Simulation of photoinduced processes in organic chromophores: mapping photochemically relevant states for accurate dynamics

The simulation of ultrafast photoinduced processes is a fundamental step towards the understanding of the underlying molecular mechanism and interpretation/prediction of experimental data. Performing a computer simulation of a complex photoinduced process is only possible introducing some approximations but, in order to obtain reliable results, the need to reduce the complexity must balance with the accuracy of the model, which should include all the relevant degrees of freedom and a quantitatively correct description of the electronic states involved in the process. This work presents new computational protocols and strategies for the parameterisation of accurate models for photochemical/photophysical processes based on state-of-the-art multiconfigurational wavefunction-based methods. The required ingredients for a dynamics simulation include potential energy surfaces (PESs) as well as electronic state couplings, which must be mapped across the wide range of geometries visited during the wavepacket/trajectory propagation. The developed procedures allow to obtain solid and extended databases reducing as much as possible the computational cost, thanks to, e.g., specific tuning of the level of theory for different PES regions and/or direct calculation of only the needed components of vectorial quantities (like gradients or nonadiabatic couplings). The presented approaches were applied to three case studies (azobenzene, pyrene, visual rhodopsin), all requiring an accurate parameterisation but for different reasons. The resulting models and simulations allowed to elucidate the mechanism and time scale of the internal conversion, reproducing or even predicting new transient experiments. The general applicability of the developed protocols to systems with different peculiarities and the possibility to parameterise different types of dynamics on an equal footing (classical vs purely quantum) prove that the developed procedures are flexible enough to be tailored for each specific system, and pave the way for exact quantum dynamics with multiple degrees of freedom.

Analytics and optimization for emergency healthcare processes

This thesis deals with the analysis and management of emergency healthcare processes through the use of advanced analytics and optimization approaches. Emergency processes are among the most complex within healthcare. This is due to their non-elective nature and their high variability. This thesis is divided into two topics. The first one concerns the core of emergency healthcare processes, the emergency department (ED). In the second chapter, we describe the ED that is the case study. This is a real case study with data derived from a large ED located in northern Italy. In the next two chapters, we introduce two tools for supporting ED activities. The first one is a new type of analytics model. Its aim is to overcome the traditional methods of analyzing the activities provided in the ED by means of an algorithm that analyses the ED pathway (organized as event log) as a whole. The second tool is a decision-support system, which integrates a deep neural network for the prediction of patient pathways, and an online simulator to evaluate the evolution of the ED over time. Its purpose is to provide a set of solutions to prevent and solve the problem of the ED overcrowding. The second part of the thesis focuses on the COVID-19 pandemic emergency. In the fifth chapter, we describe a tool that was used by the Bologna local health authority in the first part of the pandemic. Its purpose is to analyze the clinical pathway of a patient and from this automatically assign them a state. Physicians used the state for routing the patients to the correct clinical pathways. The last chapter is dedicated to the description of a MIP model, which was used for the organization of the COVID-19 vaccination campaign in the city of Bologna, Italy.

Study and implementation of control strategies for polymerization processes assisted by atmospheric pressure plasma jets

In recent years, polymerization processes assisted by atmospheric pressure plasma jets (APPJs) have received increasing attention in numerous industrially relevant sectors since they allow to coat complex 3D substrates without requiring expensive vacuum systems. Therefore, advancing the comprehension of these processes has become a high priority topic of research. This PhD dissertation is focused on the study and the implementation of control strategies for a polymerization process assisted by an atmospheric pressure single electrode plasma jet. In the first section, a study of the validity of the Yasuda parameter (W/FM) as controlling parameter in the polymerization process assisted by the plasma jet and an aerosolized fluorinated silane precursor is proposed. The surface characterization of coatings deposited under different W/FM values reveals the presence of two very well-known deposition domains, thus suggesting the validity of W/FM as controlling parameter. In addition, the key role of the Yasuda parameter in the process is further demonstrated since coatings deposited under the same W/FM exhibit similar properties, regardless of how W/FM is obtained. In the second section, the development of a methodology for measuring the energy of reactions in the polymerization process assisted by the plasma jet and vaporized hexamethyldisiloxane is presented. The values of energy per precursor molecule are calculated through the identification and resolution of a proper equivalent electrical circuit. To validate the methodology, these energy values are correlated to the bond energies in the precursor molecule and to the properties of deposited thin films. It is shown that the precursor fragmentation in the discharge and the coating characteristics can be successfully explained according to the obtained values of energy per molecule. Through a detailed discussion of the limits and the potentialities of both the control strategies, this dissertation provides useful insights into the control of polymerization processes assisted by APPJs.

