Loriano Storchi

Loriano Storchi
Università degli Studi G. d'Annunzio Chieti e Pescara | UNICH · Department of Pharmacy

PhD

About

104
Publications
7,446
Reads
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1,634
Citations
Additional affiliations
March 2013 - present
INFN - Istituto Nazionale di Fisica Nucleare and CERN
Position
  • Research Associate
Description
  • I am collaborating with the INFN (National Isntitute of Nuclear Phisics) being involved in the research activity which is part of the CMS experiment (at CERN). Cloud Computing and Reconfigurable computing (FPGA) related projects.
December 2011 - December 2020
Università degli Studi G. d'Annunzio Chieti e Pescara
Position
  • Professor
Description
  • I am researcher in General and Inorganic Chemistry. I work also as System and Network administrator for the Theoretical Inorganic Chemistry Group, managing network, servers and HPC resources (see www-thch.unich.it).
July 2011 - December 2011
Italian National Research Council
Position
  • Researcher
Description
  • Implementation and optimization of non-relativistic and relativistic DFT codes of parallel computer architectures and multi and many cores (GPU) for advanced simulations materials and processes in organic and hybrid photovoltaics.

Publications

Publications (104)
Article
Full-text available
The molecular interaction properties and aggregation capabilities disclosed by PrP-E200K, a pathogenic mutant of the human prion protein, were investigated in detail using multilayered computational approaches. In a previous work, we reported that the electrostatic complementarity between region1 (negative) and region3 (positive) has been assumed t...
Article
Machine-learning techniques are revolutionizing the way to perform efficient materials modeling. We here propose a combinatorial machine-learning approach to obtain physical formulas based on simple and easily accessible ingredients, such as atomic properties. The latter are used to build materials features that are finally employed, through linear...
Preprint
Full-text available
The Frozen Density Embedding scheme represents an embedding method in which environmental effects onto a given subsystem are included by representing the other subsystems making up the surroundings quantum mechanically, by means of their electron densities. In the present paper, we extend the full 4-component relativistic Dirac-Kohn-Sham method, as...
Preprint
Full-text available
Machine Learning (ML) techniques are revolutionizing the way to perform efficient materials modeling. Nevertheless, not all the ML approaches allow for the understanding of microscopic mechanisms at play in different phenomena. To address the latter aspect, we propose a combinatorial machine-learning approach to obtain physical formulas based on si...
Article
The software Randentropy is designed to estimate inequality in a random system where several individuals interact moving among many communities and producing dependent random quantities of an attribute. The overall inequality is assessed by computing the Random Theil’s Entropy. Firstly, the software estimates a piecewise homogeneous Markov chain by...
Article
Future systems will be characterised by the presence of many computing core in a single device, on large scale data centers or even at the level of IoT devices. The ability to fully exploit computational architectures’ heterogeneity and concurrency will be a key point. In this manuscript we present the BondMachine (BM), an innovative prototype soft...
Article
Full-text available
The CMS Inner Tracker, made of silicon pixel modules, will be entirely replaced prior to the start of the High Luminosity LHC period. One of the crucial components of the new Inner Tracker system is the readout chip, being developed by the RD53 Collaboration, and in particular its analogue front-end, which receives the signal from the sensor and di...
Article
The cover image is based on the Full Paper Combining machine learning and quantum mechanics yields more chemically aware molecular descriptors for medicinal chemistry applications by Sara Tortorella et al., https://doi.org/10.1002/jcc.26737.
Article
Full-text available
During the operation of the CMS experiment at the High-Luminosity LHC the silicon sensors of the Phase-2 Outer Tracker will be exposed to radiation levels that could potentially deteriorate their performance. Previous studies had determined that planar float zone silicon with n-doped strips on a p-doped substrate was preferred over p-doped strips o...
Article
Full-text available
Molecular interaction fields (MIFs), describing molecules in terms of their ability to interact with any chemical entity, are one of the most established and versatile concepts in drug discovery. Improvement of this molecular description is highly desirable for in silico drug discovery and medicinal chemistry applications. In this work, we revised...
Article
The reaction of the antitumor M(I)-bis-N-heterocyclic carbene (M(I)-NHC) complexes, M = Cu, Ag, and Au, with their potential protein binding sites, i.e. cysteine and selenocysteine, was investigated by means of density functional theory approaches. Capped cysteine and selenocysteine were employed to better model the corresponding residues environme...
Article
Full-text available
A multilayered computational workflow was designed to identify a druggable binding site on the surface of the E200K pathogenic mutant of the human prion protein, and to investigate the effect of the binding of small molecules in the inhibition of the early aggregation of this protein. At this purpose, we developed an efficient computational tool to...
