Crystallizing proteins is the bottleneck to systematically determining their structures. Identifying the solution conditions under which these macromolecules crystallize should be equivalent to determining their phase diagram, yet one typically resorts to combinatorial rather than physics-guided sampling to tackle this difficult problem. Although several soft matter-based ``patchy particle'' models have been invoked to rationalize protein assembly, the interactions that drive protein crystallization are insufficiently characterized for these models to be of much practical use. As a proof of concept of their relevance we simulate solvated proteins to parameterize patchy models, and find the self-assembly phase diagram to agree with crystallization experiments. By generalizing these models, we explore the range of conditions over which crystal assembly is possible, providing guidelines for crystallizing some of the recalcitrant proteins. I will also discuss a few ideas about to push this program forward.

In the presence of a strong magnetic field, and for an integer filling of the Landau levels, Coulomb interactions favor a ferromagnetic ground-state. It has been shown already twenty years ago that when extra charges are added or removed to such system, the ferromagnetic state becomes unstable and is replaced by spin textures called Skyrmions. We (*) have generalized this notion to an arbitrary number d of internal states for the electrons, which may correspond to the combination of spin, valley, or layer indices. We first consider a fully SU(d) symmetric model, that differs from the usual CP(d-1) model by the long ranged Coulomb interaction. This additional term lifts the massive ground-state degeneracy present in the short range CP(d-1) model, and selects a hexagonal Skyrmion lattice which spontaneously breaks the underlying SU(d) symmetry. The ground state charge density modulation, which inevitably exists in these lattices, vanishes exponentially in d. We compute analytically the complete low-lying excitation spectrum, which separates into d2-1 gapless acoustic magnetic modes and a magnetophonon. We discuss the role of effective mass anisotropy for SU(3) valley Skyrmions relevant for experiments with AlAs quantum wells. Here, we find a transition, which breaks a six-fold rotational symmetry of a triangular lattice, appearing at weak anisotropy, followed by a formation of a square lattice at large values of anisotropy strength. (*) This work is the result of a collaboration with D. Kovrizhin and R. Moessner

Direct searches for Dark Matter (DM) aim at detecting the nuclear recoils arising from a scattering between DM particles and target nuclei in underground detectors. Since the physics that describes the collision between DM particles and target nuclei is deeply non-relativistic, in the first part of this seminar I’ll review a different and more general approach to study signal in direct DM searches based on the formalism of non-relativistic operators. Then I’ll present the main observables and the experimental landscape pointing out all the uncertainties that enter in this field. Finally, since the underlying relativistic theory that describes both the DM and standard model fields is unknown, in the last part of the seminar I’ll be focussed on the uncertainties coming from the nature of the interaction. On a more specific level, the last part will be divided in two: i) a model independent part, in which I’m going to present a new method and a self-contained set of numerical tools to the derive the bounds from some current direct detection experiments in a completely model independent way; ii) a model dependent part, in which I’ll show that a Dirac DM particle interacting with ordinary matter via the exchange of a light pseudo-scalar can accommodate the DAMA data while being compatible with all null direct DM searches and at the same time provide a DM explanation of the GC excess in γ-rays and achieve the correct relic density.

Il seminario è basto sui seguenti lavori:
arXiv: arXiv:1402.1507
arXiv: arXiv:1307.5955
arXiv: arXiv:1406.5542

The measurement of extensional viscosity of non-Newtonian fluids has been an area of activity for several decades. While it is in principle simple to impose a controlled shear deformation on a liquid, it is not so simple to produce a controlled extensional deformation.
This presentation will demonstrate the application of the so-called Filament Stretching Rheometer for the implementation of well controlled extensional flow. The attainment of steady flow will be shown. In addition the relaxation of stress after a defined deformation for polymeric liquids will be illustrated.

Finally the presentation will discuss instabilities that may occur in extension. These include instability at the plates and what appears to be a cohesive fracture in liquids.

Active matter constitutes a particularly interesting class of systems
in non-equilibrium statistical mechanics and soft-condensed matter physics.

In the first part of this talk talk I will focus on the dynamics of passive colloidal tracers in a bath of self-propelled particles. We demonstrate that a bath of swimming E. coli is capable of mediating effective interactions between suspended (passive) colloids. In particular we observe that a bath of motile bacteria gives rise to a short range attraction similar to depletion forces in equilibrium colloidal suspensions[1]. However, using numerical simulations, we show how this effective interactions uniquely arise from the non-equilibrium dynamics, induced by the bacterial bath. Surprisingly excluded volume effects reduce the observed "attraction", in striking contrast with an equilibrium-like depletion scenario.