Characterization of pyrolysis and oxidation processes of biomaterials, biomasses and biofuels

The urgent need for alternative solutions mitigating the impacts of human activities on the environment has strongly opened new challenges and opportunities in view of the energy transition. Indeed, the automotive industry is going through a revolutionary moment in its quest to reduce its carbon footprint, with biofuels being one of the viable alternatives. The use of different classes of biofuels as fuel additives/standalone components has attracted the attention of many researchers. Despite their beneficial effects, biofuel’s combustion can also result in the production of undesirable pollutants, requiring complete characterization of the phenomena occurring during their production and consumption. Industrial scale-up of biomass conversion is challenging owing to the complexity of its chemistry and transport phenomena involved in the process. In this view, the role of solid-phase and gas-phase chemistry is paramount. Thus, this study is devoted to detailed analysis of physical-chemical phenomena characterizing biomass pyrolysis and biofuel oxidation. The pyrolysis mechanism has been represented by 20 reactions whereas, the gas-phase kinetic models; manually upgraded model (KiBo_MU) and automated model (KiBo_AG), comprises 141 species and 453 reactions, and 631 species and 28329 reactions, respectively. The accuracy of the kinetic models was tested against experimental data and the models captured experimental trends very well. While the development and validation of detailed kinetic mechanisms is the main deliverable of this project, the realized procedure integrating schematic classifications with methodologies for the identification of common decomposition pathways and intermediates represents an additional source of novelty. Besides, the fundamentally oriented nature of the adopted method allows the identification of most relevant reactions and species under the operating conditions different industrial applications, paving the way for reduced kinetic mechanisms. Ultimately, the resulting detailed mechanisms can be used to integrate with more complex fluid dynamics model to accurately reproduce the behavior of real systems and reactors.

Decoding complex flow phenomena via Dynamic Mode Decomposition

In this thesis, the viability of the Dynamic Mode Decomposition (DMD) as a technique to analyze and model complex dynamic real-world systems is presented. This method derives, directly from data, computationally efficient reduced-order models (ROMs) which can replace too onerous or unavailable high-fidelity physics-based models. Optimizations and extensions to the standard implementation of the methodology are proposed, investigating diverse case studies related to the decoding of complex flow phenomena. The flexibility of this data-driven technique allows its application to high-fidelity fluid dynamics simulations, as well as time series of real systems observations. The resulting ROMs are tested against two tasks: (i) reduction of the storage requirements of high-fidelity simulations or observations; (ii) interpolation and extrapolation of missing data. The capabilities of DMD can also be exploited to alleviate the cost of onerous studies that require many simulations, such as uncertainty quantification analysis, especially when dealing with complex high-dimensional systems. In this context, a novel approach to address parameter variability issues when modeling systems with space and time-variant response is proposed. Specifically, DMD is merged with another model-reduction technique, namely the Polynomial Chaos Expansion, for uncertainty quantification purposes. Useful guidelines for DMD deployment result from the study, together with the demonstration of its potential to ease diagnosis and scenario analysis when complex flow processes are involved.

Circumplex Model to analyze the impact of emotions on decision-making processes in innovation management

Group work allows participants to pool their thoughts and examine difficulties from several angles. In these settings, it is possible to attempt things that an individual could not achieve, combining a variety of abilities and knowledge to tackle more complicated and large-scale challenges. That’s why nowadays collaborative work is becoming more and more widespread to solve complex innovation dilemmas. Since innovation isn’t a tangible thing, most innovation teams used to take decisions based on performance KPIs such as forecasted engagement, projected profitability, investments required, cultural impacts etc. Have you ever wondered the reason why sometimes innovation group processes come out with decisions which are not the optimal meeting point of all the KPIs? Has this decision been influenced by other factors? Some researchers account part of this phenomenon to the emotions in group-based interaction between participants. I will develop a literature review that is split into three parts: first, I will consider some emotions theories from an individual perspective; secondly, a wider view of collective interactions theories will be provided; lastly, I will supply some recent collective interaction empirical studies. After the theoretical and empirical gaps have been tackled, the study will additionally move forward with a methodological point of view, about the Circumplex Model, which is the model I used to evaluate emotions in my research. This model has been applied to SUGAR project, which is the biggest design thinking academy worldwide.

