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A. Trovato

Publications and source records attributed to A. Trovato.

15 recordsLinked to original sources

Neural network time-series classifiers for gravitational-wave searches in single-detector periods

The search for gravitational-wave signals is limited by non-Gaussian transient noises that mimic astrophysical signals. Temporal coincidence between two or more detectors is used to mitigate contamination by these instrumental glitches. However, when a single detector is in operation, coincidence is impossible, and other strategies have to be used. We explore the possibility of using neural network classifiers and present the results obtained with three types of architectures: convolutional neural network, temporal convolutional network, and inception time. The last two architectures are specifically designed to process time-series data. The classifiers are trained on a month of data from the LIGO Livingston detector during the first observing run (O1) to identify data segments that include the signature of a binary black hole merger. Their performances are assessed and compared. We then apply trained classifiers to the remaining three months of O1 data, focusing specifically on single-detector times. The most promising candidate from our search is 2016-01-04 12:24:17 UTC. Although we are not able to constrain the significance of this event to the level conventionally followed in gravitational-wave searches, we show that the signal is compatible with the merger of two black holes with masses $m_1 = 50.7^{+10.4}_{-8.9}\,M_{\odot}$ and $m_2 = 24.4^{+20.2}_{-9.3}\,M_{\odot}$ at the luminosity distance of $d_L = 564^{+812}_{-338}\,\mathrm{Mpc}$.

gr-qc

Denoising gravitational-wave signals from binary black holes with dilated convolutional autoencoder

Broadband frequency output of gravitational-wave detectors is a non-stationary and non-Gaussian time series data stream dominated by noise populated by local disturbances and transient artifacts, which evolve on the same timescale as the gravitational-wave signals and may corrupt the astrophysical information. We study a denoising algorithm dedicated to expose the astrophysical signals by employing a convolutional neural network in the encoder-decoder configuration, i.e. apply the denoising procedure of coalescing binary black hole signals in the publicly available LIGO O1 time series strain data. The denoising convolutional autoencoder neural network is trained on a dataset of simulated astrophysical signals injected into the real detector's noise and a dataset of detector noise artifacts ("glitches"), and its fidelity is tested on real gravitational-wave events from O1 and O2 LIGO-Virgo observing runs.

gr-qc

Key interaction patterns in proteins revealed by cluster expansion of the partition function

The native conformation of structured proteins is stabilized by a complex network of interactions. We analyzed the elementary patterns that constitute such network and ranked them according to their importance in shaping protein sequence design. To achieve this goal, we employed a cluster expansion of the partition function in the space of sequences and evaluated numerically the statistical importance of each cluster. An important feature of this procedure is that it is applied to a dense, finite system. We found that patterns that contribute most to the partition function are cycles with even numbers of nodes, while cliques are typically detrimental. Each cluster also gives a contribute to the sequence entropy, which is a measure of the evolutionary designability of a fold. We compared the entropies associated with different interaction patterns to their abundances in the native structures of real proteins.

q-bio.BM

Long term monitoring of the optical background in the Capo Passero deep-sea site with the NEMO tower prototype

The NEMO Phase-2 tower is the first detector which was operated underwater for more than one year at the "record" depth of 3500 m. It was designed and built within the framework of the NEMO (NEutrino Mediterranean Observatory) project. The 380 m high tower was successfully installed in March 2013 80 km offshore Capo Passero (Italy). This is the first prototype operated on the site where the italian node of the KM3NeT neutrino telescope will be built. The installation and operation of the NEMO Phase-2 tower has proven the functionality of the infrastructure and the operability at 3500 m depth. A more than one year long monitoring of the deep water characteristics of the site has been also provided. In this paper the infrastructure and the tower structure and instrumentation are described. The results of long term optical background measurements are presented. The rates show stable and low baseline values, compatible with the contribution of 40K light emission, with a small percentage of light bursts due to bioluminescence. All these features confirm the stability and good optical properties of the site.

physics.ins-det

Measurement of the atmospheric muon depth intensity relation with the NEMO Phase-2 tower

The results of the analysis of the data collected with the NEMO Phase-2 tower, deployed at 3500 m depth about 80 km off-shore Capo Passero (Italy), are presented. Cherenkov photons detected with the photomultipliers tubes were used to reconstruct the tracks of atmospheric muons. Their zenith-angle distribution was measured and the results compared with Monte Carlo simulations. An evaluation of the systematic effects due to uncertainties on environmental and detector parameters is also included. The associated depth intensity relation was evaluated and compared with previous measurements and theoretical predictions. With the present analysis, the muon depth intensity relation has been measured up to 13 km of water equivalent.

physics.ins-det

Melting a stretched DNA

We study the melting of a double stranded DNA in the presence of stretching forces, via 3D Monte-Carlo simulations, exactly solvable models and heuristic arguments. The resulting force-temperature phase diagram is dramatically different for the cases where the force is applied to only one strand or to both. Different assumptions on the monomer size of single and double stranded DNA lead to opposite conclusions as to whether DNA melts or not as it overstretches.

cond-mat.soft

Simple solvation potential for coarse-grained models of proteins

We formulate a simple solvation potential based on a coarsed-grain representation of amino acids with two spheres modeling the $C_α$ atom and an effective side-chain centroid. The potential relies on a new method for estimating the buried area of residues, based on counting the effective number of burying neighbours in a suitable way. This latter quantity shows a good correlation with the buried area of residues computed from all atom crystallographic structures. We check the discriminatory power of the solvation potential alone to identify the native fold of a protein from a set of decoys and show the potential to be considerably selective.

