Predictive Controller for Refrigeration Systems Aimed to Electrical Load Shifting and Energy Storage

The need to reduce greenhouse gas emissions is leading to an increase in the use of renewable energy sources. Due to the aleatory nature of these sources, to prevent grid imbalances, smart management of the entire system is required. Industrial refrigeration systems represent a source of flexibility in this context: being large electricity consumers, they can allow large-load shifting by varying separator levels or storing surplus energy in the products and thus balancing renewable electricity production. The work aims to model and control an industrial refrigeration system used for freezing food by applying the Model Predictive Control technique. The controller was developed in Matlab® and implemented in a Model-in-the-Loop environment. Two control objectives are proposed: the first aims to minimize total energy consumption, while the second also focuses on utilizing the maximum amount of renewable energy. The results show that the innovative controller allows energy savings and better exploitation of the available renewable electricity, with a 4.5% increase in its use, compared to traditional control methods. Since the proposed software solution is rapidly applicable without the need to modify the plant with additional hardware, its uptake can contribute to grid stability and renewable energy exploitation

Investigating the side-chain structural organization behind the stability of protein folding and binding

What are the molecular mechanisms that dictate protein-protein binding stability and whether those are related to the ones behind protein fold stability are still largely open questions. Indeed, despite many past efforts, we still lack definitive models to account for experimental quantities like protein melting temperature or complex binding affinity. Here, we investigate and compare chemical and physical features on a dataset of protein with known melting temperature as well as a large dataset of protein-protein complexes with reliable experimental binding affinity. In particular, we probed the aminoacid composition and the organization of the network of intramolecular and intermolecular interaction energies among residues. We found that hydrophobic residues present on the protein surfaces are preferentially located in the binding regions, while charged residues behave oppositely. In addition, the abundance of polar amino acid like Serine and Proline correlates with the binding affinity of the complexes. Analysing the interaction energies we found that distant Coulombic interactions are responsible for thermal stability while the total inter-molecular van der Waals energy correlates with protein-protein binding affinity.Comment: 8 pages, 3 figure

Does blood type affect the COVID-19 infection pattern?

Among the many aspects that characterize the COVID-19 pandemic, two seem particularly challenging to understand: (i) the great geographical differences in the degree of virus contagiousness and lethality which were found in the different phases of the epidemic progression, and (ii) the potential role of the infected people's blood type in both the virus infectivity and the progression of the disease. A recent hypothesis could shed some light on both aspects. Specifically, it has been proposed that in the subject-to-subject transfer SARS-CoV-2 conserves on its capsid the erythrocytes' antigens of the source subject. Thus these conserved antigens can potentially cause an immune reaction in a receiving subject that has previously acquired specific antibodies for the source subject antigens. This hypothesis implies a blood type-dependent infection rate. The strong geographical dependence of the blood type distribution could be, therefore, one of the factors at the origin of the observed heterogeneity in the epidemics spread. Here, we present an epidemiological deterministic model where the infection rules based on blood types are taken into account and compare our model outcomes with the exiting worldwide infection progression data. We found an overall good agreement, which strengthens the hypothesis that blood types do play a role in the COVID-19 infection.Comment: 6 figures, 4 table

Exploring the Association Between Sialic Acid and SARS-CoV-2 Spike Protein Through a Molecular Dynamics-Based Approach

Recent experimental evidence demonstrated the capability of SARS-CoV-2 Spike protein to bind sialic acid molecules, which was a trait not present in SARS-CoV and could shed light on the molecular mechanism used by the virus for the cell invasion. This peculiar feature has been successfully predicted by in-silico studies comparing the sequence and structural characteristics that SARS-CoV-2 shares with other sialic acid-binding viruses, like MERS-CoV. Even if the region of the binding has been identified in the N-terminal domain of Spike protein, so far no comprehensive analyses have been carried out on the spike-sialic acid conformations once in the complex. Here, we addressed this aspect performing an extensive molecular dynamics simulation of a system composed of the N-terminal domain of the spike protein and a sialic acid molecule. We observed several short-lived binding events, reconnecting to the avidic nature of the binding, interestingly occurring in the surface Spike region where several insertions are present with respect to the SARS-CoV sequence. Characterizing the bound configurations via a clustering analysis on the Principal Component of the motion, we identified different possible binding conformations and discussed their dynamic and structural properties. In particular, we analyze the correlated motion between the binding residues and the binding effect on the stability of atomic fluctuation, thus proposing regions with high binding propensity with sialic acid

Peri-Implant Bone Loss and Overload: A Systematic Review Focusing on Occlusal Analysis through Digital and Analogic Methods.