In the second part of talk I will describe how the intrinsic non-equilibrium nature of swimming bacteria appears evidently even when a simple constant external field is applied to a sample of motile E. coli bacteria[2]. To this aim we use centrifugation that is a widespread laboratory technique. We demonstrate that simple centrifugation can also be used to separate swimming cells having different motilities and we discuss the potential applications of our technique. In this experiment we apply an external centrifugal field to self-propelled bacteria and we use dynamic image correlation spectroscopy to measure the motility of bacteria after centrifugation. A significant spatial gradient in swimming-speed is observed for increasing centrifugal speeds. We show how these results can be reproduced by a diffusion equation that treats bacteria as "hot" colloidal particles having a diffusion coefficient that depends on their heterogeneous swimming speed.

In the final part of the talk I will discuss a recent experimental/numerical work studying the dynamics of a colloidal bead confined by a harmonic potential in a bath of swimming E. coli bacteria [3]. The resulting dynamics is well approximated by a Langevin equation for an overdamped oscillator driven by the combination of a white thermal noise and an exponentially correlated active noise [4]. We discuss how this scenario leads to a breakdown of the equipartition theorem and to the coexistence of two different effective temperatures that govern dynamics along the flat and the curved directions in the potential landscape.


[1] L. Angelani, C. Maggi, M. L. Bernardini, et al.
Phys. Rev. Lett. 107, 138302 (2011)

[2] C. Maggi, A. Lepore, J. Solari et al.
Soft Matter 9, 10885-10890 (2013)

[3] C. Maggi, M. Paoluzzi, N. Pellicciotta, et al.
arXiv:1409.3929

[4] N. Koumakis, C. Maggi, R. Di Leonardo,
Soft Matter, 10, 5695-5701, (2014)

"Thé au cube" est la pause café scientifique de l'axe PTh. L'orateur y expose de manière interactive et accessible au théoriciens non-spécialistes, ses intérêts scientifiques du moment.N'oubliez pas de ramener vos tasses et autres mugs préférés.

The LHC has fixed the last Standard Model (SM) parameter, the Higgs mass. Now, we can study the predictions of the SM (appropriately extended to account for neutrino oscillations and dark matter) in a vast energy range, up to the Planck scale. Although the SM does not provide a dynamical explanation of electroweak symmetry breaking (EWSB), this analysis is important for at least two reasons. It gives us information about very high energies, which we cannot even dream to reach at particle colliders, and, even more importantly, it can also tell us whether the SM has other problems, besides those that are universally accepted as SM problems. We will discuss the currently most precise determination of the bound on the Higgs mass that ensures our vacuum is stable up to Planck energies. We will find that we are very close to the border between stability and metastability, with a pronounced preference for the metastable scenario. This fact puts stringent bounds on Higgs inflation and so points towards a beyond the SM explanation of inflation. Such an explanation as well as a dynamical origin of EWSB can be achieved, remarkably, in theories of all interactions (including gravity) where fundamental scales are absent: agravity.

Based on arXiv:1307.3536; 1308.2244; 1403.4226.

The early Drosophila embryo is an ideal model to understand the transcriptional regulation of well-defined patterns of gene expression in a developing organism. The first step in the spatial organization of an organism consists of the establishment of the Anterior-Posterior polarity axis. In the fruit fly, the maternal morphogen Bicoid (Bcd) forms a spatial gradient with high concentration at the anterior pole that exponentially decreases toward the posterior. Bcd activates the target gene hunchback (hb) which shows an homogeneous and sharp a domain of expression in the anterior half of the embryo. Recently my biology collaborators developed a technique to observe live transcription in transgenic flies, by genetically modifying the hb gene with an MS2-MCP fluorescent tag, opening the possibility of studying the dynamics of gene pattern formation. We used the MS2-MCP system to visualize nascent transcripts expressed from the typical hb promoter under the control of the morphogen Bcd. We developed a segmentation and tracking algorithm to analyze the data. We find that the transgene used shows an hb expression as homogeneous as the non-modified hb gene in the anterior half of the embryo, but unlike non-modified hb it is also shows activity in the posterior, though more heterogeneously and more transiently than in the anterior. We propose that the establishment of the hb pattern relies on Bcd-dependent lengthening of transcriptional activity periods in the anterior and may require two distinct repression mechanisms in the posterior. Additionally, I discuss theoretical models that aim at understanding the details of spatial and temporal regulation in this system.

Raman spectroscopy is a useful experimental tool to investigate local deformation and structural changes in SiO2-based glasses. Using a semi-classical simulation of Raman spectra in large samples of silica glasses, we show that shear plastic flow affects the Raman measurement in the upper part of the spectrum. We relate these changes to structural modifications, as well as a detailed analysis of the vibration modes computed in the same frequency range. These results opens the door to in situ monitoring of plastic damage in silica-based structures.