Silvano Garnerone

BLISS is a versatile and quantitative method for genome-wide profiling of DNA double-strand breaks

Precisely measuring the location and frequency of DNA double-strand breaks (DSBs) along the genome is instrumental to understanding genomic fragility, but current methods are limited in versatility, sensitivity or practicality. Here we present Breaks Labeling In Situ and Sequencing (BLISS), featuring the following: (1) direct labelling of DSBs in fixed cells or tissue sections on a solid surface; (2) low-input requirement by linear amplification of tagged DSBs by in vitro transcription; (3) quantification of DSBs through unique molecular identifiers; and (4) easy scalability and multiplexing. We apply BLISS to profile endogenous and exogenous DSBs in low-input samples of cancer cells, embryonic stem cells and liver tissue. We demonstrate the sensitivity of BLISS by assessing the genome-wide off-target activity of two CRISPR-associated RNA-guided endonucleases, Cas9 and Cpf1, observing that Cpf1 has higher specificity than Cas9. Our results establish BLISS as a versatile, sensitive and efficient method for genome-wide DSB mapping in many applications.

Quantum algorithms for topological and geometric analysis of data.

Extracting useful information from large data sets can be a daunting task. Topological methods for analysing data sets provide a powerful technique for extracting such information. Persistent homology is a sophisticated tool for identifying topological features and for determining how such features persist as the data is viewed at different scales. Here we present quantum machine learning algorithms for calculating Betti numbers—the numbers of connected components, holes and voids—in persistent homology, and for finding eigenvectors and eigenvalues of the combinatorial Laplacian. The algorithms provide an exponential speed-up over the best currently known classical algorithms for topological data analysis.

Fidelity approach to the disordered quantum XY model.

We study the random XY spin chain in a transverse field by analyzing the susceptibility of the ground state fidelity, numerically evaluated through a standard mapping of the model onto quasifree fermions. It is found that the fidelity susceptibility and its scaling properties provide useful information about the phase diagram. In particular it is possible to determine the Ising critical line and the Griffiths phase regions, in agreement with previous analytical and numerical results.

Bipartite quantum states and random complex networks

We introduce a mapping between graphs and pure quantum bipartite states and show that the associated entanglement entropy conveys non-trivial information about the structure of the graph. Our primary goal is to investigate the family of random graphs known as complex networks. In the case of classical random graphs, we derive an analytic expression for the averaged entanglement entropy while for general complex networks we rely on numerics. For a large number of nodes n we find a scaling where both the prefactor c and the sub-leading O(1) term ge are characteristic of the different classes of complex networks. In particular, ge encodes topological features of the graphs and is named network topological entropy. Our results suggest that quantum entanglement may provide a powerful tool for the analysis of large complex networks with non-trivial topological properties.

Scaling of the fidelity susceptibility in a disordered quantum spin chain

The phase diagram of a quantum

Fidelity in topological quantum phases of matter

XY

Thermodynamic formalism for dissipative quantum walks

spin chain with Gaussian-distributed random anisotropies and transverse fields is investigated, with focus on the fidelity susceptibility, a recently introduced quantum information theoretical measure. Monitoring the finite-size scaling of the probability distribution of this quantity as well as its average and typical values, we detect a disorder-induced disappearance of criticality and the emergence of Griffiths phases in this model. It is found that the fidelity susceptibility is not self-averaging near the disorder-free quantum-critical lines. At the Ising critical point the fidelity susceptibility scales as a disorder-strength independent stretched exponential of the system size, in contrast with the quadratic scaling at the corresponding point in the disorder-free

Generalized quantum microcanonical ensemble from random matrix product states

XY

Pure state thermodynamics with matrix product states

chain. Along the line where the average anisotropy vanishes the fidelity susceptibility appears to scale extensively, whereas in the disorder-free case this point is quantum critical with quadratic finite-size scaling.

Entanglement and its evolution after a quench in the presence of an energy current

Quantum phase transitions that take place between two distinct topological phases remain an unexplored area for the applicability of the fidelity approach. Here, we appl y this method to spin systems in two and three dimensions and show that the fidelity susceptibility can be u sed to determine the boundary between different topological phases particular to these models, while at the same time offering information about the critical exponent of the correlation length. The success of this approach relies on its independence on local order parameters or breaking symmetry mechanisms, with which non-topological phases are usually characterized. We also consider a topological insulator/superconducting phase transition in three dimensions and point out the relevant features of fidelity susceptibility at the boundar y between these phases.