Dissertations / Theses on the topic 'Macromolecules'

In this thesis, the structure and stability of globular proteins adsorbed onto nanometer-sized hydrophilic silica particles were investigated using differential scanning calorimetry (DSC), hydrogen/deuterium exchange (HDX), and mass spectrometry (MS). The adsorption process itself was characterized with fluorescence and absorption spectroscopy and surface plasmon resonance (SPR). The combination of these methods offered a unique insight into adsorption-induced changes within proteins related to their adsorption characteristics. DSC contributed with thermodynamic information on the overall structural stability within the protein population. HDX in combination with MS contributed information on the structure and stability of adsorbed proteins with focus on changes within the secondary structure elements. In order to increase the structural resolution in this part of the investigation, proteolysis was performed prior to the MS analyzing step. Knowledge on the protein adsorption process was utilized in a practical approach called ligand fishing. In this approach, SPR was used to monitor the chip-based affinity purification of a protein with MS used for protein identification.

Adsorption isotherms revealed that electrostatic interactions play an important role in the adsorption of proteins to hydrophilic surfaces. DSC investigation revealed that the thermal stability of proteins reduces with increasing electrostatic attraction between the protein and the surface and that this effect diminishes at higher surface coverage. The mass-increase due to exchange between protein hydrogen atoms and deuterium atoms in solution was investigated as a function of time. This gave insight into adsorption-induced changes in the structural stability of proteins. By combining DSC and HDX-MS, it was possible to differentiate between adsorption-induced changes in the secondary and tertiary structure. Additionally, if limited proteolysis was performed, the investigations gave insight into the orientation and protein segment specific changes in the stability of proteins adsorbed to silica surfaces. The adsorption of proteins to silica particles also provided the basis for a new experimental design that allows handling of minute amounts of proteins in a ligand fishing application, as used in the field of functional proteomics.

Orientador: Gisele Zoccal Mingoti
Banca: Fernanda da Cruz Landim
Banca: Joaquim Mansano Garcia
Resumo: O objetivo desse estudo foi avaliar os efeitos da suplementação do meio com diferentes fontes de macromoléculas, com bloqueadores da meiose e com antioxidantes durante o transporte de oócitos bovinos por 6 horas sobre: 1) progressão da maturação nuclear; 2) maturação citoplasmática e 3) competência no desenvolvimento e criotolerância dos embriões produzidos. Para tanto, o meio de transporte de oócitos foi suplementado com bloqueadores da meiose (forscolina e IBMX; Experimento 1) ou com diferentes tipos de macromoléculas (SFB ou BSA; Experimento 2), sendo que estes tratamentos ainda receberam ou não a suplementação com antioxidantes (mistura de cisteína, cisteamina e catalase). Os oócitos foram incubados em incubadora portátil (Minitub®) para simulação de transporte. Posteriormente, foram submetidos à maturação in vitro (MIV) em incubadora a 5% de CO2 em ar até completar 24h e, em seguida, foram fecundados e os prováveis zigotos foram cultivados in vitro durante 7 dias. Foi feito um grupo controle adicional no experimento I: MIV em incubadora com 10% de SFB por 24h. No experimento II foram feitos dois grupos controle adicionais MIV em incubadora com 10% de SFB por 24h sem e com antioxidantes (cisteína, cisteamina e catalase). Nos experimentos 1 e 2 foi avaliada a cinética da maturação nuclear e a maturação citoplasmática (através do posicionamento de mitocôndrias, do potencial de membrana mitocondrial e do conteúdo intracelular de espécies reativas do oxigênio) após o transpor... (Resumo completo, clicar acesso eletrônico abaixo)
Abstract: The objective of this study was to evaluate the effects of supplementation of the medium with different sources of macromolecules with blockers of meiosis and antioxidants during transport of bovine oocytes for 6 hours on: 1) progression of nuclear maturation; 2) cytoplasmic maturation and 3) competence in the development and cryotolerance of embryos produced. Therefore, the medium of transport oocytes was supplemented with blocking of meiosis (forskolin and IBMX; Experiment 1) or with different types of macromolecules (FCS or BSA; Experiment 2), and these treatments yet received or not antioxidant supplementation (mixture of cysteine, cysteamine and catalase). Oocytes were incubated in a portable incubator (Minitub®) for transport simulation. Posteriorly were submitted in vitro maturation (IVM) in incubator at 5% CO2 in air until to complete 24 hours and then were fertilized and presumptive zygotes were cultured in vitro for 7 days. Has been made an additional control group in the experiment I: MIV incubator with 10% FCS for 24 hours (Control). In the second experiment were performed two additional control groups: IVM incubator with 10% FCS for 24 hours (Control); and IVM in an incubator with 10% FCS and antioxidants (cysteine, cysteamine and catalase) for 24 hours (Contr+Atx). In Experiments 1 and 2 were evaluated after nuclear maturation kinetics and cytoplasmic maturation (made by positioning mitochondria, the mitochondrial membrane potential and intracellular content of ... (Complete abstract click electronic access below)
Mestre