q-bio.BM

Physics of thick polymers

We present the results of analytic calculations and numerical simulations of the behaviour of a new class of chain molecules which we call thick polymers. The concept of the thickness of such a polymer, viewed as a tube, is encapsulated by a special three body interaction and impacts on the behaviour both locally and non-locally. When thick polymers undergo compaction due to an attractive self-interaction, we find a new type of phase transition between a compact phase and a swollen phase at zero temperature on increasing the thickness. In the vicinity of this transition, short tubes form space filling helices and sheets as observed in protein native state structures. Upon increasing the chain length, or the number of chains, we numerically find a crossover from secondary structure motifs to a quite distinct class of structures akin to the semi-crystalline phase of polymers or amyloid fibers in polypeptides.

cond-mat.soft

Design of amino acid sequences to fold into C_alpha-model proteins

In order to extend the results obtained with minimal lattice models to more realistic systems, we study a model where proteins are described as a chain of 20 kinds of structureless amino acids moving in a continuum space and interacting through a contact potential controlled by a 20x20 quenched random matrix. The goal of the present work is to design and characterize amino acid sequences folding to the SH3 conformation, a 60-residues recognition domain common to many regulatory proteins. We show that a number of sequences can fold, starting from a random conformation, to within a distance root mean square deviation (dRMSD) of 2.6A from the native state. Good folders are those sequences displaying in the native conformation an energy lower than a sequence--independent threshold energy.

q-bio.BM

Continuum model for polymers with finite thickness

We consider the continuum limit of a recently-introduced model for discretized thick polymers, or tubes. We address both analytically and numerically how the polymer thickness influences the decay of tangent-tangent correlations and find how the persistence length scales with the thickness and the torsional rigidity of the tube centerline. At variance with the worm-like chain model, the phase diagram that we obtain for a continuous tube is richer; in particular, for a given polymer thickness there exists a threshold value for the centerline torsional rigidity separating a simple exponential decay of the tangent-tangent correlation from an oscillatory one.

cond-mat.stat-mech

A new perspective on the analysis of helix-helix packing preferences in globular proteins

For many years it had been believed that steric compatibility of helix interfaces could be the source of the observed preference for particular angles between neighbouring helices as emerging from statistical analysis of protein databanks. Several elegant models describing how side chains on helices can interdigitate without steric clashes were able to account quite reasonably for the observed distributions. However, it was later recognized (Bowie, 1997 and Walther, 1998) that the ``bare'' measured angle distribution should be corrected to avoid statistical bias. Disappointingly, the rescaled distributions dramatically lost their similarity with theoretical predictions casting many doubts on the validity of the geometrical assumptions and models. In this report we elucidate a few points concerning the proper choice of the random reference distribution. In particular we show the existence of crucial corrections due to the correct implementation of the approach used to discriminate whether two helices are in contact or not and to measure their relative orientations. By using this new rescaling, the ``true'' packing angle preferences are well described, even more than with the original ``bare'' distribution, by regular packing models.

cond-mat.soft

Geometry of compact tubes and protein structures

Proteins form a very important class of polymers. In spite of major advances in the understanding of polymer science, the protein problem has remained largely unsolved. Here, we show that a polymer chain viewed as a tube not only captures the well-known characteristics of polymers and their phases but also provides a natural explanation for many of the key features of protein behavior. There are two natural length scales associated with a tube subject to compaction -- the thickness of the tube and the range of the attractive interactions. For short tubes, when these length scales become comparable, one obtains marginally compact structures, which are relatively few in number compared to those in the generic compact phase of polymers. The motifs associated with the structures in this new phase include helices, hairpins and sheets. We suggest that Nature has selected this phase for the structures of proteins because of its many advantages including the few candidate strucures, the ability to squeeze the water out from the hydrophobic core and the flexibility and versatility associated with being marginally compact. Our results provide a framework for understanding the common features of all proteins.

physics.bio-ph

Phase diagram of force-induced DNA unzipping in exactly solvable models

The mechanical separation of the double helical DNA structure induced by forces pulling apart the two DNA strands (``unzipping'') has been the subject of recent experiments. Analytical results are obtained within various models of interacting pairs of directed walks in the (1,1,...,1) direction on the hypercubic lattice, and the phase diagram in the force-temperature plane is studied for a variety of cases. The scaling behaviour is determined at both the unzipping and the melting transition. We confirm the existence of a cold denaturation transition recently observed in numerical simulations: for a finite range of forces the system gets unzipped by {\it decreasing} the temperature. The existence of this transition is rigorously established for generic lattice and continuum space models.

cond-mat.stat-mech

Heteropolymers in a Solvent at an Interface

Exact bounds are obtained for the quenched free energy of a polymer with random hydrophobicities in the presence of an interface separating a polar from a non polar solvent. The polymer may be ideal or have steric self-interactions. The bounds allow to prove that a ``neutral'' random polymer is localized near the interface at any temperature, whereas a ``non-neutral'' chain is shown to undergo a delocalization transition at a finite temperature. These results are valid for a quite general a priori probability distribution for both independent and correlated hydrophobic charges. As a particular case we consider random AB-copolymers and confirm recent numerical studies.

cond-mat.stat-mech

Swollen-Collapsed Transition in Random Hetero-Polymers

A lattice model of a hetero-polymer with random hydrophilic-hydrophobic charges interacting with the solvent is introduced, whose continnuum counterpart has been proposed by T. Garel, L. Leibler and H. Orland {J. Phys. II France 4, 2139 (1994)]. The transfer matrix technique is used to study various constrained annealed systems which approximate at various degrees of accuracy the original quenched model. For highly hydrophobic chains an ordinary $θ$-point transition is found from a high temperature swollen phase to a low temperature compact phase. Depending on the type of constrained averages, at very low temperatures a swollen phase or a coexistence between compact and swollen phases are found. The results are carefully compared with the corresponding ones obtained in the continuum limit, and various improvements in the original calculations are discussed.

cond-mat.stat-mech