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Optical diffraction tomography (ODT) is a label-free technique for three dimensional imaging of micron-sized objects. Coherence and limited sampling of 3D Fourier space are often responsible for the appearance of artifacts. Here we present an ODT microscope that uses low temporal coherence light and spatial light modulators to retrieve reliable 3D maps of the refractive index. A common-path interferometer, based on a spatial light modulator, measures the complex fields transmitted by a sample. Measured fields, acquired while scanning the illumination direction using a digital micro-mirror device, are fed into a Rytov reconstruction algorithm to obtain refractive index maps whose accuracy is directly evaluated on microfabricated 3D test objects. Even for challenging shapes such as pyramids, bridges, and dumbbells, we obtain volumetric reconstructions that compare very well with electron microscopy images.

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We demonstrate that Digital Holographic Microscopy can be used for accurate 3D tracking and sizing of a colloidal probe trapped in a diamond anvil cell (DAC). Polystyrene beads were optically trapped in water up to Gigapascal pressures while simultaneously recording in-line holograms at 1 KHz frame rate. Using Lorenz-Mie scattering theory to fit interference patterns, we detected a 10% shrinking in the bead's radius due to the high applied pressure. Accurate bead sizing is crucial for obtaining reliable viscosity measurements and provides a convenient optical tool for the determination of the bulk modulus of probe material. Our technique may provide a new method for pressure measurements inside a DAC.

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We numerically study the dynamics of run-and-tumble particles confined in two chambers connected by thin channels. Two dominant dynamical behaviors emerge: (i) an oscillatory pumping state, in which particles periodically fill the two vessels, and (ii) a circulating flow state, dynamically maintaining a near constant population level in the containers when connected by two channels. We demonstrate that the oscillatory behavior arises from the combination of a narrow channel, preventing bacteria reorientation, and a density-dependent motility inside the chambers.

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Swimming bacteria display a remarkable tendency to move along flat surfaces for prolonged times. This behavior may have a biological importance but can also be exploited by using microfabricated structures to manipulate bacteria. The main physical mechanism behind the surface entrapment of swimming bacteria is, however, still an open question. By studying the swimming motion of Escherichia coli cells near microfabricated pillars of variable size, we show that cell entrapment is also present for convex walls of sufficiently low curvature. Entrapment is, however, markedly reduced below a characteristic radius. Using a simple hydrodynamic model, we predict that trapped cells swim at a finite angle with the wall and a precise relation exists between the swimming angle at a flat wall and the critical radius of curvature for entrapment. Both predictions are quantitatively verified by experimental data. Our results demonstrate that the main mechanism for wall entrapment is hydrodynamic in nature and show the possibility of inhibiting cell adhesion, and thus biofilm formation, using convex features of appropriate curvature.

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E. coli bacteria swim following a run and tumble pattern. In the run state all flagella join in a single helical bundle that propels the cell body along approximately straight paths. When one or more flagellar motors reverse direction the bundle unwinds and the cell randomizes its orientation. This basic picture represents an idealization of a much more complex dynamical problem. Although it has been shown that bundle formation can occur at either pole of the cell, it is still unclear whether these two run states correspond to asymmetric propulsion features. Using holographic microscopy we record the 3D motions of individual bacteria swimming in optical traps. We find that most cells possess two run states characterized by different propulsion forces, total torque, and bundle conformations. We analyze the statistical properties of bundle reversal and compare the hydrodynamic features of forward and backward running states. Our method is naturally multi-particle and opens up the way towards controlled hydrodynamic studies of interacting swimming cells.

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An assessment of trace element and polycyclic aromatic hydrocarbon (PAH) contamination based on surface sediments collected in summer 2012 was carried out in Priolo Bay adjoining one of the most polluted areas of the Mediterranean Sea, the industrial Augusta harbour (Italy, Central Mediterranean). Inorganic and organic contaminants were generally not remarkable. Occasional elevated concentrations of Hg, Cd, Ni and PAHs exceeding sediment quality guidelines were detected in the northern sector of Priolo Bay, close to Augusta harbour, possibly as a result of water drainage of industrialised and urbanised areas and/or potential direct export of contaminated material from Augusta harbour, whose influence on the adjoining Priolo Bay ecosystem cannot be ruled out. By domino effect, Priolo sediments may therefore become a potential source of pollutants and may represent a threat to the biota.