All living organisms utilize thousands of molecular building blocks to perform mechanical tasks. These building blocks are mostly proteins, and their mechanical properties define the way they can be utilized by the cell. The spectrum ranges from rope like structures that give hold and stability to our bodies to microscopic engines helping us to perform or sense mechanical work. An increasing number of biological processes are revealed to be driven by force and well-directed distribution of strain is the very base of many of these mechanisms. We need to be able to observe the distribution of strain within bio-molecules if we want to gain detailed insight into the function of these highly complex nano-machines. Only by theoretical understanding and prediction of mechanical processes on the molecular level will we be able to rationally tailor proteins to mimic specific biological functions. This thesis aims at understanding the molecular mechanics of a wide range of biological molecules, such as the muscle protein titin or silk fibers. We introduce Force Distribution Analysis (FDA), a new approach to directly study the forces driving molecular processes, instead of indirectly observing them by means of coordinate changes.

In this thesis, new biomaterials were developed by incorporating surface modifying macromolecules (SMMs) that enriched the surface with a fluoro-chemistry. The SMMs contained a linear polyurethane as the prepolymer component and the prepolymer was end-capped by a fluorinated alcohol. The SMM materials and the blend of these SMMs with the polyester-urea-urethane base polymer were characterized with respect to their bulk and the surface properties, response to their biodegradation in the presence of enzyme and their fibrinogen adsorption characteristics. The SMMs were found to have selectively migrated to the surface of the polymer mixtures as expected. The bulk thermal (e.g. glass transition temperature) were found to be unaltered for polyurethane samples containing up to 5% SMM. The "fluorine tail" of the SMMs allowed the substrate surfaces to achieve very low surface wettability. Contact angle values (water/air) for the new materials were as high as $116\sp\circ,$ which is higher than that of $\rm Teflon\sp{R}.$ Measurements of fibrinogen adsorption, an indication of the tendency of surfaces to stimulate thrombosis, showed that the SMM blended materials significantly reduced fibrinogen adsorption. A biodegradation test of a polyether-urea-urethane containing one of the SMMs optimized for the polyester-urea-urethane showed that the SMM was unable to inhibit degradation of the polyether-urea-urethane. This suggested that the SMM was not universally effective and that the microstructure of, and the interaction between, SMMs and the base polymer were also important factors to be considered during the investigations of the stability of polyurethanes. (Abstract shortened by UMI.)

A computer model for simulating experiments done on surface organelles(so called pili) on the Escherichia Coli bacteria have been developedand implemented. The objective of the computer simulation wasto mimic the results of experiments done with optical tweezers and to displaya graphical, three dimensional, representation of these experiments.The experiments measured the force response to elongation of pili.This force response can be divided into three regions of elongation, regionI, II and III, each with different properties. Region I is characterized by aconstant increase in force, in region II the pilus is unfolded under constantforce, and in region III the force versus elongation curve assumes a nontrivialshape with increasing force. The pili are also able to retract to itsoriginal length giving a similar force response curve. The computer modelshould be able to handle all these properties. The developed model couldhandle elongation in region I and II. In region III, the force response givenby the simulation differed from the one given by the experiments.

