Hydrotalcite intercalated siRNA:computational characterization of the interlayer environment

Using molecular dynamics (MD) simulations, we explore the structural and dynamical properties of siRNA within the intercalated environment of a Mg:Al 2:1 Layered Double Hydroxide (LDH) nanoparticle. An ab initio force field (Condensed-phase Optimized Molecular Potentials for Atomistic Simulation Studies: COMPASS) is used for the MD simulations of the hybrid organic-inorganic systems. The structure, arrangement, mobility, close contacts and hydrogen bonds associated with the intercalated RNA are examined and contrasted with those of the isolated RNA. Computed powder X-ray diffraction patterns are also compared with related LDH-DNA experiments. As a method of probing whether the intercalated environment approximates the crystalline or rather the aqueous state, we explore the stability of the principle parameters (e.g., the major groove width) that differentiate both A- and A'- crystalline forms of siRNA and contrast this with recent findings for the same siRNA simulated in water. We find the crystalline forms remain structurally distinct when intercalated, whereas this is not the case in water. Implications for the stability of hybrid LDH-RNA systems are discussed.

Computational characterization of carbazole-benzonitrile derivatives for applications in Organic Light Emitting Diodes

The technology of Organic Light-Emitting Diodes has reached such a high level of reliability that it can be used in various applications. The required light emission efficiency can be achieved by transforming the triplet excitons into singlet states through Reverse InterSystem Crossing (RISC), which is the main process of a general mechanism called thermally activated delayed fluorescence (TADF). In this thesis, we theoretically analyzed two carbazole-benzonitrile (donor-acceptor) derivatives, 2,5-di(9H-carbazol-9-yl)benzonitrile (p-2CzBN) and 2,3,4,5,6-penta(9H-carbazol-9-yl)benzonitrile (5CzBN), and addressed the problem of how donor-acceptor (D-A) or donor-acceptor-donor (D-A-D) flexible molecular architectures influence the nature of the excited states and the emission intensity. Furthermore, we analyzed the RISC rates as a function of the conformation of the carbazole lateral groups, considering the first electronic states, S0, S1, T1 and T2, involved in TADF process. The two prototype molecules, p-2CzBN and 5CzBN, have a similar energy gap between the first singlet and triplet states (∆EST, a key parameter in the RISC rate), but different TADF performances. Therefore, other parameters must be considered to explain their different behavior. The oscillator strength of p-2CzBN, never tested as emitter in OLEDs, is similar to that of 5CzBN, which is an active TADF molecule. We also note that the presence of a second T2 triplet state, lower in energy than S1 only in 5CzBN, and the reorganization energies, associated with RISC processes involving T1 and T2, are important factors in differentiating the rates in p-2CzBN and 5CzBN. For p-2CzBN, the RISC rate from T2 to S1 is surprisingly higher than that from T1 to S1, in disagreement with El-Sayed rules, due to a large reorganization energy associated to the T1 to S1, process; while the contrary occurs for 5CzBN. These insights are important for designing new TADF emitters based on the benzo-carbazole architecture.

EPIPOX:immunoinformatic characterization of the shared T-cell epitome between variola virus and related pathogenic orthopoxviruses

Concerns that variola viruses might be used as bioweapons have renewed the interest in developing new and safer smallpox vaccines. Variola virus genomes are now widely available, allowing computational characterization of the entire T-cell epitome and the use of such information to develop safe and yet effective vaccines. To this end, we identified 124 proteins shared between various species of pathogenic orthopoxviruses including variola minor and major, monkeypox, cowpox, and vaccinia viruses, and we targeted them for T-cell epitope prediction. We recognized 8,106, and 8,483 unique class I and class II MHC-restricted T-cell epitopes that are shared by all mentioned orthopoxviruses. Subsequently, we developed an immunological resource, EPIPOX, upon the predicted T-cell epitome. EPIPOX is freely available online and it has been designed to facilitate reverse vaccinology. Thus, EPIPOX includes key epitope-focused protein annotations: time point expression, presence of leader and transmembrane signals, and known location on outer membrane structures of the infective viruses. These features can be used to select specific T-cell epitopes suitable for experimental validation restricted by single MHC alleles, as combinations thereof, or by MHC supertypes.