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The random energy landscapes developed by speckle fields can be used to confine and manipulate a large number of micro-particles with a single laser beam. By means of molecular dynamics simulations, we investigate the static and dynamic properties of an active suspension of swimming bacteria embedded into speckle patterns. Looking at the correlation of the density fluctuations and the equilibrium density profiles, we observe a crossover phenomenon when the forces exerted by the speckles are equal to the bacteria's propulsion.

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We theoretically and numerically investigate the transport of active colloids to target regions, delimited by asymmetric energy barriers. We show that it is possible to introduce a generalized effective temperature that is related to the local variance of particle velocities. The stationary probability distributions can be derived from a simple diffusion equation in the presence of an inhomogeneous effective temperature resulting from the action of external force fields. In particular, transition rates over asymmetric energy barriers can be unbalanced by having different effective temperatures over the two slopes of the barrier. By varying the type of active noise, we find that equal values of diffusivity and persistence time may produce strongly varied effective temperatures and thus stationary distributions.

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We solve the problem of first-passage time for run-and-tumble particles in one dimension. Exact expression is derived for the mean first-passage time in the general case, considering external force fields and chemotactic fields, giving rise to space-dependent swim speed and tumble rate. Agreement between theoretical formulae and numerical simulations is obtained in the analyzed case studies --constant and sinusoidal force fields, constant gradient chemotactic field. Reported findings can be useful to get insights into very different phenomena involving active particles, such as bacterial motion in external fields, intracellular transport, cell migration, animal foraging.

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Digital Holographic Microscopy allows to numerically retrieve three dimensional information encoded in a single 2D snapshot of the coherent superposition of a reference and a scattered beam. Since no mechanical scans are involved, holographic techniques have a superior performance in terms of achievable frame rates. Unfortunately, numerical reconstructions of scattered field by back-propagation leads to a poor axial resolution. Here we show that overlapping the three numerical reconstructions obtained by tilted red, green and blue beams results in a great improvement over the axial resolution and sectioning capabilities of holographic microscopy. A strong reduction in the coherent background noise is also observed when combining the volumetric reconstructions of the light fields at the three different wavelengths. We discuss the performance of our technique with two test objects: an array of four glass beads that are stacked along the optical axis and a freely diffusing rod shaped E.coli bacterium.

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The use of individual multimode optical fibers in endoscopy applications has the potential to provide highly miniaturized and noninvasive probes for microscopy and optical micromanipulation. A few different strategies have been proposed recently, but they all suffer from intrinsically low resolution related to the low numerical aperture of multimode fibers. Here, we show that two-photon polymerization allows for direct fabrication of micro-optics components on the fiber end, resulting in an increase of the numerical aperture to a value that is close to 1. Coupling light into the fiber through a spatial light modulator, we were able to optically scan a submicrometer spot (300 nm FWHM) over an extended region, facing the opposite fiber end. Fluorescence imaging with improved resolution is also demonstrated.

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The possibility of exploiting motile microorganisms as tiny propellers represents a fascinating strategy for the transport of colloidal cargoes. However, delivery on target sites usually requires external control fields to steer propellers and trigger cargo release. The need for a constant feedback mechanism prevents the design of compact devices where biopropellers could perform their tasks autonomously. Here we show that properly designed three-dimensional (3D) microstructures can define accumulation areas where bacteria spontaneously and efficiently store colloidal beads. The process is stochastic in nature and results from the rectifying action of an asymmetric energy landscape over the fluctuating forces arising from collisions with swimming bacteria. As a result, the concentration of colloids over target areas can be strongly increased or depleted according to the topography of the underlying structures. Besides the significance to technological applications, our experiments pose some important questions regarding the structure of stationary probability distributions in non-equilibrium systems.

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E. coli bacteria swim in straight runs interrupted by sudden reorientation events called tumbles. The resulting random walks give rise to density fluctuations that can be derived analytically in the limit of non-interacting particles or equivalently of very low concentrations. However, in situations of practical interest, the concentration of bacteria is always large enough to make interactions an important factor. Using molecular dynamics simulations, we study the dynamic structure factor of a model bacterial bath for increasing values of densities. We show that it is possible to reproduce the dynamics of density fluctuations in the system using a free run-and-tumble model with effective fitting parameters. We discuss the dependence of these parameters, e.g., the tumbling rate, tumbling time and self-propulsion velocity, on the density of the bath.

