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Jurij Kotar

Publications and source records attributed to Jurij Kotar.

14 recordsLinked to original sources
arXiv2023

Using Old Laboratory Equipment with Modern Web-of-Things Standards: a Smart Laboratory with LabThings Retro

There has been an increasing, and welcome, Open Hardware trend towards science teams building and sharing their designs for new instruments. These devices, often built upon low-cost microprocessors and micro-controllers, can be readily connected to enable complex, automated, and smart experiments. When designed to use open communication web standards, devices from different laboratories and manufacturers can be controlled using a single protocol, and even communicate with each other. However, science labs still have a majority of old, perfectly functional, equipment which tends to use older, and sometimes proprietary, standards for communications. In order to encourage the continued and integrated use of this equipment in modern automated experiments, we develop and demonstrate LabThings Retro. This allows us to retrofit old instruments to use modern web-of-things standards, which we demonstrate with closed-loop feedback involving an optical microscope, digital imaging and fluid pumping.

physics.ins-det↗
arXiv2020

Direct Measurement of Unsteady Microscale Stokes Flow Using Optically Driven Microspheres

A growing body of work on the dynamics of eukaryotic flagella has noted that their oscillation frequencies are sufficiently high that the viscous penetration depth of unsteady Stokes flow is comparable to the scales over which flagella synchronize. Incorporating these effects into theories of synchronization requires an understanding of the global unsteady flows around oscillating bodies. Yet, there has been no precise experimental test on the microscale of the most basic aspects of such unsteady Stokes flow: the orbits of passive tracers and the position-dependent phase lag between the oscillating response of the fluid at a distant point and that of the driving particle. Here, we report the first such direct Lagrangian measurement of this unsteady flow. The method uses an array of $30$ submicron tracer particles positioned by a time-shared optical trap at a range of distances and angular positions with respect to a larger, central particle, which is then driven by an oscillating optical trap at frequencies up to $400$ Hz. In this microscale regime, the tracer dynamics is considerably simplified by the smallness of both inertial effects on particle motion and finite-frequency corrections to the Stokes drag law. The tracers are found to display elliptical Lissajous figures whose orientation and geometry are in agreement with a low-frequency expansion of the underlying dynamics, and the experimental phase shift between motion parallel and orthogonal to the oscillation axis exhibits a predicted scaling form in distance and angle. Possible implications of these results for synchronization dynamics are discussed.

cond-mat.soft↗
arXiv2019

Two Microspheres in an External Flow: a Dance of Cause and Effect

In low Reynolds number swimming and pumping, differently to everyday experience, a net motion (or flow) can be achieved only if the constructing parts of the swimmer (or pump) follow a non-trivial pattern of motion, in order to break time reciprocity. The case of a driven fan, which spins to create a flow of air, but conversely rotates when turned off and subjected to a strong external flow, is a familiar example of reciprocal connection between physical cause and effect. We explore here in a well controlled low Reynolds number system whether such an exchange of the cause and effect also holds in the low Reynolds number regime. As a case study we investigate the motion of two microspheres which interact hydrodynamically through their surrounding fluid. Each sphere is constrained in a fixed optical trap potential, allowing local fluctuations around an equilibrium position. An external flow is shown to induce non-trivial coupled motion. We find a signature of reciprocity: the nonequilibrium sphere fluctuations mimic the symmetry of the motions that one would impose in order for them to produce a constant flow.

cond-mat.soft↗
arXiv2017

Optical trapping of colloids at a liquid-liquid interface

We demonstrate the realization of (laterally) optically bounded colloidal structures on a liquid-liquid interface of an emulsion droplet. We use DNA tethers to graft the particles to the droplet surface, effectively confining them to a quasi-2D plane with minimum constraints on the lateral movement even when optically trapped in a common single-beam configuration. We show that relatively weak interactions such as depletion can be measured in the optically bounded crystals by video-microscopy imaging and analysis. This illustrates the possible use of our system as template to study optically controlled quasi two-dimensional colloidal assembly on liquid-liquid interfaces.

cond-mat.soft↗
arXiv2016

Long-range interactions and phase defects in chains of fluid-coupled oscillators

Eukaryotic cilia and flagella are chemo-mechanical oscillators capable of generating long-range coordinated motions known as metachronal waves. Pair synchronization is a fundamental requirement for these collective dynamics, but it is generally not sufficient for collective phase-locking, chiefly due to the effect of long-range interactions. Here we explore experimentally and numerically a minimal model for a ciliated surface; hydrodynamically coupled oscillators rotating above a no-slip plane. Increasing their distance from the wall profoundly effects the global dynamics, due to variations in hydrodynamic interaction range. The array undergoes a transition from a traveling wave to either a steady chevron pattern or one punctuated by periodic phase defects. Within the transition between these regimes the system displays behavior reminiscent of chimera states.

physics.bio-ph↗
arXiv2015

Volume and porosity thermal regulation in lipid mesophases by coupling mobile ligands to soft membranes

Short DNA linkers are increasingly being exploited for driving specific self-assembly of Brownian objects. DNA-functionalised colloids can assemble into ordered or amorphous materials with tailored morphology. Recently, the same approach has been applied to compliant units, including emulsion droplets and lipid vesicles. The liquid structure of these substrates introduces new degrees of freedom: the tethers can diffuse and rearrange, radically changing the physics of the interactions. Unlike droplets, vesicles are extremely deformable and DNA-mediated adhesion causes significant shape adjustments. We investigate experimentally the thermal response of pairs and networks of DNA-tethered liposomes and observe two intriguing and possibly useful collective properties: negative thermal expansion and tuneable porosity of the liposome networks. A model providing a thorough understanding of this unexpected phenomenon is developed, explaining the emergent properties out of the interplay between the temperature-dependent deformability of the vesicles and the DNA-mediated adhesive forces.

