Silvia Bonfanti
Assistant Professor at NOMATEN, Warsaw.

My research focuses on Physics of Complex Systems: glasses, mechanical metamaterials, machine learning and biophysics.

Recently I am working on High Entropy Alloys.

– Research Works –

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ML prediction of failure in silica glasses

Predicting the failure of two-dimensional silica glasses. Nature communications, 13(1), 1-11.


We use our automatic method to design metamaterial (see below) to get chiral metamaterials: metamaterials that rotate under compression!

Combining 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 how to design efficient actuators by training a deep neural network.

Our review paper on digital strategies to design metamaterials has been selected as a cover of APL Materials!

Tailoring mechanical metamaterials through density of beams


We report investigations of a model of silica glass at finite temperature; here the bare forces include binary and ternary interactions. We can establish the validity of the universal law of the density of quasi-localized modes also in this richer and more realistic model glass.

Universality of glassy vibrational modes for the first time in a realistic glass system: Silica. We present analysis of the quasilocalized modes in silica and conclude that in three dimensions silica exhibits the very same frequency dependence at low frequencies, suggesting that this universal form is a generic consequence of amorphous glassiness.

We study atomic-scale plastic instabilities in a three-dimensional molecular dynamics model of silica glass under quasistatic shear. We identify two distinct types of elementary plastic events, one is a standard quasilocalized atomic rearrangement while the second is a bond-breaking event that is absent in simplified models of fragile glass formers.

The origin of the brittle-to-ductile transition, experimentally observed in amorphous silica nanofibers as the sample size is reduced, is still debated. Here we investigate the issue by extensive molecular dynamics simulations at low and room temperatures for a broad range of sample sizes, with open and periodic boundary conditions.

Frictional Spheres

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.


Active particles 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 and self-propulsive forces. We also study the interplay between self-propulsion and self-rotation and derive a phase diagram. We provide 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.

Bio-ispired Metamaterials

Metamaterial architecture from a self-shaping carnivorous plant

Computational Biophysics

The nuclear morphology of eukaryotic cells is determined by the interplay between the lamina forming the nuclear skeleton, the chromatin inside the nucleus, and the coupling with the cytoskeleton. Nuclear alterations of the lamina are often associated with pathological conditions as in Hutchinson-Gilford progeria syndrome, in which a mutation in the lamin A gene yields an altered form of the protein, named progerin, and an aberrant nuclear shape. Here, we introduce an inducible cellular model of Hutchinson-Gilford progeria syndrome in HeLa cells in which increased progerin expression leads to alterations in the coupling of the lamin shell with cytoskeletal or chromatin tethers as well as with polycomb group proteins.

Protein Aggregation: Mutant vs wild type HTT

Energy Landscapes

Saddle point search without using Hessian matrix
Energy Landscape of Frictional System

About Me

Triathlete, experiencing interdisciplinarity
at all levels!


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