The present review aimed to assess the possible relationship between occlusal overload and peri-implant bone loss. In accordance with the PRISMA guidelines, the MEDLINE, Scopus, and Cochrane databases were searched from January 1985 up to and including December 2021. The search strategy applied was: (dental OR oral) AND implants AND (overload OR excessive load OR occlusal wear) AND (bone loss OR peri-implantitis OR failure). Clinical studies that reported quantitative analysis of occlusal loads through digital contacts and/or occlusal wear were included. The studies were screened for eligibility by two independent reviewers. The quality of the included studies was assessed using the Risk of Bias in Non-randomized Studies of Interventions (ROBINS-I) tool. In total, 492 studies were identified in the search during the initial screening. Of those, 84 were subjected to full-text evaluation, and 7 fulfilled the inclusion criteria (4 cohort studies, 2 cross-sectional, and 1 case-control). Only one study used a digital device to assess excessive occlusal forces. Four out of seven studies reported a positive correlation between the overload and the crestal bone loss. All of the included studies had moderate to serious overall risk of bias, according to the ROBINS-I tool. In conclusion, the reported data relating the occlusal analysis to the peri-implant bone level seem to reveal an association, which must be further investigated using new digital tools that can help to standardize the methodology

Shape Complementarity Optimization of Antibody-Antigen Interfaces: the Application to SARS-CoV-2 Spike Protein

Many factors influence biomolecules binding, and its assessment constitutes an elusive challenge in computational structural biology. In this respect, the evaluation of shape complementarity at molecular interfaces is one of the main factors to be considered. We focus on the particular case of antibody-antigen complexes to quantify the complementarities occurring at molecular interfaces. We relied on a method we recently developed, which employs the 2D Zernike descriptors, to characterize investigated regions with an ordered set of numbers summarizing the local shape properties. Collected a structural dataset of antibody-antigen complexes, we applied this method and we statistically distinguished, in terms of shape complementarity, pairs of interacting regions from non-interacting ones. Thus, we set up a novel computational strategy based on \textit{in-silico} mutagenesis of antibody binding site residues. We developed a Monte Carlo procedure to increase the shape complementarity between the antibody paratope and a given epitope on a target protein surface. We applied our protocol against several molecular targets in SARS-CoV-2 spike protein, known to be indispensable for viral cell invasion. We, therefore, optimized the shape of template antibodies for the interaction with such regions. As the last step of our procedure, we performed an independent molecular docking validation of the results of our Monte Carlo simulations.Comment: 13 pages, 4 figure

Politica industriale e sviluppo sostenibile

Il libro riproduce ed amplia le relazioni presentate al workshop del 3 ottobre 2014 presso il Dipartimento di Economia dell’Università di Parma, ad opera di studiosi appartenenti all’Università di Ferrara, allo Iefe-Università Bocconi di Milano, all’Università di Modena, alla Scuola Sant’Anna di Pisa, nonché alla stessa Università di Parma. I cinque contributi qui presentati fotografano cinque diversi aspetti del rapporto fra politica industriale (più in generale crescita economica diretta dalle istituzioni pubbliche) e sviluppo sostenibile: a livello nazionale, il possibile trade-off fra i due obiettivi di politica industriale e di sostenibilità ambientale nel tentativo di gerarchizzare i “settori strategici”, e la necessità che questo trade-off sia parzialmente compensato a livello di sforzo innovativo (Di Tommaso e Tassinari); a livello internazionale, la possibilità che politiche industriali nazionali non operino all’interno di un gioco a somma zero, ma diano risultati favorevoli al raggiungimento di un bene pubblico globale quale il cambiamento climatico (Fabbri e Ninni); a livello di imprese, la tendenziale riduzione delle contraddizioni fra incentivi al loro operare e “impronta” ambientale, grazie agli accordi volontari e in particolare all’importante ruolo della certificazione (Frey); a livello di istituzioni, l’esistenza di tipologie diverse di obiettivi e di strumenti a livello nazionale e a livello locale, e l’analisi in un confronto tra paesi europei delle caratteristiche delle politiche ambientali impostate a livello sub-nazionale (Croci e Molteni); a livello di mercato del lavoro, l’effetto sul tessuto industriale delle politiche di aumento della flessibilità del lavoro nella singola impresa, come aspetto particolare di una ridiscussione più ampia del concetto di sostenibilità ambientale e dei suoi rapporti con la politica nei confronti delle imprese (Giovannetti)

A computational approach to investigate TDP-43 C-terminal fragments aggregation in Amyotrophic Lateral Sclerosis

Many of the molecular mechanisms underlying the pathological aggregation of proteins observed in neurodegenerative diseases are still not fully understood. Among the diseases associated with protein aggregates, for example, Amyotrophic Lateral Sclerosis (ALS) is of relevant importance. Although understanding the processes that cause the disease is still an open challenge, its relationship with protein aggregation is widely known. In particular, human TDP-43, an RNA/DNA binding protein, is a major component of pathological cytoplasmic inclusions described in ALS patients. The deposition of the phosphorylated full-length TDP-43 in spinal cord cells has been widely studied, and it has been shown that the brain cortex presents an accumulation of phosphorylated C-terminal fragments (CTFs). Even if it is debated whether CTFs represent a primary cause of ALS, they are a hallmark of TDP-43 related neurodegeneration in the brain. Here, we investigate the CTFs aggregation process, providing a possible computational model of interaction based on the evaluation of shape complementarity at the interfaces. To this end, extensive Molecular Dynamics (MD) simulations were conducted for different types of fragments with the aim of exploring the equilibrium configurations. Adopting a newly developed approach based on Zernike polynomials, for finding complementary regions of the molecular surface, we sampled a large set of exposed portions of the molecular surface of CTFs structures as obtained from MD simulations. The analysis proposes a set of possible associations between the CTFs, which could drive the aggregation process of the CTFs.Comment: 9 pages, 4 figures, 1 tabl