Geochemistry Of Acid Mine Drainage From A Coal Mining Area And Processes Controlling Metal Attenuation In Stream Waters, Southern Brazil.

Acid drainage influence on the water and sediment quality was investigated in a coal mining area (southern Brazil). Mine drainage showed pH between 3.2 and 4.6 and elevated concentrations of sulfate, As and metals, of which, Fe, Mn and Zn exceeded the limits for the emission of effluents stated in the Brazilian legislation. Arsenic also exceeded the limit, but only slightly. Groundwater monitoring wells from active mines and tailings piles showed pH interval and chemical concentrations similar to those of mine drainage. However, the river and ground water samples of municipal public water supplies revealed a pH range from 7.2 to 7.5 and low chemical concentrations, although Cd concentration slightly exceeded the limit adopted by Brazilian legislation for groundwater. In general, surface waters showed large pH range (6 to 10.8), and changes caused by acid drainage in the chemical composition of these waters were not very significant. Locally, acid drainage seemed to have dissolved carbonate rocks present in the local stratigraphic sequence, attenuating the dispersion of metals and As. Stream sediments presented anomalies of these elements, which were strongly dependent on the proximity of tailings piles and abandoned mines. We found that precipitation processes in sediments and the dilution of dissolved phases were responsible for the attenuation of the concentrations of the metals and As in the acid drainage and river water mixing zone. In general, a larger influence of mining activities on the chemical composition of the surface waters and sediments was observed when enrichment factors in relation to regional background levels were used.

Construction Of A Manual Of Work Processes And Techniques From Centro De Dispensação De Medicamentos De Alto Custo (cedmac), Hospital De Clínicas, Unicamp.

The Centers for High Cost Medication (Centros de Medicação de Alto Custo, CEDMAC), Health Department, São Paulo were instituted by project in partnership with the Clinical Hospital of the Faculty of Medicine, USP, sponsored by the Foundation for Research Support of the State of São Paulo (Fundação de Amparo à Pesquisa do Estado de São Paulo, FAPESP) aimed at the formation of a statewide network for comprehensive care of patients referred for use of immunobiological agents in rheumatological diseases. The CEDMAC of Hospital de Clínicas, Universidade Estadual de Campinas (HC-Unicamp), implemented by the Division of Rheumatology, Faculty of Medical Sciences, identified the need for standardization of the multidisciplinary team conducts, in face of the specificity of care conducts, verifying the importance of describing, in manual format, their operational and technical processes. The aim of this study is to present the methodology applied to the elaboration of the CEDMAC/HC-Unicamp Manual as an institutional tool, with the aim of offering the best assistance and administrative quality. In the methodology for preparing the manuals at HC-Unicamp since 2008, the premise was to obtain a document that is participatory, multidisciplinary, focused on work processes integrated with institutional rules, with objective and didactic descriptions, in a standardized format and with electronic dissemination. The CEDMAC/HC-Unicamp Manual was elaborated in 10 months, with involvement of the entire multidisciplinary team, with 19 chapters on work processes and techniques, in addition to those concerning the organizational structure and its annexes. Published in the electronic portal of HC Manuals in July 2012 as an e-Book (ISBN 978-85-63274-17-5), the manual has been a valuable instrument in guiding professionals in healthcare, teaching and research activities.

Albumin Is Synthesized In Epididymis And Aggregates In A High Molecular Mass Glycoprotein Complex Involved In Sperm-egg Fertilization.