This Thesis investigates computationally the behaviour of two novel microporous materials,organic molecules of intrinsic microporosity (OMIMs) and polymers of intrinsic microporosity(PIMs). OMIMs and PIMs are organic amorphous materials, which achieve microporosityby packing inefficiently. The design of amorphous materials is challenging because their self-assembly process is not known. Predictive molecular simulations can help in recognising thefeatures that affect the properties of these materials, and guiding in the design of new structures with desired performances. OMIMs are highly concave shaped molecules, consisting of a core and a series of termini, which provide the geometry and the general chemical environment of these structures, respectively. PIMs are polymers consisting of fundamental units such as stiff segments and contortionsites, which form either linear or network like porous structures. While chronologically olderthan OMIMs, they share with them a common design philosophy. This Thesis is presented in alternative format, and the results, consisting of five journal articles,can be divided into three main parts. The first part focuses on recognising a reliable method to generate representative models ofOMIMs. Different computational protocols and molecular mechanics descriptions were investigated; the development of the utilised simulation protocol was based on comparison of several simulation methods and force fields to experimental wide angle X-ray scattering (WAXS) patterns. Our work suggests that OMIMs can be described successfully by both PCFF and UFF; the final packed material can be generated using a 21-step compression-decompression molecular dynamics protocol, previously developed to generate virtual model of PIMs. The examination of the simulated structures has provided a deeper understanding of the features that affect the packing behaviour of this class of materials, suggesting that OMIMs have a greater microporosity when the molecules are the most shape-persistent, which required rigid structures and bulky end groups. The adsorption behaviour described by different generic force fields (Dreiding, OPLS and UFF) was also investigated to guide on the selection of the solid-fluid interactions when modelling OMIMs, for future comparison with experimental data. Our results suggest that very strong interactions between argon adsorbate and OMIM-based framework are described by UFF, while the weakest adsorbent is obtained using OPLS force field. The second part of the research focuses on assessing the effect that different termini’s chemistry and bulkiness have over the packing behaviour, adsorption properties and solubility of the OMIMs. The microporous frameworks generated by two selected families of cruciform OMIMs (benzene and naphthalene- based) were investigated with respect to their packing behaviour, porosity and adsorption properties. Our analysis suggests that the final density of the material, as well as the surface area and pore volume, depend on the ending group’s bulkiness. Bulkier molecules lead to materials with lower densities, but it was found that the adsorption behaviour is not just related to the material’s density, but also to the pore size and shape, which are determined by the way the molecules pack. The relationship between adsorption capacity and physical properties was analysed and the role of surface area, free volume and enthalpic interaction was used to identify different adsorption regimes. It was found that the uptake of argon at low pressure is proportional to the strength of the adsorbent-adsorbate interaction while at moderate pressure it is dependent on the free volume and surface area. The dissolution of three cruciform OMIMs was investigated in dichloromethane, ethyl acetateand toluene. Direct interface molecular dynamics simulations showed that the solubility process consists of two steps; the diffusion of the solvent in the OMIM-rich phase, and the departure of the OMIMs in the solvent bulk. We proposed a simple model to represent this mechanism. Furthermore, results from infinite dilution simulations show that the solvent-OMIMs interactions can be related to the chemistry of the OMIMs and to the solvent’s properties. We found that, in general, increasing the length of the OMIM’s arm affects negatively the solubility of the material, while adding bulky alkyl groups favours the interaction with the solvent molecules. The third part concentrates on the characterisation of PIMs and their application as CO2 adsorbent. Properties of four polymers of intrinsic microporosity containing Tröger’s base units were assessed for CO2 capture experimentally and computationally. Structural properties included average pore size, pore size distribution, surface area, and accessible pore volume, whereas thermodynamic properties focused on density, CO2 sorption isotherms, and enthalpies of adsorption. It was found that the shape of the contortion site plays a more important role than the polymer density when assessing the capacity of the material, and that the presence of a Tröger base unit only slightly affects the amount adsorbed at low pressures, but it does not have any significant influence on the enthalpy of adsorption fingerprint. A comparison of the materials studied with those reported in the literature allowed us to propose a set of guidelines for the design of polymers for CO2 capture applications.

Thesis (Ph. D.)--University of Oregon, 2008.
Typescript. Includes vita and abstract. Includes bibliographical references (leaves 69-81). Also available online in ProQuest, free to University of Oregon users.

This thesis comprises of the study performed on the extraction, isolation and structural characterisation of macromolecular components from the three members of the family Cucurbitaceae. In particular, the polysaccharides from C.moschata, C. maxima and C. pepo (butternut squash, zucchini and pumpkin, respectively) and oil bodies from the seeds of C. pepo are selected on the basis of their antidiabetic potential. The study centred around structural characterisation of the polysaccharides using hydrodynamical methods such as analytical ultracentrifugation (sedimentation velocity and sedimentation equilibrium), viscometry and dynamic light scattering followed by the use of gas chromatography and gas chromatography coupled with mass spectrophotometry for the assessment of monosaccharide composition. Bioactivity of these polysaccharides was also examined using complement fixation assay. Pumpkin seed oil bodies were extracted, isolated and characterised under various laboratory conditions to establish the zeta potential and size distribution of oil bodies in the solvent provided. Although the selection of the biomaterial for this study from the three species was based on their antidiabetic potential, other health benefits and practical applications are also associated with them. For example, the characterisation of these macromolecules could act as a stepping stone for the future investigation in therapeutics. These biomaterials can potentially be used in the pharmaceutical industry to act as a drug themselves or can be used as a part of any formulation or otherwise can be used as a nutraceutical compound.

