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Pietro Cicuta

Publications and source records attributed to Pietro Cicuta.

At least 37 records · Page 2Linked to original sources

Self-assembly of repulsive interfacial particles via collective sinking

Charged colloidal particles trapped at an air--water interface are well known to form an ordered crystal, stabilized by a long ranged repulsion, the details of this repulsion remain something of a mystery, but all experiments performed to date have confirmed a dipolar-repulsion, at least at dilute concentrations. More complex arrangements are often observed, especially at higher concentration, and these seem to be incompatible with a purely repulsive potential. In addition to electrostatic repulsion, interfacial particles may also interact via deformation of the surface: so-called capillary effects. Pair-wise capillary interactions are well understood, and are known to be too small (for these colloidal particles) to overcome thermal effects. Here we show that collective effects may significantly modify the simple pair-wise interactions and become important at higher density, though we remain well below close packing throughout. In particular, we show that the interaction of many interfacial particles can cause much larger interfacial deformations than do isolated particles, and show that the energy of interaction per particle due to this "collective sinking" grows as the number of interacting particles grows. Though some of the parameters in our simple model are unknown, the scaling behaviour is entirely consistent with experimental data, strongly indicating that estimating interaction energy based solely on pair-wise potentials may be too simplistic for surface particle layers.

cond-mat.soft↗

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↗

Individuality and universality in the growth-division laws of single E. coli cells

The mean size of exponentially dividing E. coli cells cultured in different nutrient conditions is known to depend on the mean growth rate only. However, the joint fluctuations relating cell size, doubling time and individual growth rate are only starting to be characterized. Recent studies in bacteria (i) revealed the near constancy of the size extension in a single cell cycle (adder mechanism), and (ii) reported a universal trend where the spread in both size and doubling times is a linear function of the population means of these variables. Here, we combine experiments and theory and use scaling concepts to elucidate the constraints posed by the second observation on the division control mechanism and on the joint fluctuations of sizes and doubling times. We found that scaling relations based on the means both collapse size and doubling-time distributions across different conditions, and explain how the shape of their joint fluctuations deviates from the means. Our data on these joint fluctuations highlight the importance of cell individuality: single cells do not follow the dependence observed for the means between size and either growth rate or inverse doubling time. Our calculations show that these results emerge from a broad class of division control mechanisms (including the adder mechanism as a particular case) requiring a certain scaling form of the so-called "division hazard rate function", which defines the probability rate of dividing as a function of measurable parameters. This gives a rationale for the universal body-size distributions observed in microbial ecosystems across many microbial species, presumably dividing with multiple mechanisms. Additionally, our experiments show a crossover between fast and slow growth in the relation between individual-cell growth rate and division time, which can be understood in terms of different regimes of genome replication control.

q-bio.CB↗

The Role of Optical Projection in the Analysis of Membrane Fluctuations

We propose a methodology to measure the mechanical properties of membranes from their fluctuations and apply this to optical microscopy measurements of giant unilamellar vesicles of lipids. We analyze the effect of the projection of thermal shape undulations across the focal depth of the microscope. We derive an analytical expression for the mode spectrum that varies with the focal depth and accounts for the projection of fluctuations onto the equatorial plane. A comparison of our model with existing approaches, that use only the apparent equatorial fluctuations without averaging out of this plane, reveals a significant and systematic reduction in the inferred value of the bending rigidity. Our results are in full agreement with the values measured through X-ray scattering and other micromechanical manipulation techniques, resolving a long standing discrepancy with these other experimental methods.

cond-mat.soft↗

Realizing the physics of motile cilia synchronization with driven colloids

Cilia and flagella in biological systems often show large scale cooperative behaviors such as the synchronization of their beats in "metachronal waves". These are beautiful examples of emergent dynamics in biology, and are essential for life, allowing diverse processes from the motility of eukaryotic microorganisms, to nutrient transport and clearance of pathogens from mammalian airways. How these collective states arise is not fully understood, but it is clear that individual cilia interact mechanically,and that a strong and long ranged component of the coupling is mediated by the viscous fluid. We review here the work by ourselves and others aimed at understanding the behavior of hydrodynamically coupled systems, and particularly a set of results that have been obtained both experimentally and theoretically by studying actively driven colloidal systems. In these controlled scenarios, it is possible to selectively test aspects of the living motile cilia, such as the geometrical arrangement, the effects of the driving profile and the distance to no-slip boundaries. We outline and give examples of how it is possible to link model systems to observations on living systems, which can be made on microorganisms, on cell cultures or on tissue sections. This area of research has clear clinical application in the long term, as severe pathologies are associated with compromised cilia function in humans.