Assembling a xylanase-lichenase chimera through all-atom molecular dynamics simulations

Multifunctional enzyme engineering can improve enzyme cocktails for emerging biofuel technology. Molecular dynamics through structure-based models (SB) is an effective tool for assessing the tridimensional arrangement of chimeric enzymes as well as for inferring the functional practicability before experimental validation. This study describes the computational design of a bifunctional xylanase-lichenase chimera (XylLich) using the xynA and bglS genes from Bacillus subtilis. In silico analysis of the average solvent accessible surface area (SAS) and the root mean square fluctuation (RMSF) predicted a fully functional chimera, with minor fluctuations and variations along the polypeptide chains. Afterwards, the chimeric enzyme was built by fusing the xynA and bglS genes. XylLich was evaluated through small-angle X-ray scattering (SAXS) experiments, resulting in scattering curves with a very accurate fit to the theoretical protein model. The chimera preserved the biochemical characteristics of the parental enzymes, with the exception of a slight variation in the temperature of operation and the catalytic efficiency (k cat/Km). The absence of substantial shifts in the catalytic mode of operation was also verified. Furthermore, the production of chimeric enzymes could be more profitable than producing a single enzyme separately, based on comparing the recombinant protein production yield and the hydrolytic activity achieved for XylLich with that of the parental enzymes. © 2013 Elsevier B.V. All rights reserved.

A biomimetic piezoelectric pump: Computational and experimental characterization

Flow pumps have been developed for classical applications in Engineering, and are important instruments in areas such as Biology and Medicine. Among applications for this kind of device we notice blood pump and chemical reagents dosage in Bioengineering. Furthermore, they have recently emerged as a viable thermal management solution for cooling applications in small-scale electronic devices. This work presents the performance study of a novel principle of a piezoelectric flow pump which is based oil the use of a bimorph piezoelectric actuator inserted in fluid (water). Piezoelectric actuators have some advantages over classical devices, such as lower noise generation and ease of miniaturization. The main objective is the characterization of this piezoelectric pump principle through computational simulations (using finite element software), and experimental tests through a manufactured prototype. Computational data, Such as flow rate and pressure curves, have also been compared with experimental results for validation purposes. (C) 2009 Elsevier B.V. All rights reserved.

Experimental and computational study on the synthesis and characterization of self-assembling meso/macroporous materials in highly concentrated emulsions

Report for the scientific sojourn carried out at Massachusetts General Hospital Cancer Center-Harvard Medical School, Estats Units, from 2010 to 2011. The project aims to study the aggregation behavior of amphiphilic molecules in the continuous phase of highly concentrated emulsions, which can be used as templates for the synthesis of meso/macroporous materials. At this stage of the project, we have investigated the self-assembly of diblock and triblock surfactants under the effect of a confined geometry being surrounded by the droplets of the dispersed phase. These droplets limit the growth of the aggregates, deeply modify their orientation and hence alter their spatial arrangement as compared to the self-assembly taking place far enough from any boundary surface, that is in the bulk. By performing Monte Carlo simulations, we have showed that the interface between the dispersed and continuous phases as well as its shape has a significant impact on the structural order of the resulting aggregates and hence on the potential applications of highly concentrated emulsions as reaction media, drug delivery systems, or templates for meso/macroporous materials. Due to the combined effect of symmetry breaking and morphological frustration, very intriguing structures, such as square columnar liquid crystals, twisted X-shaped aggregates, and helical phases of cylindrical aggregates, never observed in the bulk for the same model surfactant, have been found. The presence of other more conventional structures, such as micelles and cubic and hexagonal liquid crystals, formed at low and high amphiphilic concentrations, respectively, further enhance the interest on this already rich aggregation behavior.