Hubble Space Telescope survey of Magellanic Cloud star clusters: photometry and astrometry of 113 clusters and early results

In the past few years, we have undertaken an extensive investigation of star clusters and their stellar populations in the Large and Small Magellanic Clouds (LMC and SMC) based on archival images collected with the Hubble Space Telescope. We present photometry and astrometry of stars in 101 fields observed with the Wide Field Channel of the Advanced Camera for Surveys and the Ultraviolet and Visual Channel and the Near-Infrared Channel of Wide Field Camera 3. These fields comprise 113 star clusters. We provide differential-reddening maps for those clusters with significant reddening variations across the field of view. We illustrate various scientific outcomes that arise from the early inspection of the photometric catalogs. In particular, we provide new insights into the extended main-sequence turnoff (eMSTO) phenomenon: (i) We detected eMSTOs in two clusters, KMHK 361 and NGC 265, which had no previous evidence of multiple populations. This finding corroborates the conclusion that the eMSTO is a widespread phenomenon among clusters younger than ~2 Gyr. (ii) The homogeneous color-magnitude diagrams (CMDs) of 19 LMC clusters reveal that the distribution of stars along the eMSTO depends on cluster age. (iii) We discovered a new feature along the eMSTO of NGC 1783, which consists of a distinct group of stars on the red side of the eMSTO in CMDs composed of UV filters. Furthermore, we derived the proper motions of stars in the fields of view of clusters with multi-epoch images. Proper motions allowed us to separate the bulk of bright field stars from cluster members and investigate the internal kinematics of stellar populations in various LMC and SMC fields. As an example, we analyze the field around NGC 346 to disentangle the motions of its stellar populations, including NGC 364 and BS 90, young and pre-main-sequence stars in the star-forming region associated with NGC 346, and young and old field stellar populations of the SMC. Based on these results and the fields around five additional clusters, we find that young SMC stars exhibit elongated proper-motion distributions that point toward the LMC, thus providing new evidence for a kinematic connection between the LMC and SMC.We thank the anonymous referee for various suggestions that improved the quality of the manuscript. This work has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research innovation programme (Grant Agreement ERC-StG 2016, No. 716082 ’GALFOR’, PI: Milone, http://progetti.dfa.unipd. it/GALFOR) and from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 101034319 and from the European Union – NextGenerationEU, beneficiary: Ziliotto. A.P.M., M.T., and E.D. acknowledge support from MIUR through the FARE project R164RM93XW SEMPLICE (PI: Milone). A.P.M. and M.T. have been supported by MIUR under PRIN program 2017Z2HSMF (PI: Bedin). This research was supported in part by the Australian Research Council Centre of Excellence for All Sky Astrophysics in 3 Dimensions (ASTRO 3D) through project number CE170100013. This work is based on observations made with the NASA/ESA Hubble Space Telescope, obtained from the data archive at the Space Telescope Science Institute (STScI). STScI is operated by the Association of Universities for Research in Astronomy, Inc. under NASA contract NAS 5-26555.Peer ReviewedPostprint (published version

Differences in the organization of interface residues tunes the stability of the SARS-CoV-2 spike-ACE2 complex

The continuous emergence of novel variants represents one of the major problems in dealing with the SARS-CoV-2 virus. Indeed, also due to its prolonged circulation, more than ten variants of concern emerged, each time rapidly overgrowing the current viral version due to improved spreading features. As, up to now, all variants carry at least one mutation on the spike Receptor Binding Domain, the stability of the binding between the SARS-CoV-2 spike protein and the human ACE2 receptor seems one of the molecular determinants behind the viral spreading potential. In this framework, a better understanding of the interplay between spike mutations and complex stability can help to assess the impact of novel variants. Here, we characterize the peculiarities of the most representative variants of concern in terms of the molecular interactions taking place between the residues of the spike RBD and those of the ACE2 receptor. To do so, we performed molecular dynamics simulations of the RBD-ACE2 complexes of the seven variants of concern in comparison with a large set of complexes with different single mutations taking place on the RBD solvent-exposed residues and for which the experimental binding affinity was available. Analyzing the strength and spatial organization of the intermolecular interactions of the binding region residues, we found that (i) mutations producing an increase of the complex stability mainly rely on instaurating more favorable van der Waals optimization at the cost of Coulombic ones. In particular, (ii) an anti-correlation is observed between the shape and electrostatic complementarities of the binding regions. Finally, (iii) we showed that combining a set of dynamical descriptors is possible to estimate the outcome of point mutations on the complex binding region with a performance of 0.7. Overall, our results introduce a set of dynamical observables that can be rapidly evaluated to probe the effects of novel isolated variants or different molecular systems