation through environments with time dependent mobility

We consider single particle and polymer translocation where the frictional properties experienced from the environment are changing in time. This work is motivated by the interesting frequency responsive behaviour observed when a polymer is passing through a pore with an oscillating width. In order to explain this better we construct general diffusive and non-diffusive frequency response of the gain in translocation time for a single particle in changing environments and look at some specific variations. For two state confinement, where the particle either has constant drift velocity or is stationary, we find exact expressions for both the diffusive and non-diffusive gain. We then apply this approach to polymer translocation under constant forcing through a pore with a sinusoidally varying width. We find good agreement for small polymers at low frequency oscillation with deviations occurring at longer lengths and higher frequencies. Unlike periodic forcing of a single particle at constant mobility, constant forcing with time dependent mobility is amenable to exact solution through manipulation of the Fokker-Planck equation.

cond-mat.soft↗
arXiv2012

Hydrodynamic Synchronization between Objects with Cyclic Rigid Trajectories

Synchronization induced by long-range hydrodynamic interactions is attracting attention as a candidate mechanism behind coordinated beating of cilia and flagella. Here we consider a minimal model of hydrodynamic synchronization in the low Reynolds number limit. The model consists of rotors, each of which assumed to be a rigid bead making a fixed trajectory under periodically varying driving force. By a linear analysis, we derive the necessary and sufficient conditions for a pair of rotors to synchronize in phase. We also derive a non-linear evolution equation for their phase difference, which is reduced to minimization of an effective potential. The effective potential is calculated for a variety of trajectory shapes and geometries (either bulk or substrated), for which the stable and metastable states of the system are identified. Finite size of the trajectory induces asymmetry of the potential, which also depends sensitively on the tilt of the trajectory. Our results show that flexibility of cilia or flagella is {\it not} a requisite for their synchronized motion, in contrast to previous expectations. We discuss the possibility to directly implement the model and verify our results by optically driven colloids.

cond-mat.soft↗
arXiv2012

Emergent Run-and-Tumble Behavior in a Simple Model of Chlamydomonas with Intrinsic Noise

Recent experiments on the green alga Chlamydomonas that swims using synchronized beating of a pair of flagella have revealed that it exhibits a run-and-tumble behavior similar to that of bacteria such as E. Coli. Using a simple purely hydrodynamic model that incorporates a stroke cycle and an intrinsic Gaussian white noise, we show that a stochastic run-and-tumble behavior could emerge, due to the nonlinearity of the combined synchronization-rotation-translation dynamics. This suggests the intriguing possibility that the alga might exploit nonlinear mechanics---as opposed to sophisticated biochemical circuitry as used by bacteria---to control its behavior.

q-bio.CB↗
arXiv2012

Length scale dependence of DNA mechanical properties

Although mechanical properties of DNA are well characterized at the kilo base-pair range, a number of recent experiments have suggested that DNA is more flexible at shorter length scales, which correspond to the regime that is crucial for cellular processes such as DNA packaging and gene regulation. Here, we perform a systematic study of the effective elastic properties of DNA at different length scales by probing the conformation and fluctuations of DNA from single base-pair level up to four helical turns, using trajectories from atomistic simulation. We find evidence that supports cooperative softening of the stretch modulus and identify the essential modes that give rise to this effect. The bend correlation exhibits modulations that reflect the helical periodicity, while it yields a reasonable value for the effective persistence length, and the twist modulus undergoes a smooth crossover---from a relatively smaller value at the single base-pair level to the bulk value---over half a DNA-turn.

q-bio.BM↗
arXiv2012

Chiral Structure of F-actin Bundle Formed by Multivalent Counterions?

