Digital Video Microscopy Enhanced by Deep Learning published in Optica

Digital video microscopy enhanced by deep learning

Digital video microscopy enhanced by deep learning
Saga Helgadottir, Aykut Argun & Giovanni Volpe
Optica 6(4), 506—513 (2019)
doi: 10.1364/OPTICA.6.000506
arXiv: 1812.02653
GitHub: DeepTrack

Single particle tracking is essential in many branches of science and technology, from the measurement of biomolecular forces to the study of colloidal crystals. Standard methods rely on algorithmic approaches; by fine-tuning several user-defined parameters, these methods can be highly successful at tracking a well-defined kind of particle under low-noise conditions with constant and homogenous illumination. Here, we introduce an alternative data-driven approach based on a convolutional neural network, which we name DeepTrack. We show that DeepTrack outperforms algorithmic approaches, especially in the presence of noise and under poor illumination conditions. We use DeepTrack to track an optically trapped particle under very noisy and unsteady illumination conditions, where standard algorithmic approaches fail. We then demonstrate how DeepTrack can also be used to track multiple particles and non-spherical objects such as bacteria, also at very low signal-to-noise ratios. In order to make DeepTrack readily available for other users, we provide a Python software package, which can be easily personalized and optimized for specific applications.

Invited talk by G. Volpe at the 10th Nordic Workshop on Statistical Physics, Stockholm, 20-22 Mar 2019

Soft Matter Meets Deep Learning
Giovanni Volpe
The 10th Nordic Workshop on Statistical Physics: Biological, Complex and Non-equilibrium Systems, NORDITA, Stockholm, Sweden
20-22 March 2019

I will present an overview of recent projects where we have proposed new approaches to the experimental study of active matter. In particular, I will present a new algorithm for the measurement of microscopic force fields and a deep-learning approach to the tracking of microscopic particles.

Active Colloidal Molecules published in J. Chem. Phys.

Light-controlled Assembly of Active Colloidal Molecules
Light-controlled Assembly of Active Colloidal Molecules

Light-controlled Assembly of Active Colloidal Molecules
Falko Schmidt, Benno Liebchen, Hartmut Löwen & Giovanni Volpe
Journal of Chemical Physics 150(9), 094905 (2019)
doi: 10.1063/1.5079861
arXiv: 1801.06868

Thanks to a constant energy input, active matter can self-assemble into phases with complex architectures and functionalities such as living clusters that dynamically form, reshape, and break-up, which are forbidden in equilibrium materials by the entropy maximization (or free energy minimization) principle. The challenge to control this active self-assembly has evoked widespread efforts typically hinging on engineering of the properties of individual motile constituents. Here, we provide a different route, where activity occurs as an emergent phenomenon only when individual building blocks bind together in a way that we control by laser light. Using experiments and simulations of two species of immotile microspheres, we exemplify this route by creating active molecules featuring a complex array of behaviors, becoming migrators, spinners, and rotators. The possibility to control the dynamics of active self-assembly via light-controllable nonreciprocal interactions will inspire new approaches to understand living matter and to design active materials.

Ordering of binary colloidal crystals by random potentials on ArXiv

Ordering of binary colloidal crystals by random potentials

Ordering of binary colloidal crystals by random potentials
André S. Nunes, Sabareesh K. P. Velu, Iryna Kasianiuk, Denys Kasyanyuk, Agnese Callegari, Giorgio Volpe, Margarida M. Telo da Gama, Giovanni Volpe & Nuno A. M. Araújo
arXiv: 1903.01579

Structural defects are ubiquitous in condensed matter, and not always a nuisance. For example, they underlie phenomena such as Anderson localization and hyperuniformity, and they are now being exploited to engineer novel materials. Here, we show experimentally that the density of structural defects in a 2D binary colloidal crystal can be engineered with a random potential. We generate the random potential using an optical speckle pattern, whose induced forces act strongly on one species of particles (strong particles) and weakly on the other (weak particles). Thus, the strong particles are more attracted to the randomly distributed local minima of the optical potential, leaving a trail of defects in the crystalline structure of the colloidal crystal. While, as expected, the crystalline ordering initially decreases with increasing fraction of strong particles, the crystalline order is surprisingly recovered for sufficiently large fractions. We confirm our experimental results with particle-based simulations, which permit us to elucidate how this non-monotonic behavior results from the competition between the particle-potential and particle-particle interactions.