Preprint
The software Randentropy is designed to estimate inequality in a random system where several individuals interact moving among many communities and producing dependent random quantities of an attribute. The overall inequality is assessed by computing the Random Theil's Entropy. Firstly, the software estimates a piecewise homogeneous Markov chain by...
Article
Full-text available
The CMS detector at the CERN LHC features a silicon pixel detector as its innermost subdetector. The original CMS pixel detector has been replaced with an upgraded pixel system (CMS Phase-1 pixel detector) in the extended year-end technical stop of the LHC in 2016/2017. The upgraded CMS pixel detector is designed to cope with the higher instantaneo...
Article
Full-text available
The production of seeds without sex is considered the holy grail of plant biology. The transfer of apomixis to various crop species has the potential to transform plant breeding, since it will allow new varieties to retain valuable traits thorough asexual reproduction. Therefore, a greater molecular understanding of apomixis is fundamental. In a pr...
Article
Full-text available
The programmed cell death protein 1 (PD-1) and its ligand, PD-L1, constitute an important co-inhibitory immune checkpoint leading to downregulation of immune system. Tumor cells developed a strategy to trigger PD-1/PD-L1 pathway reducing the T cell anticancer activity. Anti-PD-L1 small drugs, generally with improved pharmacokinetic and technologica...
Article
Frozen Density Embedding (FDE) represents a versatile embedding scheme to describe the environmental effect on the electron dynamics in molecular systems. The extension of the general theory of FDE to the real-time time-dependent Kohn-Sham method has previously been presented and implemented in plane-waves and periodic boundary conditions (Pavanell...
Preprint
Full-text available
Frozen Density Embedding (FDE) represents a versatile embedding scheme to describe the environmental effect on the electron dynamics in molecular systems. The extension of the general theory of FDE to the real-time time-dependent Kohn-Sham method has previously been presented and implemented in plane-waves and periodic boundary conditions (Pavanell...
Article
In this paper, we present and review the most recent computational advances in the BERTHA code. BERTHA can be regarded as the state of the art in fully relativistic four-component Dirac–Kohn–Sham (DKS) software. Thanks to the implementation of various parallelization and memory open-ended distribution schemes in combination with efficient “density...
Article
Full-text available
During the high-luminosity phase of the LHC (HL-LHC), planned to start in 2027, the accelerator is expected to deliver an instantaneous peak luminosity of up to 7.5 x 10(34) cm(-2) s(-1). A total integrated luminosity of 3000 or even 4000 fb(-1) is foreseen to be delivered to the general purpose detectors ATLAS and CMS over a decade, thereby increa...
Chapter
While since mid-seventies it has been clearly shown that relativistic effects play a crucial role for the complete understanding of the chemistry of molecules especially when heavy elements are involved, still nowadays in most of the case the relativistic effects are introduced via approximate methods. The main motivation behind the introduction of...
Article
We present a real-time time-dependent four-component Dirac-Kohn-Sham (RT-TDDKS) implementation based on the BERTHA code. This new implementation takes advantage of modern software engineering, including the prototyping techniques. The software design follows a three step approach: i) the prototype implementation of time-propagation algorithm in non...
Article
The effect of spin-orbit coupling (SOC) on the halogen bond involving astatine has been investigated using state-of-the-art two- and four-component relativistic calculations. Adducts between Cl-X (X = Cl, Br, I and At) and ammonia have been selected to establish a trend on going down the periodic table. The SOC influence has been explored not only...
Conference Paper
The chemical characterization of super heavy elements (SHE), achieved by studying their interaction with a heavy metal surface, is currently of fundamental importance for the placement of new elements in the periodic table. Effects described by relativity theory on SHE chemistry are known to alter expectations dramatically. We use the 4-component D...
Conference Paper
Full-text available
Metals play an important role in many biological systems, not to mention that their use in the formulation of drugs with novel modes of action has boosted the investigations aimed at elucidating their reaction mechanisms. At variance with carbon-based (or purely organic) molecules which nowadays may be described rather satisfactorily with molecular...
Article
Full-text available
In 2017 a new pixel detector was installed in the CMS detector. This so-called Phase-1 pixel detector features four barrel layers in the central region and three disks per end in the forward regions. The upgraded pixel detector requires an upgraded data acquisition (DAQ) system to accept a new data format and larger event sizes. A new DAQ and contr...
Article
We present a four-component relativistic density functional theory study of the chemical bond and s-d hybridization in the group 11 cyanides M-CN (M = Cu, Ag, and Au). The analysis is carried out within the charge-displacement/natural orbital for chemical valence (CD-NOCV) scheme, which allows us to single out meaningful contributions to the total...
