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Overlap fermions preserve a remnant of chiral symmetry on the lattice. They are a powerful tool to investigate the topological structure of the vacuum of Yang-Mills theory and full QCD. Recent results concerning the localization of…
We analyze data from confocal microscopy experiments of a colloidal suspension to validate predictions of rapid sporadic events responsible for structural relaxation in a glassy sample. The trajectories of several thousand colloidal…
In this paper, we investigate induced and nonlinear fiber topological pressure for random dynamical systems. We define a non-averaged induced fiber pressure via spanning and separated sets, characterize it as the pseudo-inverse of the…
We study the microrheology of nanoparticle shells [Dinsmore et al. Science 298, 1006 (2002)] and viral capsids [Ivanovska et al. PNAS 101, 7600 (2004)] by computing the mechanical response function and thermal fluctuation spectrum of a…
Many models of physics beyond the Standard Model include towers of particles whose masses follow an approximately periodic pattern with little spacing between them. These resonances might be too weak to detect individually, but could be…
We investigate the dynamics of an epidemiological susceptible-infected-susceptible (SIS) model on an adaptive network. This model combines epidemic spreading (dynamics on the network) with rewiring of network connections (topological…
A coarse-grained computational model is used to investigate the effect of a fluctuating fluid membrane on the dynamics of patchy-particle assembly into virus capsid-like cores. Results from simulations for a broad range of parameters are…
The notion of topology in physical systems is associated with the existence of a nonlocal ordering that is insensitive to a large class of perturbations. This brings robustness to the behaviour of the system and can serve as a ground for…
With Monte Carlo methods we study the dynamic relaxation of a vortex state at the Kosterlitz-Thouless phase transition of the two-dimensional XY model. A local pseudo-magnetization is introduced to characterize the symmetric structure of…
We introduce a new method for temporal pattern analysis of scientific collaboration networks. We investigate in particular virus research activities through five epidemic or pandemic outbreaks in the recent two decades and in the ongoing…
We propose a novel model-based clustering approach for samples of time series. We assume as a unique commonality that two observations belong to the same group if structural changes in their behaviours happen at the same time. We resort to…
In molecular dynamics simulations, rare events, such as protein folding, are typically studied using enhanced sampling techniques, most of which are based on the definition of a collective variable (CV) along which acceleration occurs.…
The dynamics of neural networks is often characterized by collective behavior and quasi-synchronous events, where a large fraction of neurons fire in short time intervals, separated by uncorrelated firing activity. These global temporal…
We develop and present a unified multi-scale model (involving three scales of spatial organisation) to study the dynamics of rigid aggregating particles suspended in a viscous fluid medium and subject to a steady poiseuille flow. At…
The phenomenon of solidification of a substance from its liquid phase is of the greatest practical and theoretical importance, and atomistic simulations can provide precious information towards its understanding and control. Unfortunately,…
It has been known for some time that human autoimmune diseases can be triggered by viral infections. Several possible mechanisms of interactions between a virus and immune system have been analysed, with a prevailing opinion being that the…
Mesoscopic spin ensembles coupled to a cavity offer the exciting prospect of observing complex nonclassical phenomena that pool the microscopic features from a few spins with those of macroscopic spin ensembles. Here, we demonstrate how the…
We investigate numerically and analytically the coupled dynamics of transmembrane voltage and intracellular calcium cycling in paced cardiac cells using a detailed physiological model and its reduction to a three-dimensional discrete map.…
We investigate the dynamics of a single, overdamped colloidal particle, which is driven by a constant force through a one-dimensional periodic potential. We focus on systems with large barrier heights where the lowest-order cumulants of the…
We develop equilibrium and kinetic theories that describe the assembly of viral capsid proteins on a charged central core, as seen in recent experiments in which brome mosaic virus (BMV) capsids assemble around nanoparticles functionalized…