The epididymis has an important role in the maturation of sperm for fertilization, but little is known about the epididymal molecules involved in sperm modifications during this process. We have previously described the expression pattern for an antigen in epididymal epithelial cells that reacts with the monoclonal antibody (mAb) TRA 54. Immunohistochemical and immunoblotting analyses suggest that the epitope of the epididymal antigen probably involves a sugar moiety that is released into the epididymal lumen in an androgen-dependent manner and subsequently binds to luminal sperm. Using column chromatography, SDS-PAGE with in situ digestion and mass spectrometry, we have identified the protein recognized by mAb TRA 54 in mouse epididymal epithelial cells. The ∼65 kDa protein is part of a high molecular mass complex (∼260 kDa) that is also present in the sperm acrosomal vesicle and is completely released after the acrosomal reaction. The amino acid sequence of the protein corresponded to that of albumin. Immunoprecipitates with anti-albumin antibody contained the antigen recognized by mAb TRA 54, indicating that the epididymal molecule recognized by mAb TRA 54 is albumin. RT-PCR detected albumin mRNA in the epididymis and fertilization assays in vitro showed that the glycoprotein complex containing albumin was involved in the ability of sperm to recognize and penetrate the egg zona pellucida. Together, these results indicate that epididymal-derived albumin participates in the formation of a high molecular mass glycoprotein complex that has an important role in egg fertilization.

Interplay Between Cell Growth And Cell Cycle In Plants.

The growth of organs and whole plants depends on both cell growth and cell-cycle progression, but the interaction between both processes is poorly understood. In plants, the balance between growth and cell-cycle progression requires coordinated regulation of four different processes: macromolecular synthesis (cytoplasmic growth), turgor-driven cell-wall extension, mitotic cycle, and endocycle. Potential feedbacks between these processes include a cell-size checkpoint operating before DNA synthesis and a link between DNA contents and maximum cell size. In addition, key intercellular signals and growth regulatory genes appear to target at the same time cell-cycle and cell-growth functions. For example, auxin, gibberellin, and brassinosteroid all have parallel links to cell-cycle progression (through S-phase Cyclin D-CDK and the anaphase-promoting complex) and cell-wall functions (through cell-wall extensibility or microtubule dynamics). Another intercellular signal mediated by microtubule dynamics is the mechanical stress caused by growth of interconnected cells. Superimposed on developmental controls, sugar signalling through the TOR pathway has recently emerged as a central control point linking cytoplasmic growth, cell-cycle and cell-wall functions. Recent progress in quantitative imaging and computational modelling will facilitate analysis of the multiple interconnections between plant cell growth and cell cycle and ultimately will be required for the predictive manipulation of plant growth.

Effects Of Partial Inhibition Of Respiratory Complex I On H2o 2 Production By Isolated Brain Mitochondria In Different Respiratory States.

The aim of this work was to characterize the effects of partial inhibition of respiratory complex I by rotenone on H2O2 production by isolated rat brain mitochondria in different respiratory states. Flow cytometric analysis of membrane potential in isolated mitochondria indicated that rotenone leads to uniform respiratory inhibition when added to a suspension of mitochondria. When mitochondria were incubated in the presence of a low concentration of rotenone (10 nm) and NADH-linked substrates, oxygen consumption was reduced from 45.9 ± 1.0 to 26.4 ± 2.6 nmol O2 mg(-1) min(-1) and from 7.8 ± 0.3 to 6.3 ± 0.3 nmol O2 mg(-1) min(-1) in respiratory states 3 (ADP-stimulated respiration) and 4 (resting respiration), respectively. Under these conditions, mitochondrial H2O2 production was stimulated from 12.2 ± 1.1 to 21.0 ± 1.2 pmol H2O2 mg(-1) min(-1) and 56.5 ± 4.7 to 95.0 ± 11.1 pmol H2O2 mg(-1) min(-1) in respiratory states 3 and 4, respectively. Similar results were observed when comparing mitochondrial preparations enriched with synaptic or nonsynaptic mitochondria or when 1-methyl-4-phenylpyridinium ion (MPP(+)) was used as a respiratory complex I inhibitor. Rotenone-stimulated H2O2 production in respiratory states 3 and 4 was associated with a high reduction state of endogenous nicotinamide nucleotides. In succinate-supported mitochondrial respiration, where most of the mitochondrial H2O2 production relies on electron backflow from complex II to complex I, low rotenone concentrations inhibited H2O2 production. Rotenone had no effect on mitochondrial elimination of micromolar concentrations of H2O2. The present results support the conclusion that partial complex I inhibition may result in mitochondrial energy crisis and oxidative stress, the former being predominant under oxidative phosphorylation and the latter under resting respiration conditions.