Article
In this paper, we propose a methodology based on piecewise homogeneous Markov chain for credit ratings and a multivariate model of the credit spreads to evaluate the financial risk in the European Union (EU). Two main aspects are considered: how the financial risk is distributed among the European countries and how large is the value of the total r...
Article
Full-text available
Hydrogen economy has been suggested as a possible green alternative to produce energy, also in the framework of transport applications. According to the specific transport means, different kinds of materials can be adopted. The choice of the most suitable materials should then be addressed according to a systematic analysis of available data. In th...
Preprint
In this paper, we propose a methodology based on piece-wise homogeneous Markov chain for credit ratings and a multivariate model of the credit spreads to evaluate the financial risk in European Union (EU). Two main aspects are considered: how the financial risk is distributed among the European countries and how large is the value of the total risk...
Article
In the present work, we investigate the sensitivity of the dynamic Theil index computed under a Markov reward model with respect to structured perturbations affecting the underlying Markov process. The model is applied to the sovereign credit spread evolution as a proxy for financial risk, which are driven by the sovereign credit rating dynamic. Th...
Article
Interferon responsive factor 1 (IRF-1) is a pleiotropic transcription factor, possessing non-redundant biological activities that depend on its interaction with different protein partners and multiple post-translational modifications including phosphorylation. In particular, a 5′-SXXXSXS-3′ motif of the protein represents the target of the IκB-rela...
Article
Full-text available
The structure of the CMS inner tracking system has been studied using nuclear interactions of hadrons striking its material. Data from proton-proton collisions at a center-of-mass energy of 13 TeV recorded in 2015 at the LHC are used to reconstruct millions of secondary vertices from these nuclear interactions. Precise positions of the beam pipe an...
Article
In the original publication, second author’s name was incorrectly published as ‘Leonardo Belapassi’. The correct name should read as ‘Leonardo Belpassi’.
Article
The elucidation of the molecular mechanisms subtending the pathogenesis of prion diseases, and, the particular, of the events leading to the formation of prion particles is a nowadays challenge in the field of neurochemistry. A notable example is represented by pathogenic mutants of prion protein characterized by both an intrinsic tendency to aggre...
Article
Full-text available
In this paper, we apply information theory measures and Markov processes in order to analyse the inequality in the distribution of the financial risk in a pool of countries. The considered financial variables are sovereign credit ratings and interest rates of sovereign government bonds of European countries. This paper extends the methodology propo...
Article
Quantum chemistry is nowadays a term referring to a wide set of theoretical frameworks and models mainly relying on non-relativistic quantum mechanics. While, in most cases, the picture of the molecular structure and of the chemical reality provided by non-relativistic quantum chemistry is appropriate, we live in a universe with a finite speed of l...
Article
In Italy Botrytis cinerea represents the most significant disease in strawberry crops and causes major quality and quantity losses in postharvest storage. An alternative strategy to the synthetic fungicides in crop defence could be the use of bioactive compounds with high antifungal activity. This research regards the use of Punica granatum peel ex...
Article
Full-text available
A new CMS Tracker is under development for operation at the High Luminosity LHC from 2026 onwards. It includes an outer tracker based on dedicated modules that will reconstruct short track segments, called stubs, using spatially coincident clusters in two closely spaced silicon sensor layers. These modules allow the rejection of low transverse mome...
Article
A methodology based on Markov chains and dynamic entropy measures is proposed for measuring and forecasting the evolution of the inequality of financial risks in the European Union (EU). The proposed methodology requires knowledge of the past evolution of sovereign credit rating for the EU member states and historical data concerning harmonized int...
Article
We have recently introduced a simple yet powerful tool for analyzing quantitatively the coordination bond in terms of the donation and back-donation constituents of the Dewar-Chatt-Duncanson model. Our approach is based on the decomposition, via natural orbitals for chemical valence (NOCV), of the so-called charge-displacement (CD) function into ad...
Article
Full-text available
The high luminosity upgrade of the Large Hadron Collider, foreseen for 2026, necessitates the replacement of the CMS experiment’s silicon tracker. The innermost layer of the new pixel detector will be exposed to severe radiation, corresponding to a 1 MeV neutron equivalent fluence of up to \(\Phi _{eq} = 2 \times 10^{16}\) cm\(^{-2}\), and an ionis...
Conference Paper
The Grid Empowered Molecular Simulator GEMS enabling fully ab initio virtual experiments through rigorous theoretical and computational procedures has been upgraded with a novel scheme for automated generation of three-atom potential energy surfaces. The scheme is based on a space-reduced formulation of the so-called bond-order variables allowing f...
Article
Full-text available
The upgrade of the LHC to the High-Luminosity LHC (HL-LHC) is expected to increase the LHC design luminosity by an order of magnitude. This will require silicon tracking detectors with a significantly higher radiation hardness. The CMS Tracker Collaboration has conducted an irradiation and measurement campaign to identify suitable silicon sensor ma...
