arXiv subjects

Ramin Golestanian

Publications and source records attributed to Ramin Golestanian.

At least 145 records · Page 8Linked to original sources

arXiv2016

Multicellular self-organization of P. aeruginosa due to interactions with secreted trails

Guided movement in response to slowly diffusing polymeric trails provides a unique mechanism for self-organization of some microorganisms. To elucidate how this signaling route leads to microcolony formation, we experimentally probe the trajectory and orientation of Pseudomonas aeruginosa that propel themselves on a surface using type IV pili motility appendages, which preferentially attach to deposited exopolysaccharides. We construct a stochastic model by analyzing single-bacterium trajectories, and show that the resulting theoretical prediction for the many-body behavior of the bacteria is in quantitative agreement with our experimental characterization of how cells explore the surface via a power law strategy.

q-bio.CB↗

arXiv2016

Reply to Comment on "Enhanced diffusion of enzymes that catalyze exothermic reactions"

Catalytically active enzymes have recently been observed to exhibit enhanced diffusion. In a recent work [C. Riedel et al., Nature 517, 227 (2015)], it has been suggested that this phenomenon is correlated with the degree of exothermicity of the reaction, and a mechanism was proposed to explain the phenomenon based on channeling the released heat into the center of mass kinetic energy of the enzyme. I addressed this question by comparing four different mechanisms, and concluded that collective heating is the strongest candidate out of those four to explain the phenomenon, and in particular, several orders of magnitude stronger than the mechanism proposed by Riedel et al. In a recent preprint (arXiv:1608.05433), K. Tsekouras, C. Riedel, R. Gabizon, S. Marqusee, S. Presse, and C. Bustamante present a comment on my paper [R. Golestanian, Phys. Rev. Lett. 115, 108102 (2015); arXiv:1508.03219], which I address here in this reply.

physics.bio-ph↗

arXiv2016

Current fluctuations in nanopores: the effects of electrostatic and hydrodynamic interactions

Using nonequilibrium Langevin dynamics simulations of an electrolyte with explicit solvent particles, we investigate the effect of hydrodynamic interactions on the power spectrum of ionic nanopore currents. At low frequency, we find a power-law dependence of the power spectral density, with an exponent depending on the ion density. Surprisingly, however, the exponent is not affected by the presence of the neutral solvent particles. We conclude that hydrodynamic interactions do not affect the shape of the power spectrum in the frequency range studied.

cond-mat.soft↗

arXiv2016

Effective dynamics of microorganisms that interact with their own trail

Like ants, some microorganisms are known to leave trails on surfaces to communicate. We explore how trail-mediated self-interaction could affect the behavior of individual microorganisms when diffusive spreading of the trail is negligible on the timescale of the microorganism using a simple phenomenological model for an actively moving particle and a finite-width trail. The effective dynamics of each microorganism takes on the form of a stochastic integral equation with the trail interaction appearing in the form of short-term memory. For moderate coupling strength below an emergent critical value, the dynamics exhibits effective diffusion in both orientation and position after a phase of superdiffusive reorientation. We report experimental verification of a seemingly counterintuitive perpendicular alignment mechanism that emerges from the model.

physics.bio-ph↗

arXiv2016

Active micromachines: Microfluidics powered by mesoscale turbulence

Dense active matter, from bacterial suspensions and microtubule bundles driven by motor proteins to cellular monolayers and synthetic Janus particles, is characterised by mesoscale turbulence, the emergence of chaotic flow structures. By immersing an ordered array of symmetric rotors in an active fluid, we introduce a microfluidic system that exploits spontaneous symmetry breaking in mesoscale turbulence to generate work. The lattice of rotors self-organises into a spin-state where neighbouring discs continuously rotate in permanent alternating directions due to combined hydrodynamic and elastic effects. Our virtual prototype demonstrates a new research direction for the design of micromachines powered by the nematohydrodynamic properties of active turbulence.

cond-mat.soft↗

arXiv2015

The Power Spectrum of Ionic Nanopore Currents: The Role of Ion Correlations

We calculate the power spectrum of electric-field-driven ion transport through cylindrical nanometer-scale pores using both linearized mean-field theory and Langevin dynamics simulations. With the atom-sized cutoff radius as the only fitting parameter, the linearized mean-field theory accurately captures the dependence of the simulated power spectral density on the pore radius and the applied electric field. Remarkably, the linearized mean-field theory predicts a plateau in the power spectral density at low frequency $ω$, which is confirmed by the Langevin dynamics simulations at low ion concentration. At high ion concentration, however, the power spectral density follows a power law that is reminiscent of the $1/ω^α$ dependence found experimentally at low frequency. Based on simulations with and without ion-ion interactions, we attribute the low-frequency power law dependence to ion-ion correlations. Finally, we show that the surface charge density has no effect on the frequency dependence of the power spectrum.