cond-mat.soft↗
arXiv2013

Multistep kinetic self-assembly of DNA-coated colloids

Self-assembly is traditionally described as the process through which an initially disordered system relaxes towards an equilibrium ordered phase only driven by local interactions between its building blocks. However, This definition is too restrictive. Nature itself provides examples of amorphous, yet functional, materials assembled upon kinetically arresting the pathway towards the ground state. Kinetic self-assembly is intrinsically more flexible and reliable than its equilibrium counterpart, allowing control over the morphology of the final phase by tuning both the interactions and the thermodynamic pathway leading to kinetic arrest. Here we propose strategies to direct the gelation of two-component colloidal mixtures by sequentially activating selective interspecies and intra-species interactions. We investigate morphological changes in the structure of the arrested phases by means of event driven molecular dynamics (MD) simulations and experimentally using DNA-coated colloids (DNACCs). Our approach can be exploited to finely tune the morphology of multicomponent nano- or micro-porous materials with possible applications in hybrid photovoltaics, photonics and drug delivery.

cond-mat.soft↗
arXiv2011

Hydrodynamically synchronized states in active colloidal arrays

Colloidal particles moving in a fluid interact via the induced velocity field. The collective dynamic state for a class of actively forced colloids, driven by harmonic potentials via a rule that couples forces to configurations, to perform small oscillations around an average position, is shown by experiment, simulation and theoretical arguments to be determined by the eigenmode structure of the coupling matrix. It is remarkable that the dynamical state can therefore be predicted from the mean spatial configuration of the active colloids, or from an analysis of the fluctuations near equilibrium. This has the surprising consequence that while 2 particles, or polygonal arrays of 4 or more colloids, synchronize with the nearest neighbors in anti-phase, a system of 3 equally spaced colloids synchronizes in-phase. In the absence of thermal fluctuations, the stable dynamical state is predominantly formed by the eigenmode with longest relaxation time.

cond-mat.soft↗
arXiv2011

Interactions between colloids induced by a soft cross-linked polymer substrate

Using video-microscopy imaging we demonstrate the existence of a short-ranged equilibrium attraction between heavy silica colloids diffusing on soft surfaces of cross-linked polymer gels. The inter-colloid potential can be tuned by changing the gel stiffness or by coating the colloids with a polymer layer. On sufficiently soft substrates, the interaction induced by the polymer matrix leads to large-scale colloidal aggregation. We correlate the in-plane interaction with a colloid-surface attraction.

cond-mat.soft↗
arXiv2010

Real-time monitoring of complex moduli from micro-rheology

We describe an approach to online analysis of micro-rheology data using a multi-scale time-correlation method. The method is particularly suited to process high-volume data streams and compress the relevant information in real time. Using this, we can obtain complex moduli of visco-elastic media without suffering from the high-frequency artefacts that are associated with the truncation errors in the most widely used versions of micro-rheology. Moreover, the present approach obviates the need to choose the time interval for data acquisition beforehand. We test our approach first on an artificial data set and then on experimental data obtained both for an optically trapped colloidal probe in water and a similar probe in poly-ethylene glycol solutions at various concentrations. In all cases, we obtain good agreement with the bulk rheology data in the region of overlap. We compare our method with the conventional Kramers-Kronig transform approach and find that the two methods agree over most of the frequency regime. For the same data set, the present approach is superior to Kramers-Kronig at high frequencies and can be made to perform at least comparable at low frequencies.

cond-mat.soft↗
arXiv2010

Minimal two-sphere model of the generation of fluid flow at low Reynolds numbers

Locomotion and generation of flow at low Reynolds number are subject to severe limitations due to the irrelevance of inertia: the "scallop theorem" requires that the system have at least two degrees of freedom, which move in non-reciprocal fashion, i.e. breaking time-reversal symmetry. We show here that a minimal model consisting of just two spheres driven by harmonic potentials is capable of generating flow. In this pump system the two degrees of freedom are the mean and relative positions of the two spheres. We have performed and compared analytical predictions, numerical simulation and experiments, showing that a time-reversible drive is sufficient to induce flow.

cond-mat.soft↗
arXiv2007

Non-linear mechanical response of the Red Blood Cell

We measure the dynamical mechanical properties of human red blood cells. Single cell response is measured with optical tweezers. We investigate both the stress relaxation following a fast deformation, and the effect of varying the strain rate. We find a power law decay of the stress as a function of time, down to a plateau stress, and a power law increase of the cell's elasticity as a function of the strain rate. Interestingly, the exponents of these quantities violate the linear superposition principle, indicating a nonlinear response. We propose that this is due to breaking of a fraction of the crosslinks during the deformation process. The Soft Glassy Rheology Model accounts for the relation between the exponents we observe experimentally. This picture is consistent with recent models of bond remodeling in the red blood cell's molecular structure. Our results imply that the blood cell's mechanical behavior depends critically on the deformation process.

cond-mat.soft↗
arXiv2003

CCD based phase resolved stroboscopic photometry of pulsars

A stroboscope designed to observe pulsars in the optical spectrum is presented. The absolute phase of the stroboscope is synchronized to better than 2.5 microseconds with the known radio ephemerides for a given pulsar. The absolute timing is provided by the GPS clock. With such a device phase resolved photometry of pulsars can be performed. We demonstrate the instrument's capabilities with the results of a set of observations of the Crab pulsar, the brightest of the known optical pulsars, with a visual magnitude of 16.5, and a rotational frequency of ~29Hz.

astro-ph↗