Article
Full-text available
A new pixel detector for the CMS experiment was built in order to cope with the instantaneous luminosities anticipated for the Phase I Upgrade of the LHC . The new CMS pixel detector provides four-hit tracking with a reduced material budget as well as new cooling and powering schemes. A new front-end readout chip mitigates buffering and bandwidth l...
Article
Full-text available
The CMS tracker consists of 206 m² of silicon strip sensors assembled on carbon fibre composite structures and is designed for operation in the temperature range from −25 to +25°C. The mechanical stability of tracker components during physics operation was monitored with a few μm resolution using a dedicated laser alignment system as well as partic...
Article
Full-text available
The CMS tracker consists of 206 m2 of silicon strip sensors assembled on carbon fibre composite structures and is designed for operation in the temperature range from −25 to +25◦C. The mechanical stability of tracker components during physics operation was monitored with a few µm resolution using a dedicated laser alignment system as well as partic...
Article
Full-text available
The propensity of cellular prion protein to aggregation is reputed essential for the initiation of the amyloid cascade that ultimately lead to the accumulation of neurotoxic aggregates. In this paper, we extended and applied an already reported computational workflow [Proteins 2015; 83: 1751–1765] to elucidate in details the aggregation propensity...
Data
Anchoring of N-terminus at globule domain of PrPC. Reported systems: Ib (left), IIb (middle), and Vb (right). (TIF)
Data
Octamer of Ca2+-bound PrPC units. Hydrophobic and hydrophilic clusters are depicted with yellow and red spheres, respectively. Also shown: interunit region 1-region 1 and H1-H2 hydrophobic approach (purple dashed circles); region1-region3 interface (green dashed circles). (TIF)
Data
Trajectory stabilization. Root mean squared deviations of the backbone atom coordinates along the trajectory of (A) Ia-Va and (B) Ib-Vb systems. Root mean squared deviations of the charged residues atom coordinates along the trajectory of (C) Ia-Va and (D) Ib-Vb systems. (TIF)
Data
Averaged MEP isosurfaces. From the top to below Ia, IIa, and Va (left) and Ib, IIb, and Vb (right). Positive and negative isosurfaces are depicted as blue and red meshes, respectively. (TIF)
Data
Detailed view of the region 1-region 3 interface detected in the octamer of Ca2+-bound PrPC. (TIF)
Data
Computational details. (DOCX)
Data
Percentage of trajectory with Ca2+-residue distance within 0.25 nm. (DOC)
Data
Octamer of wild type PrPC units. Hydrophobic and hydrophilic clusters are depicted with yellow and red spheres, respectively. Also shown: interunit hydrophobic matches at the region 1-region 3 interface (purple dashed circles) and H1-H2 hydrophobic approach (dashed arrows). (TIF)
Data
Clustering analysis (last 100 ns) based on the alignment and positional deviation of ionizable residues. (DOC)
Article
The increment of luminosity at HL-LHC will require the introduction of tracker information at Level-1 trigger system for the experiments in order to maintain an acceptable trigger rate for selecting interesting events despite the one order of increased magnitude in the minimum bias interactions. In order to extract the track information in the requ...
Article
The increase of luminosity at HL-LHC will require the introduction of tracker information at Level-1 trigger system for the experiments to maintain an acceptable trigger rate to select interesting events despite the one order of magnitude increase in the minimum bias interactions. To extract in the required latency the track information a dedicated...
Article
Full-text available
The chemistry of superheavy elements (Z ≥ 104) is actively investigated in atom-at-a-time experiments of volatility through adsorption on gold surfaces. In this context, common guidelines for interpretation based on group trends in the periodic table should be used cautiously, because relativistic effects play a central role and may cause predictio...
Article
Full-text available
The degradation of signal in silicon sensors is studied under conditions expected at the CERN High-Luminosity LHC. 200 $\mu$m thick n-type silicon sensors are irradiated with protons of different energies to fluences of up to $3 \cdot 10^{15}$ neq/cm$^2$. Pulsed red laser light with a wavelength of 672 nm is used to generate electron-hole pairs in...
Article
The amyloid conversion is a massive detrimental modification affecting several proteins upon specific physical or chemical stimuli characterizing a plethora of diseases. In many cases, the amyloidogenic stimuli induce specific structural features to the protein conferring the propensity to misfold and form amyloid deposits. The investigation of mut...
Article
We present an innovative methodology for the computer simulation of mesoporous nanoparticulated oxide films based on the random packing of faceted nanopolyhedra in the form of bifrustums, reproducing the experimentally observed TiO2 anatase bifrustum shape. A computer simulation employing nanospheres as packing objects was preliminary considered to...