physics.bio-ph↗

arXiv2015

Intrinsic Free Energy in Active Nematics

Basing our arguments on the theory of active liquid crystals, we demonstrate both analytically and numerically, that the activity can induce an effective free energy which enhances ordering in extensile systems of active rods and in contractile suspensions of active discs. We argue that this occurs because any ordering fluctuation is enhanced by the flow field it produces. A phase-diagram in the temperature-activity plane compares ordering due to a thermodynamic free energy to that resulting from the activity. We also demonstrate that activity can drive variations in concentration, but for a different physical reason that relies on the separation of hydrodynamic and diffusive timescales.

cond-mat.soft↗

arXiv2015

Enhanced Diffusion of Enzymes that Catalyze Exothermic Reactions

Enzymes have been recently found to exhibit enhanced diffusion due to their catalytic activities. A recent experiment [C. Riedel et al., Nature 517, 227 (2015)] has found evidence that suggests this phenomenon might be controlled by the degree of exothermicity of the catalytic reaction involved. Four mechanisms that can lead to this effect, namely, self-thermophoresis, boost in kinetic energy, stochastic swimming, and collective heating, are critically discussed, and it is shown that only the last two could be strong enough to account for the observations. The resulting quantitative description is used to examine the biological significance of the effect.

q-bio.BM↗

arXiv2015

Driven active and passive nematics

We investigate similarities in the micro-structural dynamics between externally driven and actively driven nematics. Walls, lines of strong deformations in the director field, and topological defects are characteristic features of an active nematic. Similar structures form in driven passive nematics when there are inhomogeneities in imposed velocity gradients due to non-linear flow fields or geometrical constraints. Specifically, pressure driven flow of a tumbling passive nematic in an expanding-contracting channel produces walls and defects similar to those seen in active nematics. We also study the response of active nematics to external driving, confirming that imposed shear suppresses the hydrodynamic instabilities. We show that shear fields can lead to wall alignments and the localisation of active turbulence.

cond-mat.soft↗

arXiv2015

Self-assembly of Active Colloidal Molecules with Dynamic Function

Catalytically active colloids maintain non-equilibrium conditions in which they produce and deplete chemicals and hence effectively act as sources and sinks of molecules. While individual colloids that are symmetrically coated do not exhibit any form of dynamical activity, the concentration fields resulting from their chemical activity decay as $1/r$ and produce gradients that attract or repel other colloids depending on their surface chemistry and ambient variables. This results in a non-equilibrium analogue of ionic systems, but with the remarkable novel feature of action-reaction symmetry breaking. We study solutions of such chemically active colloids in dilute conditions when they join up to form molecules via generalized ionic bonds, and discuss how we can achieve structures with time dependent functionality. In particular, we study a molecule that adopts a spontaneous oscillatory pattern of conformations, and another that exhibits a run-and-tumble dynamics similar to bacteria. Our study shows that catalytically active colloids could be used for designing self-assembled structures that posses dynamical functionalities that are determined by their prescribed 3D structures, a strategy that follows the design principle of proteins.

cond-mat.soft↗

arXiv2015

Collective Dynamics of Dividing Chemotactic Cells

The large scale behaviour of a population of cells that grow and interact through the concentration field of the chemicals they secrete is studied using dynamical renormalization group methods. The combination of the effective long-range chemotactic interaction and lack of number conservation leads to a rich variety of phase behaviour in the system, which includes a sharp transition from a phase that has moderate (or controlled) growth and regulated chemical interactions to a phase with strong (or uncontrolled) growth and no chemical interactions. The transition point has nontrivial critical exponents. Our results might help shed light on the interplay between chemical signalling and growth in tissues and colonies, and in particular on the challenging problem of cancer metastasis.

q-bio.CB↗

arXiv2014

A steering mechanism for phototaxis in Chlamydomonas

Chlamydomonas shows both positive and negative phototaxis. It has a single eyespot near its equator and as the cell rotates during forward motion the light signal received by the eyespot varies. We use a simple mechanical model of Chlamydomonas that couples the flagellar beat pattern to the light intensity at the eyespot to demonstrate a mechanism for phototactic steering that is consistent with observations. The direction of phototaxis is controlled by a parameter in our model and the steering mechanism is robust to noise. Our model shows switching between directed phototaxis when the light is on and run-and-tumble behaviour in the dark.