Synthesis, characterization and computational studies of (E)-2-{[(2-aminopyridin-3-yl)imino]-methyl}-4,6-di-tert-butylphenol

(E)-2-{[(2-Aminopyridin-3-yl)imino]-methyl}-4,6-di-tert-butyl-phenol ( 3: ), a ligand containing an intramolecular hydrogen bond, was prepared according to a previous literature report, with modifications, and was characterized by UV-vis, FTIR, ¹H-NMR, 13C-NMR, HHCOSY, TOCSY and cyclic voltammetry. Computational analyses at the level of DFT and TD-DFT were performed to study its electronic and molecular structures. The results of these analyses elucidated the behaviors of the UV-vis and electrochemical data. Analysis of the transitions in the computed spectrum showed that the most important band is primarily composed of a HOMO→LUMO transition, designated as an intraligand (IL) charge transfer.

Computational analysis and physico-chemical characterization of an inclusion compound between praziquantel and methyl-beta-cyclodextrin for use as an alternative in the treatment of schistosomiasis

Schistosomiasis is still an endemic disease in many regions, with 250 million people infected with Schistosoma and about 500,000 deaths per year. Praziquantel (PZQ) is the drug of choice for schistosomiasis treatment, however it is classified as Class II in the Biopharmaceutics Classification System, as its low solubility hinders its performance in biological systems. The use of cyclodextrins is a useful tool to increase the solubility and bioavailability of drugs. The aim of this work was to prepare an inclusion compound of PZQ and methyl-beta-cyclodextrin (MeCD), perform its physico-chemical characterization, and explore its in vitro cytotoxicity. SEM showed a change of the morphological characteristics of PZQ:MeCD crystals, and IR data supported this finding, with changes after interaction with MeCD including effects on the C-H of the aromatic ring, observed at 758 cm(-1). Differential scanning calorimetry measurements revealed that complexation occurred in a 1:1 molar ratio, as evidenced by the lack of a PZQ transition temperature after inclusion into the MeCD cavity. In solution, the PZQ UV spectrum profile in the presence of MeCD was comparable to the PZQ spectrum in a hydrophobic solvent. Phase solubility diagrams showed that there was a 5.5-fold increase in PZQ solubility, and were indicative of a type A(L) isotherm, that was used to determine an association constant (K(a)) of 140.8 M(-1). No cytotoxicity of the PZQ:MeCD inclusion compound was observed in tests using 3T3 cells. The results suggest that the association of PZQ with MeCD could be a good alternative for the treatment of schistosomiasis.

Computational and experimental characterization of a low-cost piezoelectric valveless diaphragm pump

Flow pumps act as important devices in areas such as Bioengineering, Medicine, and Pharmacy, among other areas of Engineering, mainly for delivering liquids or gases at small-scale and precision flow rate quantities. Principles for pumping fluids based on piezoelectric actuators have been widely studied, since they allow the construction of pump systems for displacement of small fluid volumes with low power consumption. This work studies valveless piezoelectric diaphragm pumps for flow generation, which uses a piezoelectric ceramic (PZT) as actuator to move a membrane (diaphragm) up and down as a piston. The direction of the flow is guaranteed by valveless configuration based on a nozzle-diffuser system that privileges the flow in just one pumping direction. Most research efforts on development of valveless flow pump deal either with computational simulations based on simplified models or with simplified physical approaches based on analytical models. The main objective of this work is the study of a methodology to develop a low-cost valveless piezoelectric diaphragm flow pump using computational simulations, parametric study, prototype manufacturing, and experimental characterization. The parametric study has shown that the eccentricity of PZT layer and metal layer plays a key role in the performance of the pump.