The mechanism of multivalent counterion-induced bundle formation by filamentous actin (F-actin) is studied using a coarse-grained model and molecular dynamics simulation. Real diameter size, helically ordered charge distribution and twist rigidity of F-actin are taken into account in our model. The attraction between parallel F-actins induced by multivalent counterions is studied in detail and it is found that the maximum attraction occurs between their closest charged domains. The model F-actins aggregate due to the like-charge attraction and form closely packed bundles. Counterions are mostly distributed in the narrowest gaps between neighboring F-actins inside the bundles and the channels between three adjacent F-actins correspond to low density of the counterions. Density of the counterions varies periodically with a wave length comparable to the separation between consecutive G-actin monomers along the actin polymers. Long-lived defects in the hexagonal order of F-actins in the bundles are observed that their number increases with increasing the bundles size. Combination of electrostatic interactions and twist rigidity has been found not to change the symmetry of F-actin helical conformation from the native 13/6 symmetry. Calculation of zero-temperature energy of hexagonally ordered model F-actins with the charge of the counterions distributed as columns of charge domains representing counterion charge density waves has shown that helical symmetries commensurate with the hexagonal lattice correspond to local minima of the energy of the system. The global minimum of energy corresponds to 24/11 symmetry with the columns of charge domains arranged in the narrowest gaps between the neighboring F-actins.

cond-mat.soft↗
arXiv2012

Stochastic sensing of polynucleotides using patterned nanopores

The effect of the microscopic structure of a pore on polymer translocation is studied using Langevin dynamics simulation, and the consequence of introducing patterned stickiness inside the pore is investigated. It is found that the translocation process is extremely sensitive to the detailed structure of such patterns with faster than exponential dependence of translocation times on the stickiness of the pore. The stochastic nature of the translocation process leads to discernable differences between how polymers with different sequences go through specifically patterned pores. This notion is utilized to propose a stochastic sensing protocol for polynucleotides, and it is demonstrated that the method, which would be significantly faster than the existing methods, could be made arbitrarily robust.

cond-mat.soft↗
arXiv2011

Active polymer translocation through flickering pores

Single file translocation of a homopolymer through an active channel under the presence of a driving force is studied using Langevin dynamics simulation. It is shown that a channel with sticky walls and oscillating width could lead to significantly more efficient translocation as compared to a static channel that has a width equal to the mean width of the oscillating pore. The gain in translocation exhibits a strong dependence on the stickiness of the pore, which could allow the polymer translocation process to be highly selective.

cond-mat.soft↗
arXiv2011

Collective Thermotaxis of Thermally Active Colloids

Colloids with patchy metal coating under laser irradiation could act as local sources of heat due to the absorption of light. While for asymmetric colloids this could induce self-propulsion, it also leads to the generation of a slowly decaying temperature profile that other colloids could interact with. The collective behavior of a dilute solution of such thermally active particles is studied using a stochastic formulation. It is found that when the Soret coefficient is positive, the system could be described in stationary-state by the nonlinear Poisson-Boltzmann equation and could adopt density profiles with significant depletion in the middle region when confined. For colloids with negative Soret coefficient, the system can be described as a dissipative equivalent of a gravitational system. It is shown that in this case the thermally active colloidal solution could undergo an instability at a critical laser intensity, which has similarities to supernova explosion.

cond-mat.soft↗
arXiv2011

Effect of interactions on the cellular uptake of nanoparticles

We present a simple two-state model to understand the size-dependent endocytosis of nanoparticles. Using this model, we elucidate the relevant energy terms required to understand the size-dependent uptake mechanism and verify it by correctly predicting the behavior at large and small particle sizes. In the absence of interactions between the nanoparticles we observe an asymmetric distribution of sizes with maximum uptake at intermediate sizes and a minimum size cut-off below which there can be no endocytosis. Including the effect of interactions in our model has remarkable effects on the uptake characteristics. Attractive interactions shift the minimum size cut-off and increase the optimal uptake while repulsive interactions make the distribution more symmetric lowering the optimal uptake.

cond-mat.soft↗
arXiv2010

Generic Conditions for Hydrodynamic Synchronization

Synchronization of actively oscillating organelles such as cilia and flagella facilitates self-propulsion of cells and pumping fluid in low Reynolds number environments. To understand the key mechanism behind synchronization induced by hydrodynamic interaction, we study a model of rigid-body rotors making fixed trajectories of arbitrary shape under driving forces that are arbitrary functions of the phases. For a wide class of geometries, we obtain the necessary and sufficient conditions for synchronization of a pair of rotors. We also find a novel synchronized pattern with a time-dependent phase shift. Our results shed light on the role of hydrodynamic interactions in biological systems, and could help in developing efficient mixing and transport strategies in microfluidic devices.

cond-mat.soft↗