cond-mat.soft↗

Microscopic Origin of the Hofmeister Effect in Gelation Kinetics of Colloidal Silica

The gelation kinetics of silica nanoparticles is a central process in physical chemistry, yet it is not fully understood. Gelation times are measured to increase by over 4 orders of magnitude, simply changing the monovalent salt species from CsCl to LiCl. This striking effect has no microscopic explanation within current paradigms. The trend is consistent with the Hofmeister series, pointing to short-ranged solvation effects not included in the standard colloidal (DLVO) interaction potential. By implementing a simple form for short-range repulsion within a model that relates the gelation timescale to the colloidal interaction forces, we are able to explain the many orders of magnitude difference in the gelation times at fixed salt concentration. The model allows us to estimate the magnitude of the non-DLVO hydration forces, which dominate the interparticle interactions on the length scale of the hydrated ion diameter. This opens the possibility of finely tuning the gelation time scale of nanoparticles by just adjusting the background electrolyte species

cond-mat.soft↗

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↗

Correlation between crystalline order and vitrification in colloidal monolayers

We investigate experimentally the relationship between local structure and dynamical arrest in a quasi-2d colloidal model system which approximates hard discs. We introduce polydispersity to the system to suppress crystallisation. Upon compression, the increase in structural relaxation time is accompanied by the emergence of local hexagonal symmetry. Examining the dynamical heterogeneity of the system, we identify three types of motion : "zero-dimensional" corresponding to beta-relaxation, "one-dimensional" or stringlike motion and "two-dimensional" motion. The dynamic heterogeneity is correlated with the local order, that is to say locally hexagonal regions are more likely to be dynamically slow. However we find that lengthscales corresponding to dynamic heterogeneity and local structure do not appear to scale together approaching the glass transition.

cond-mat.soft↗

The role of mechanical forces in the planar-to-bulk transition in growing Escherichia coli microcolonies

Mechanical forces are obviously important in the assembly of three-dimensional multicellular structures, but their detailed role is often unclear. We have used growing microcolonies of the bacterium \emph{Escherichia coli} to investigate the role of mechanical forces in the transition from two-dimensional growth (on the interface between a hard surface and a soft agarose pad) to three-dimensional growth (invasion of the agarose). We measure the position within the colony where the invasion transition happens, the cell density within the colony, and the colony size at the transition as functions of the concentration of the agarose. We use a phenomenological theory, combined with individual-based computer simulations, to show how mechanical forces acting between the bacterial cells, and between the bacteria and the surrounding matrix, lead to the complex phenomena observed in our experiments - in particular a non-trivial dependence of the colony size at the transition on the agarose concentration. Matching these approaches leads to a prediction for how the friction coefficient between the bacteria and the agarose should vary with agarose concentration. Our experimental conditions mimic numerous clinical and environmental scenarios in which bacteria invade soft matrices, as well as shedding more general light on the transition between two- and three-dimensional growth in multicellular assemblies.

q-bio.CB↗

Elastometry of Deflated Capsules: Elastic Moduli from Shape and Wrinkle Analysis

Elastic capsules, prepared from droplets or bubbles attached to a capillary (as in a pendant drop tensiometer), can be deflated by suction through the capillary. We study this deflation and show that a combined analysis of the shape and wrinkling characteristics enables us to determine the elastic properties in situ. Shape contours are analyzed and fitted using shape equations derived from nonlinear membrane-shell theory to give the elastic modulus, Poisson ratio and stress distribution of the membrane. We include wrinkles, which generically form upon deflation, within the shape analysis. Measuring the wavelength of wrinkles and using the calculated stress distribution gives the bending stiffness of the membrane. We compare this method with previous approaches using the Laplace-Young equation and illustrate the method on two very different capsule materials: polymerized octadecyltrichlorosilane (OTS) capsules and hydrophobin (HFBII) coated bubbles. Our results are in agreement with the available rheological data. For hydrophobin coated bubbles the method reveals an interesting nonlinear behavior consistent with the hydrophobin molecules having a rigid core surrounded by a softer shell.

cond-mat.soft↗

Physical descriptions of the bacterial nucleoid at large scales, and their biological implications