Integration of computational models and experimental characterization to study internal frost damage in cementitious materials

The objective of this doctoral research is to investigate the internal frost damage due to crystallization pore pressure in porous cement-based materials by developing computational and experimental characterization tools. As an essential component of the U.S. infrastructure system, the durability of concrete has significant impact on maintenance costs. In cold climates, freeze-thaw damage is a major issue affecting the durability of concrete. The deleterious effects of the freeze-thaw cycle depend on the microscale characteristics of concrete such as the pore sizes and the pore distribution, as well as the environmental conditions. Recent theories attribute internal frost damage of concrete is caused by crystallization pore pressure in the cold environment. The pore structures have significant impact on freeze-thaw durability of cement/concrete samples. The scanning electron microscope (SEM) and transmission X-ray microscopy (TXM) techniques were applied to characterize freeze-thaw damage within pore structure. In the microscale pore system, the crystallization pressures at sub-cooling temperatures were calculated using interface energy balance with thermodynamic analysis. The multi-phase Extended Finite Element Modeling (XFEM) and bilinear Cohesive Zone Modeling (CZM) were developed to simulate the internal frost damage of heterogeneous cement-based material samples. The fracture simulation with these two techniques were validated by comparing the predicted fracture behavior with the captured damage from compact tension (CT) and single-edge notched beam (SEB) bending tests. The study applied the developed computational tools to simulate the internal frost damage caused by ice crystallization with the two dimensional (2-D) SEM and three dimensional (3-D) reconstructed SEM and TXM digital samples. The pore pressure calculated from thermodynamic analysis was input for model simulation. The 2-D and 3-D bilinear CZM predicted the crack initiation and propagation within cement paste microstructure. The favorably predicted crack paths in concrete/cement samples indicate the developed bilinear CZM techniques have the ability to capture crack nucleation and propagation in cement-based material samples with multiphase and associated interface. By comparing the computational prediction with the actual damaged samples, it also indicates that the ice crystallization pressure is the main mechanism for the internal frost damage in cementitious materials.

Computational analysis and physico-chemical characterization of an inclusion compound between praziquantel and methyl-beta-cyclodextrin for use as an alternative in the treatment of schistosomiasis

Schistosomiasis is still an endemic disease in many regions, with 250 million people infected with Schistosoma and about 500,000 deaths per year. Praziquantel (PZQ) is the drug of choice for schistosomiasis treatment, however it is classified as Class II in the Biopharmaceutics Classification System, as its low solubility hinders its performance in biological systems. The use of cyclodextrins is a useful tool to increase the solubility and bioavailability of drugs. The aim of this work was to prepare an inclusion compound of PZQ and methyl-beta-cyclodextrin (MeCD), perform its physico-chemical characterization, and explore its in vitro cytotoxicity. SEM showed a change of the morphological characteristics of PZQ:MeCD crystals, and IR data supported this finding, with changes after interaction with MeCD including effects on the C-H of the aromatic ring, observed at 758 cm(-1). Differential scanning calorimetry measurements revealed that complexation occurred in a 1:1 molar ratio, as evidenced by the lack of a PZQ transition temperature after inclusion into the MeCD cavity. In solution, the PZQ UV spectrum profile in the presence of MeCD was comparable to the PZQ spectrum in a hydrophobic solvent. Phase solubility diagrams showed that there was a 5.5-fold increase in PZQ solubility, and were indicative of a type A(L) isotherm, that was used to determine an association constant (K(a)) of 140.8 M(-1). No cytotoxicity of the PZQ:MeCD inclusion compound was observed in tests using 3T3 cells. The results suggest that the association of PZQ with MeCD could be a good alternative for the treatment of schistosomiasis.

Computational resources for structural and metagenomic characterization of functions in bacteria and bacterial communities. Antimicrobial resistance, pathways for xenobiotic degradation and relationship between gut microbiome and ageing.

