arXiv subjects

Silvia Bonfanti

Publications and source records attributed to Silvia Bonfanti.

27 records · Page 2Linked to original sources

arXiv2020

Unjamming of active rotators

Active particle assemblies can exhibit a wide range of interesting dynamical phases depending on internal parameters such as density, adhesion strength or self-propulsion. Active self-rotations are rarely studied in this context, although they can be relevant for active matter systems, as we illustrate by analyzing the motion of Chlamydomonas reinhardtii algae under different experimental conditions. Inspired by this example, we simulate the dynamics of a system of interacting active disks endowed with active torques. At low packing fractions, adhesion causes the formation of small rotating clusters, resembling those observed when algae are stressed. At higher densities, the model shows a jamming to unjamming transition promoted by active torques and hindered by adhesion. Our results yield a comprehensive picture of the dynamics of active rotators, providing useful guidance to interpret experimental results in cellular systems where rotations might play a role.

cond-mat.soft↗

arXiv2020

Automatic Design of Mechanical Metamaterial Actuators

Mechanical metamaterials actuators achieve pre-determined input--output operations exploiting architectural features encoded within a single 3D printed element, thus removing the need of assembling different structural components. Despite the rapid progress in the field, there is still a need for efficient strategies to optimize metamaterial design for a variety of functions. We present a computational method for the automatic design of mechanical metamaterial actuators that combines a reinforced Monte Carlo method with discrete element simulations. 3D printing of selected mechanical metamaterial actuators shows that the machine-generated structures can reach high efficiency, exceeding human-designed structures. We also show that it is possible to design efficient actuators by training a deep neural network, eliminating the need for lengthy mechanical simulations. The elementary actuators devised here can be combined to produce metamaterial machines of arbitrary complexity for countless engineering applications.

cond-mat.soft↗

arXiv2020

Protein driven lipid domain nucleation in biological membranes

Lipid rafts are heterogeneous dynamic lipid domains of the cell membranes that are involved in several biological processes, like protein and lipids specific transport and signaling. Our understanding of lipid raft formation is still limited, due to the transient and elusive nature of these domains {\it in vivo}, in contrast to the stable phase-separated domains observed in artificial membranes. Inspired by experimental findings highlighting the relevance of transmembrane proteins for lipid rafts, we investigate lipid domain nucleation by coarse-grained molecular dynamics and Ising model simulations. We find that the presence of a transmembrane protein can trigger lipid domain nucleation in a flat membrane from an otherwise mixed lipid phase. Furthermore, we study the role of the lipid domain in the diffusion of the protein showing that its mobility is hindered by the presence of the raft. The results of our coarse-grained molecular dynamics and Ising model simulations thus coherently support the important role played by transmembrane proteins in lipid domain formation and stability.

physics.bio-ph↗

arXiv2019

Elementary plastic events in amorphous silica

Plastic instabilities in amorphous materials are often studied using idealized models of binary mixtures that do not capture accurately molecular interactions and bonding present in real glasses. Here we study atomic scale plastic instabilities in a three dimensional molecular dynamics model of silica glass under quasi-static shear. We identify two distinct types of elementary plastic events, one is a standard quasi-localized atomic rearrangement while the second is a bond breaking event that is absent in simplified models of fragile glass formers. Our results show that both plastic events can be predicted by a drop of the lowest non-zero eigenvalue of the Hessian matrix that vanishes at a critical strain. Remarkably, we find very high correlation between the associated eigenvectors and the non-affine displacement fields accompanying the bond breaking event, predicting the locus of structural failure. Both eigenvectors and non-affine displacement fields display an Eshelby-like quadrupolar structure for both failure modes, rearrangement or bond-breaking. Our results thus clarify the nature of atomic scale plastic instabilities in silica glasses providing useful information for the development of mesoscale models of amorphous plasticity.

cond-mat.dis-nn↗

arXiv2019

Oscillatory Instabilities in 3-Dimensional Frictional Granular Matter

The dynamics of amorphous granular matter with frictional interactions cannot be derived in general from a Hamiltonian and therefore displays oscillatory instabilities stemming from the onset of complex eigenvalues in the stability matrix. These instabilities were discovered in the context of one and two dimensional systems, while the three dimensional case was never studied in detail. Here we fill this gap by deriving and demonstrating the presence of oscillatory instabilities in a three dimensional granular packing. We study binary assemblies of spheres of two sizes interacting via classical Hertz and Mindlin force laws for the longitudinal and tangent interactions, respectively. We formulate analytically the stability matrix in 3D and observe that a couple of complex eigenvalues emerges at the onset of the instability as in the case of frictional disks in two-dimensions. The dynamics then shows oscillatory exponential growth in the Mean-Square-Displacement, followed by a catastrophic event. The generality of these results for any choice of forces that break the symplectic Hamiltonian symmetry is discussed.