physics.bio-ph↗

arXiv2014

Active nematic materials with substrate friction

Active turbulence in dense active systems is characterized by high vorticity on a length scale that is large compared to that of individual entities. We describe the properties of active turbulence as momentum propagation is screened by frictional damping. As friction is increased, the spacing between the walls in the nematic director field decreases as a consequence of the more rapid velocity decays. This leads to, first, a regime with more walls and an increased number of topological defects, and then to a jammed state in which the walls deliminate bands of opposing flow, analogous to the shear bands observed in passive complex fluids.

cond-mat.soft↗

arXiv2014

Hydrodynamic suppression of phase separation in active suspensions

We simulate with hydrodynamics a suspension of active disks squirming through a Newtonian fluid. We explore numerically the full range of squirmer area fractions from dilute to close packed and show that "motility induced phase separation" (MIPS), which was recently proposed to arise generically in active matter, and which has been seen in simulations of active Brownian disks, is strongly suppressed by hydrodynamic interactions. We give an argument for why this should be the case and support it with counterpart simulations of active Brownian disks in a parameter regime that provides a closer counterpart to hydrodynamic suspensions than in previous studies.

cond-mat.soft↗

arXiv2014

Mechanosensitive Channel Activation by Diffusio-Osmotic Force

For ion channel gating, the appearance of two distinct conformational states and the discrete transitions between them is essential, and therefore of crucial importance to all living organisms. We show that the physical interplay between two structural elements that are commonly present in bacterial mechanosensitive channels, namely a charged vestibule and a hydrophobic constriction, creates two distinct conformational states, open and closed, as well as the gating between them. We solve the nonequilibrium Stokes-Poisson-Nernst-Planck equations, extended to include a molecular potential of mean force, and show that a first order transition between the closed and open states arises naturally from the diffusio-osmotic stress caused by the ions and water inside the channel and the elastic restoring force from the membrane. Our proposed gating mechanism is likely to be important for a broad range of ion channels, as well as for biomimetic channels and ion channel-targeting therapeutics.

cond-mat.soft↗

arXiv2014

Vorticity, Defects and Correlations in Active Turbulence

We describe a numerical investigation of a continuum model of an active nematic, concentrating on the regime of active turbulence. Results are presented for the effect of three parameters, activity, elastic constant and rotational diffusion constant, on the order parameter and flow fields. Defects and distortions in the director field act as sources of vorticity, and thus vorticity is strongly correlated to the director field. In particular the characteristic length of decay of vorticity and order parameter correlations is controlled by the defect density. By contrast the decay of velocity correlations is determined by a balance between activity and dissipation. We highlight the role of microscopic flow generation mechanisms in determining the flow patterns and characteristic scales of active turbulence and contrast the behaviour of extensile and contractile active nematics.

cond-mat.soft↗

arXiv2014

Clusters, asters and collective oscillations in chemotactic colloids

The creation of synthetic systems that emulate the defining properties of living matter, such as motility, gradient-sensing, signalling and replication, is a grand challenge of biomimetics. Such imitations of life crucially contain active components that transform chemical energy into directed motion. These artificial realizations of motility point in the direction of a new paradigm in en- gineering, through the design of emergent behavior by manipulating properties at the scale of the individual components. Catalytic colloidal swimmers are a particularly promising example of such systems. Here we present a comprehensive theoretical description of gradient-sensing of an individual swimmer, leading controllably to chemotactic or anti-chemotactic behavior, and use it to construct a framework for studying their collective behavior. We find that both the positional and the orientational degrees of freedom of the active colloids can exhibit condensation, signalling formation of clusters and asters. The kinetics of catalysis introduces a natural control parameter for the range of the interaction mediated by the diffusing chemical species. For various regimes in parameter space in the long-ranged limit our system displays precise analogs to gravitational collapse, plasma oscillations and electrostatic screening. We present prescriptions for how to tune the surface properties of the colloids during fabrication to achieve each type of behavior.

cond-mat.soft↗

arXiv2014

Self-assembly of catalytically active colloidal molecules: Tailoring activity through surface chemistry

A heterogeneous and dilute suspension of catalytically active colloids is studied as a non-equilibrium analogue of ionic systems, which has the remarkable feature of action-reaction symmetry breaking. Symmetrically coated colloids are found to join up to form self-assembled molecules that could be inert or have spontaneous activity in the form of net translational velocity and spin depending on their symmetry properties and their constituents. The type of activity can be adjusted by changing the surface chemistry and ambient variables that control the surface reactions and the phoretic drift.

cond-mat.soft↗