Prokaryotic organisms are one of the most successful forms of life, they are present in all known ecosystems. The deluge diversity of bacteria reflects their ability to colonise every environment. Also, human beings host trillions of microorganisms in their body districts, including skin, mucosae, and gut. This symbiosis is active for all other terrestrial and marine animals, as well as plants. With the term holobiont we refer, with a single word, to the systems including both the host and its symbiotic microbial species. The coevolution of bacteria within their ecological niches reflects the adaptation of both host and guest species, and it is shaped by complex interactions that are pivotal for determining the host state. Nowadays, thanks to the current sequencing technologies, Next Generation Sequencing, we have unprecedented tools for investigating the bacterial life by studying the prokaryotic genome sequences. NGS revolution has been sustained by the advancements in computational performance, in terms of speed, storage capacity, algorithm development and hardware costs decreasing following the Moore’s Law. Bioinformaticians and computational biologists design and implement ad hoc tools able to analyse high-throughput data and extract valuable biological information. Metagenomics requires the integration of life and computational sciences and it is uncovering the deluge diversity of the bacterial world. The present thesis work focuses mainly on the analysis of prokaryotic genomes under different aspects. Being supervised by two groups at the University of Bologna, the Biocomputing group and the group of Microbial Ecology of Health, I investigated three different topics: i) antimicrobial resistance, particularly with respect to missense point mutations involved in the resistant phenotype, ii) bacterial mechanisms involved in xenobiotic degradation via the computational analysis of metagenomic samples, and iii) the variation of the human gut microbiota through ageing, in elderly and longevous individuals.

Spectroscopic characterization of schiff base-copper complexes immobilized in smectite clays

Herein, the immobilization of some Schiff base-copper(II) complexes in smectite clays is described as a strategy for the heterogenization of homogeneous catalysts. The obtained materials were characterized by spectroscopic techniques, mostly UV/Vis, EPR, XANES and luminescence spectroscopy. SWy-2 and synthetic Laponite clays were used for the immobilization of two different complexes that have previously shown catalytic activity in the dismutation of superoxide radicals, and disproportionation of hydrogen peroxide. The obtained results indicated the occurrence of an intriguing intramolecular redox process involving copper and the imine ligand at the surface of the clays. These studies are supported by computational calculations.

Finite element computational modeling of externally bonded CFRP composites flexural behavior in RC beams

This paper focuses on the flexural behavior of RC beams externally strengthened with Carbon Fiber Reinforced Polymers (CFRP) fabric. A non-linear finite element (FE) analysis strategy is proposed to support the beam flexural behavior experimental analysis. A development system (QUEBRA2D/FEMOOP programs) has been used to accomplish the numerical simulation. Appropriate constitutive models for concrete, rebars, CFRP and bond-slip interfaces have been implemented and adjusted to represent the composite system behavior. Interface and truss finite elements have been implemented (discrete and embedded approaches) for the numerical representation of rebars, interfaces and composites.

Design and Characterization of a Biomimetic Piezoelectric Pump Inspired on Group Fish Swimming Effect

Flow pumps are important tools in several engineering areas, such as in the fields of bioengineering and thermal management solutions for electronic devices. Nowadays, many of the new flow pump principles are based on the use of piezoelectric actuators, which present some advantages such as miniaturization potential and lower noise generation. In previous work, authors presented a study of a novel pump configuration based on placing an oscillating bimorph piezoelectric actuator in water to generate flow. It was concluded that this oscillatory behavior (such as fish swimming) yields vortex interaction, generating flow rate due to the action and reaction principle. Thus, following this idea the objective of this work is to explore this oscillatory principle by studying the interaction among generated vortex from two bimorph piezoelectric actuators oscillating inside the same pump channel, which is similar to the interaction of vortex generated by frontal fish and posterior ones when they swim together in a group formation. It is shown that parallel-series configurations of bimorph piezoelectric actuators inside the same pump channel provide higher flow rates and pressure for liquid pumping than simple parallel-series arrangements of corresponding single piezoelectric pumps, respectively. The scope of this work includes structural simulations of bimorph piezoelectric actuators, fluid flow simulations, and prototype construction for result validation.