cond-mat.stat-mech↗

arXiv2018

Density scaling in the mechanics of a disordered mechanical meta-material

Nature provides examples of self-assemble lightweight disordered network structures with remarkable mechanical properties which are desirable for many applications purposes but challenging to reproduce artificially. Previous experimental and computational studies investigated the mechanical responses of random network structures focusing on topological and geometrical aspects in terms of variable connectivity or probability to place beam elements. However for practical purposes an ambitious challenge is to design new materials with the possibility to taylor their mechanical features such as stiffness. Here, we design a two dimensional disordered mechanical meta-material exhibiting unconventional stiffness-density scaling in the regime where both bending and stretching are relevant for deformation. In this regime, the mechanical meta-material covers a wide interval of the Young modulus - density plane, simultaneously exhibiting high critical stress and critical strain. Our results, supported by finite element simulations, provides the guiding principles to design on demand disordered metamaterials, bridging the gap between artificial and naturally occurring materials.

cond-mat.soft↗

arXiv2017

Methods to locate Saddle Points in Complex Landscapes

We present a class of simple algorithms that allows to find the reaction path in systems with a complex potential energy landscape. The approach does not need any knowledge on the product state and does not require the calculation of any second derivatives. The underlying idea is to use two nearby points in configuration space to locate the path of slowest ascent. By introducing a weak noise term, the algorithm is able to find even low-lying saddle points that are not reachable by means of a slowest ascent path. Since the algorithm makes only use of the value of the potential and its gradient, the computational effort to find saddles is linear in the number of degrees of freedom, if the potential is short-ranged. We test the performance of the algorithm for two potential energy landscapes. For the Müller-Brown surface we find that the algorithm always finds the correct saddle point. For the modified Müller-Brown surface, which has a saddle point that is not reachable by means of a slowest ascent path, the algorithm is still able to find this saddle point with high probability.

cond-mat.dis-nn↗

arXiv2015

Realistic Tunneling States for the Magnetic Effects in Non-Metallic Real Glasses

The discovery of magnetic and compositional effects in the low temperature properties of multi-component glasses has prompted the need to extend the standard two-level systems (2LSs) tunneling model. A possible extension \cite{Jug2004} assumes that a subset of tunneling quasi-particles is moving in a three-welled potential (TWP) associated with the ubiquitous inhomogeneities of the disordered atomic structure of the glass. We show that within an alternative, cellular description of the intermediate-range atomic structure of glasses the tunneling TWP can be fully justified. We then review how the experimentally discovered magnetic effects can be explained within the approach where only localized atomistic tunneling 2LSs and quasi-particles tunneling in TWPs are allowed. We discuss the origin of the magnetic effects in the heat capacity, dielectric constant (real and imaginary parts), polarization echo and SQUID magnetization in several glassy systems. We conclude by commenting on a strategy to reveal the mentioned tunneling states (2LSs and TWPs) by means of atomistic computer simulations and discuss the microscopic nature of the tunneling states in the context of the potential energy landscape of glass-forming systems.

cond-mat.dis-nn↗

arXiv2015

On the Paramagnetic Impurity Concentration of Silicate Glasses from Low-Temperature Physics

The concentration of paramagnetic trace impurities in glasses can be determined via precise SQUID measurements of the sample's magnetization in a magnetic field. However the existence of quasi-ordered structural inhomogeneities in the disordered solid causes correlated tunneling currents that can contribute to the magnetization, surprisingly, also at the higher temperatures. We show that taking into account such tunneling systems gives rise to a good agreement between the concentrations extracted from SQUID magnetization and those extracted from low-temperature heat capacity measurements. Without suitable inclusion of such magnetization contribution from the tunneling currents we find that the concentration of paramagnetic impurities gets considerably over-estimated. This analysis represents a further positive test for the structural inhomogeneity theory of the magnetic effects in the cold glasses.

cond-mat.dis-nn↗