Agrin And Perlecan Mediate Tumorigenic Processes In Oral Squamous Cell Carcinoma.

Oral squamous cell carcinoma is the most common type of cancer in the oral cavity, representing more than 90% of all oral cancers. The characterization of altered molecules in oral cancer is essential to understand molecular mechanisms underlying tumor progression as well as to contribute to cancer biomarker and therapeutic target discovery. Proteoglycans are key molecular effectors of cell surface and pericellular microenvironments, performing multiple functions in cancer. Two of the major basement membrane proteoglycans, agrin and perlecan, were investigated in this study regarding their role in oral cancer. Using real time quantitative PCR (qRT-PCR), we showed that agrin and perlecan are highly expressed in oral squamous cell carcinoma. Interestingly, cell lines originated from distinct sites showed different expression of agrin and perlecan. Enzymatically targeting chondroitin sulfate modification by chondroitinase, oral squamous carcinoma cell line had a reduced ability to adhere to extracellular matrix proteins and increased sensibility to cisplatin. Additionally, knockdown of agrin and perlecan promoted a decrease on cell migration and adhesion, and on resistance of cells to cisplatin. Our study showed, for the first time, a negative regulation on oral cancer-associated events by either targeting chondroitin sulfate content or agrin and perlecan levels.

A New Platinum Complex With Tryptophan: Synthesis, Structural Characterization, Dft Studies And Biological Assays In Vitro Over Human Tumorigenic Cells.

A new platinum(II) complex with the amino acid L-tryptophan (trp), named Pt-trp, was synthesized and characterized. Elemental, thermogravimetric and ESI-QTOF mass spectrometric analyses led to the composition [Pt(C11H11N2O2)2]⋅6H2O. Infrared spectroscopic data indicate the coordination of trp to Pt(II) through the oxygen of the carboxylate group and also through the nitrogen atom of the amino group. The (13)C CP/MAS NMR spectroscopic data confirm coordination through the oxygen atom of the carboxylate group, while the (15)N CP/MAS NMR data confirm coordination of the nitrogen of the NH2 group to the metal. Density functional theory (DFT) studies were applied to evaluate the cis and trans coordination modes of trp to platinum(II). The trans isomer was shown to be energetically more stable than the cis one. The Pt-trp complex was evaluated as a cytotoxic agent against SK-Mel 103 (human melanoma) and Panc-1 (human pancreatic carcinoma) cell lines. The complex was shown to be cytotoxic over the considered cells.

Encephalization And Diversification Of The Cranial Base In Platyrrhine Primates.

The cranial base, composed of the midline and lateral basicranium, is a structurally important region of the skull associated with several key traits, which has been extensively studied in anthropology and primatology. In particular, most studies have focused on the association between midline cranial base flexion and relative brain size, or encephalization. However, variation in lateral basicranial morphology has been studied less thoroughly. Platyrrhines are a group of primates that experienced a major evolutionary radiation accompanied by extensive morphological diversification in Central and South America over a large temporal scale. Previous studies have also suggested that they underwent several evolutionarily independent processes of encephalization. Given these characteristics, platyrrhines present an excellent opportunity to study, on a large phylogenetic scale, the morphological correlates of primate diversification in brain size. In this study we explore the pattern of variation in basicranial morphology and its relationship with phylogenetic branching and with encephalization in platyrrhines. We quantify variation in the 3D shape of the midline and lateral basicranium and endocranial volumes in a large sample of platyrrhine species, employing high-resolution CT-scans and geometric morphometric techniques. We investigate the relationship between basicranial shape and encephalization using phylogenetic regression methods and calculate a measure of phylogenetic signal in the datasets. The results showed that phylogenetic structure is the most important dimension for understanding platyrrhine cranial base diversification; only Aotus species do not show concordance with our molecular phylogeny. Encephalization was only correlated with midline basicranial flexion, and species that exhibit convergence in their relative brain size do not display convergence in lateral basicranial shape. The evolution of basicranial variation in primates is probably more complex than previously believed, and understanding it will require further studies exploring the complex interactions between encephalization, brain shape, cranial base morphology, and ecological dimensions acting along the species divergence process.