Seminar by G. Volpe at Tel Aviv University, 6 Mar 2019

Emergent Complex Behaviour in Active Matter
Giovanni Volpe
Light Matter Interaction Center, Tel Aviv University, Israel
6 March 2019

After a brief introduction of active particles, I’ll present some recent advances on the study of active particles in complex and crowded environments.
First, I’ll show that active particles can work as microswimmers and microengines powered by critical fluctuations and controlled by light.
Then, I’ll discuss some examples of behavior of active particles in crowded environments: a few active particles alter the overall dynamics of a system; active particles create metastable clusters and channels; active matter leads to non-Boltzmann distributions and alternative non-equilibrium relations; and active colloidal molecules can be created and controlled by light.
Finally, I’ll present some examples of the behavior of active particles in complex environments: active particles often perform 2D active Brownian motion; active particles at liquid-liquid interfaces behave as active interstitials or as active atoms; and the environment alters the optimal search strategy for active particles in complex topologies.

Controlling Colloidal Dynamics by Critical Casimir Forces published in Soft Matter

Controlling the dynamics of colloidal particles by critical Casimir forces

Controlling the dynamics of colloidal particles by critical Casimir forces
Alessandro Magazzù, Agnese Callegari, Juan Pablo Staforelli, Andrea Gambassi, Siegfried Dietrich & Giovanni Volpe
Soft Matter 15(10), 2152—2162 (2019)
doi: 10.1039/C8SM01376D
arXiv: 1806.11403

Critical Casimir forces can play an important role for applications in nano-science and nano-technology, owing to their piconewton strength, nanometric action range, fine tunability as a function of temperature, and exquisite dependence on the surface properties of the involved objects. Here, we investigate the effects of critical Casimir forces on the free dynamics of a pair of colloidal particles dispersed in the bulk of a near-critical binary liquid solvent, using blinking optical tweezers. In particular, we measure the time evolution of the distance between the two colloids to determine their relative diffusion and drift velocity. Furthermore, we show how critical Casimir forces change the dynamic properties of this two-colloid system by studying the temperature dependence of the distribution of the so-called first-passage time, i.e., of the time necessary for the particles to reach for the first time a certain separation, starting from an initially assigned one. These data are in good agreement with theoretical results obtained from Monte Carlo simulations and Langevin dynamics.

Active Matter Influence on Coffee Rings published in Soft Matter

Active Matter Alters the Growth Dynamics of Coffee Rings

Active Matter Alters the Growth Dynamics of Coffee Rings
Tuğba Andaç, Pascal Weigmann, Sabareesh K. P. Velu, Erçağ Pinçe, Agnese Callegari, Giorgio Volpe, Giovanni Volpe & Agnese Callegari
Soft Matter 15(7), 1488—1496 (2019)
doi: 10.1039/C8SM01350K
arXiv: 1803.02619

How particles are deposited at the edge of evaporating droplets, i.e. the coffee ring effect, plays a crucial role in phenomena as diverse as thin-film deposition, self-assembly, and biofilm formation. Recently, microorganisms have been shown to passively exploit and alter these deposition dynamics to increase their survival chances under harshening conditions. Here, we show that, as the droplet evaporation rate slows down, bacterial mobility starts playing a major role in determining the growth dynamics of the edge of drying droplets. Such motility-induced dynamics can influence several biophysical phenomena, from the formation of biofilms to the spreading of pathogens in humid environments and on surfaces subject to periodic drying. Analogous dynamics in other active matter systems can be exploited for technological applications in printing, coating, and self-assembly, where the standard coffee-ring effect is often a nuisance.

Seminar by G. Volpe at UNAM, Mexico City, 18 Feb 2019

Optical Tweezers: From critical fluctuations to nanoscopic force measurement
Seminar at Sistemas Complejos y Física Estadística
UNAM – Universidad National de Mexico, Mexico City, Mexico
18 February 2019

I will first give a brief overview of optical trapping and optical manipulation — the invention that has earned Arthur Ashkin the 2019 Nobel Prize in Physics. Then, I will focus on some recent applications where we have used optical tweezers to characterise critical Casimir forces and to manipulate active matter. Finally, I will present a new approach to the calibration of optical forces that we have recently developed in collaboration with UNAM.

 

Colloquium by G. Volpe at ICF, Cuernavaca, 13 Feb 2019

Emergent Complex Behaviour in Active Matter
Giovanni Volpe
Colloquium at Instituto de Ciencias Físicas
Cuernavaca, Morelos, Mexico
13 February 2019

After a brief introduction of active particles, I’ll present some recent advances on the study of active particles in complex and crowded environments.
First, I’ll show that active particles can work as microswimmers and microengines powered by critical fluctuations and controlled by light.
Then, I’ll discuss some examples of behavior of active particles in crowded environments: a few active particles alter the overall dynamics of a system; active particles create metastable clusters and channels; active matter leads to non-Boltzmann distributions and alternative non-equilibrium relations; and active colloidal molecules can be created and controlled by light.
Finally, I’ll present some examples of the behavior of active particles in complex environments: active particles often perform 2D active Brownian motion; active particles at liquid-liquid interfaces behave as active interstitials or as active atoms; and the environment alters the optimal search strategy for active particles in complex topologies.

https://www.fis.unam.mx/coloquios/473/qemergent-complex-behaviour-in-active-matterq