Understanding the motion of nanoparticles in polymer solutionsand melts is a problem of broad importance, with applications tomany different fields, such as material science, biophysics, andmedicine. If the nanoparticles are larger than the polymer's radiusof gyration, their structure and dynamics can be well described interms of effective pair potentials. However, much remains to beunderstood in the so-called “protein limit”, where the size of thenanoparticles becomes comparable to or smaller than that ofthe polymers. Moreover, most of the previous study consideringthis size range have only focused on the dilute nanoparticleregime, which is easier to handle since inter-nanoparticleinteraction can be neglected and the properties of the polymersolution/melt are expected to be unchanged.Using molecular dynamics simulations, we study the dynamic andstructural properties of a semidilute polymer solution containingwell dispersed spherical nanoparticles of size smaller than thepolymer's radius of gyration. We consider various nanoparticlediameters and a broad range of nanoparticle volume fractions,up to values for which the inter-nanoparticle interactionbecomes important.We find that the polymers slow down when the nanoparticleconcentration is increased, in qualitative agreement with theconfinement parameter theory (Choi et al.,ACS Macro Lett.2013,2,485−490), according to which polymers slow downbecause they have to squeeze through “bottlenecks” created bythe presence of the nanoparticles. Also the nanoparticles slowdown when their concentration is increased, with the magnitudeof the slowing down depending in a non-trivial way on their size.Surprisingly, if the concentration of the nanoparticles is increasedpast the range in which the nanoparticle dispersion is good, thediffusivities of polymers and nanoparticles reach a minimum andthen start to increase.

Proteins are the basis of cellular functions, yet key parameters regulating protein synthesis remain elusive. Understanding the fine mechanisms of regulation is a major goal of molecular and systems biology, and this knowledge will support many synthetic biology applications.We have the ambitious goal of providing a biophysical modelling framework of one of the last steps in protein synthesis, namely mRNA translation. Our work focuses on translation initiation and elongation, which relative role is highly debated in the literature: is the ribosome recruitment or the codon bias determining the expression of a gene? We explain how the transcript efficiency can be dictated by ribosome abundances, codon usage and transcript length.We propose analytical and simulation methods to investigate translation models based on an inhomogeneous exclusion process, the prototypical non-equilibrium traffic model in one dimension. We show that the first codons, together with the value of the initiation rate, are the main determinants of protein production. Finally, we interpret the obtained analytical results based on the evolutionary role of codons' choice for regulating translation rates and ribosome usage.

Dense active materials

Lectures on entropy

By combining rheology, light scattering, small angle X-ray scattering and simulations we explore the glassy dynamics of soft colloids using microgels and charged particles interacting by steric and screened Coulomb interactions, respectively. In the supercooled regime, the structural relaxation time (SRT) of both systems grows steeply with volume fraction, reminiscent of the behavior of colloidal hard sphere systems [1]. This suggests that softness has no impact on the growth of the SRT on approaching the glass transition, as confirmed by computer simulations. We show that the onset of a finite yield-stress, occurring within the supercooled regime, systematically corresponds to a minimum of the stretching exponent characterizing the decay of the two-time intensity autocorrelation function.Softness becomes relevant only at very large packing fractions, when the system falls out of equilibrium. In this non-equilibrium regime, the SRT depends surprisingly weakly on packing fraction and time correlation functions exhibit compressed exponential decays consistent with internal stress-driven relaxation. The transition to this novel regime coincides with the onset of an anomalous decrease of local order with increasing density, reminiscent of the reentrant glass transition predicted theoretically in ultrasoft systems [2,3], and corresponds to a weakening of the volume fraction dependence of the plateau modulus of the suspensions. We propose that these peculiar dynamics result from a competition between the non-equilibrium aging dynamics of the glassy state and the tendency of soft systems to refluidize at high packing fractions.

Equilibrium simulations ofsupercooled liquids beyondlaboratory timescales

The Gardner transition in glasses