Recent experimental and theoretical approaches have attempted to quantify the physical organization (compaction and geometry) of the bacterial chromosome with its complement of proteins (the nucleoid). The genomic DNA exists in a complex and dynamic protein-rich state, which is highly organised at various length scales. This has implications on modulating (when not enabling) the core biological processes of replication, transcription, segregation. We overview the progress in this area, driven in the last few years by new scientific ideas and new interdisciplinary experimental techniques, ranging from high space- and time-resolution microscopy to high-throughput genomics employing sequencing to map different aspects of the nucleoid-related interactome. The aim of this review is to present the wide spectrum of experimental and theoretical findings coherently, from a physics viewpoint. We also discuss some attempts of interpretation that unify different results, highlighting the role that statistical and soft condensed matter physics, and in particular classic and more modern tools from the theory of polymers, plays in describing this system of fundamental biological importance, and pointing to possible directions for future investigation.

physics.bio-ph↗

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↗

Patterns of synchronization in the hydrodynamic coupling of active colloids

A system of active colloidal particles driven by harmonic potentials to oscillate about the vertices of a regular polygon, with hydrodynamic coupling between all particles, is described by a piece-wise linear model which exhibits various patterns of synchronization. Analytical solutions are obtained for this class of dynamical systems. Depending only on the number of particles, the synchronization occurs into states in which nearest neighbors oscillate either in-phase, or anti-phase, or in phase-locked (time-shifted) trajectories.

cond-mat.stat-mech↗

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↗

Granular Character of Particle Rafts

We consider a monolayer of particles floating at a horizontal liquid-gas interface -- a particle raft. Upon compressing the monolayer in a Langmuir trough, the particles at first pack but ultimately the monolayer buckles out of the plane. We measure the stress profile within the raft at the onset of buckling and show for the first time that such systems exhibit a Janssen effect: the stress decays exponentially away from the compressing barriers over a length scale that depends on the width of the trough. We find quantitative agreement between the rate of decay and the simple theory presented by Janssen and others. This demonstrates that floating particle rafts have a granular, as well as elastic, character, which is neglected by current models. Finally, we suggest that our experimental setup may be suitable for exploring granular effects in two dimensions without the complications of gravity and basal friction.

cond-mat.soft↗

Line tensions, correlation lengths, and critical exponents in lipid membranes near critical points

Membranes containing a wide variety of ternary mixtures of high chain-melting temperature lipids, low chain-melting temperature lipids, and cholesterol undergo lateral phase separartion into coexisting liquid phases at a miscibility transition. When membranes are prepared from a ternary lipid mixture at a critical composition, they pass through a miscibility critical point at the transition temperature. Since the critical temperature is typically on the order of room temperature, membranes provide an unusual opportunity in which to perform a quantitative study of biophysical systems that exhibit critical phenomena in the two-dimensional Ising universality class. As a critical point is approached from either high or low temperature, the scale of fluctuations in lipid composition, set by the correlation length, diverges. In addition, as a critical point is approached from low temperature, the line tension between coexisting phases decreases to zero. Here we quantitatively evaluate the temperature dependence of line tension between liquid domains and of fluctuation correlation lengths in lipid membranes in order to extract a critical exponent, nu. We obtain nu=1.2 plus or minus 0.2, consistent with the Ising model prediction nu=1. We also evaluate the probability distributions of pixel intensities in fluoresence images of membranes. From the temperature dependence of these distributions above the critical temperature, we extract an independent critical exponent beta=0.124 plus or minus 0.03 which is consistent with the Ising prediction of beta=1/8.

cond-mat.soft↗

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↗

Diffusion of liquid domains in lipid bilayer membranes

We report diffusion coeffcients of micron-scale liquid domains in giant unilamellar vesicles of phospholipids and cholesterol. The trajectory of each domain is tracked, and the mean square displacement grows linearly in time as expected for Brownian motion. We study domain dffusion as a function of composition and temperature, and measure how diffusion depends on domain size. We find mechanisms of domain diffusion which are consistent with membrane-dominated drag in viscous Lo phases [P.G. Saffman and M. Delbruck, PNAS 72, 3111 (1975)], and bulk-dominated drag for less viscous L$_α$ phases [B.D.Hughes et al., J. Fluid Mech. 110, 349 (1981)]. Where applicable, we obtain the membrane viscosity and report activation energies of diffusion.

cond-mat.soft↗