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Hydrodynamic synchronization provides a general mechanism for the spontaneous emergence of coherent beating states in independently driven mesoscopic oscillators. A complete physical picture of those phenomena is of definite importance to the understanding of biological cooperative motions of cilia and flagella. Moreover, it can potentially suggest novel routes to exploit synchronization in technological applications of soft matter. We demonstrate that driving colloidal particles in rotating energy landscapes results in a strong tendency towards synchronization, favoring states where all beads rotate in phase. The resulting dynamics can be described in terms of activated jumps with transition rates that are strongly affected by hydrodynamics leading to an increased probability and lifetime of the synchronous states. Using holographic optical tweezers we quantitatively verify our predictions in a variety of spatial configurations of rotors.

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In this paper, we exploit an analogy of the run-and-tumble process for bacterial motility with the Lorentz model of electron conduction in order to obtain analytical results for the intermediate scattering function. This allows to obtain an analytical result for the van Hove function in real space for two-dimensional systems. We furthermore consider the 2D circling motion of bacteria close to solid boundaries with tumbling, and show that the analogy to electron conduction in a magnetic field allows to predict the effective diffusion coefficient of the bacteria. The latter is shown to be reduced by the circling motion of the bacteria.

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Hydrodynamic synchronization is a fundamental physical phenomenon by which self-sustained oscillators communicate through perturbations in the surrounding fluid and converge to a stable synchronized state. This is an important factor for the emergence of regular and coordinated patterns in the motions of cilia and flagella. When dealing with biological systems, however, it is always hard to disentangle internal signaling mechanisms from external purely physical couplings. We have used the combination of two-photon polymerization and holographic optical trapping to build a mesoscale model composed of chiral propellers rotated by radiation pressure. The two microrotors can be synchronized by hydrodynamic interactions alone although the relative torques have to be finely tuned. Dealing with a micron sized system we treat synchronization as a stochastic phenomenon and show that the phase lag between the two microrotors is distributed according to a stationary Fokker-Planck equation for an overdamped particle over a tilted periodic potential. Synchronized states correspond to minima in this potential whose locations are shown to depend critically on the detailed geometry of the propellers.

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Understanding the collective motion of self-propelling organisms in confined geometries, such as that of narrow channels, is of great theoretical and practical importance. By means of numerical simulations we study the motion of model bacteria in 2D channels under different flow conditions: fluid at rest, steady and unsteady flow. We find aggregation of bacteria near channel walls and, in the presence of external flow, also upstream swimming, which turns out to be a very robust result. Detailed analysis of bacterial velocity and orientation fields allows us to quantify the phenomenon by varying cell density, channel width and fluid velocity. The tumbling mechanism turns out to have strong influence on velocity profiles and particle flow, resulting in a net upstream flow in the case of non-tumbling organisms. Finally we demonstrate that upstream flow can be enhanced by a suitable choice of an unsteady flow pattern.

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Digital holographic microscopy provides an ideal tool for 3D tracking of microspheres while simultaneously allowing a full and accurate characterization of their main physical properties such as: radius and refractive index. We demonstrate that the combination of high resolution multipoint tracking and accurate optical sizing of tracers provides an ideal tool for precise multipoint viscosity measurements. We also report a detailed evaluation of the technique's accuracy and precision in relation to the primary sources of error.

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The dynamics of passive colloidal tracers in a bath of self-propelled particles is receiving a lot of attention in the context of nonequilibrium statistical mechanics. Here we demonstrate that active baths are also capable of mediating effective interactions between suspended bodies. In particular we observe that a bath of swimming bacteria gives rise to a short range attraction similar to depletion forces in equilibrium colloidal suspensions. Using numerical simulations and experiments we show how the features of this interaction arise from the combination of nonequilibrium dynamics (peculiar of bacterial baths) and excluded volume effects.

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Digital holographic microscopy is used to numerically refocus a recorded hologram at an arbitrary axial distance. However, as a straightforward property of coherent light fields, image reconstruction on an arbitrary tilted plane could be directly obtained by a rotation in k-space. We demonstrate that this property allows the real-time microscopic inspection of particle distribution over three mutually orthogonal planes at the same time. As a straightforward application we use the proposed technique for real-time monitoring of fluid flow over the three cross sections of a microfluidic channel.