This thesis is concerned with using diffusing molecules as a probe to understanding changes in both two- and three-dimensional polymer systems. Fluorescence correlation spectroscopy (FCS) is used to measure the diffusion coefficient of a fluorescently labelled molecule within poly (methacrylic acid) (PMAA hydrogels and adsorbed onto poly(alkyl mcthacrylate) thin films. Responsive hydrogels such as PMAA arc of great importance in controlled release systems such as drug delivery. The hydrogcls studied were found to respond to temperature, pH. and salt concentrations in ways that can be utilised for producing systems that change in predetermined ways under controlled conditions. Thin polymer films. both homopolymer and polymer blends are found to exhibit a transition process between glass and liquid states. Existing theories present the transition as a sharp. almost instantaneous process but FCS and ellipsometric measurements find this to be an insufficient model. Not only is the glass transition found to occur over a temperature range but the diffusion of adsorbed molecule and the measured friction coefficient. Are found to increase dralllatically at the transition temperature range after which they are similar to the values below the transition. Furthermore polymer blends (Ire found to exhibit two distinct transitions. each with an increase in adsorbed diffusion that are unexpected in the existing theoretical understanding of polymer blends.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Materials Science and Engineering, 2007.
Includes bibliographical references (p. 187-201).
In this thesis, the shear and self-adhesion nanomechanical properties between opposing cartilage aggrecan macromolecules were probed. In addition, nanoscale dynamic oscillatory mechanical properties of cartilage and its type II collagen network was measured. Aggrecan shear nanomechanics was assessed via microcontact printing and lateral force microscopy. Lateral force between aggrecan and the probe tip, and compression of aggrecan was simultaneously measured in 0.001 - 1.0 M NaCl aqueous solutions. Using the microsized tip (Rtip ~ 2.5 [mu]m) enabled a large assembly of ~ 103 aggrecan molecules to interact simultaneously, closely mimicking the in vivo conditions.Both electrostatic and nonelectrostatic components were identified to importantly contribute to aggrecan shear. At near physiological IS (0.1 M), significant rate dependence was observed, suggestive of visco/poroelastic interactions within the aggrecan layer. By using an aggrecan end-functionalized colloidal tip, shear of two opposing aggrecan layers was assessed in a similar fashion. Lower lateral force and a more marked rate dependence were measured compared to the shear of a single layer, due to the aggrecan inter-layer molecular interpenetration and the different local z-dependent charge density distribution. The addition of Ca2+, at physiological-like 2 mM concentration, significantly affects cartilage shear by its electrostatic screening and binding effects. Marked aggrecan self-adhesion upon separation was discovered after static compression in the presence of electrostatic repulsion in physiological-like conditions.
(cont.) Aggrecan self-adhesion increases as increasing equilibration time and bath IS. Molecular origins of the adhesion, also present in vivo, include van der Waals, hydrogen bonding, Ca2+-mediated bridging, and molecular entanglements between the glycosaminogly-can branches of aggrecan. This self-adhesion could be an important factor in protecting cartilage matrix structural integrity and function via these energy-dissipative mechanisms. The nanoscale oscillatory dynamic deformation properties of both nontreated and proteoglycan(PG)-depleted (left mostly type II collagen) calf knee cartilage disks (- 0.5 mm thick) was measured by connecting an external electronic wave generator to the AFM. A significant increase in effective stiffness E and phase lag A (deformation with respect to force) as increasing frequency for both disks suggests poro/viscoelasticity are more critical at higher frequency. The PG-depleted disk shows a more marked dependence of E and A on deformation amplitude - 2 - 100 nm, as the nanostructure and nanomechanical properties of porous collagen network are more heterogeneous without the entrapment of aggrecan motif. A unique - 23 nm banding pattern along the type II collagen fibrils was observed, which may be relative to the cartilage swelling properties and the molecular interaction between aggrecan and the collagen network. Taken together, this study provides insights into molecular-level deformation of cartilage extracellular matrix (ECM) macromolecules (e.g., aggrecan, type II collagen) that are important to the understanding of cartilage biomechanical function. Ongoing studies are probing the age, disease (osteoarthritis), source and species related variations of cartilage ECM properties at the molecular level.
by Lin Han.
Ph.D.

Animals, plants and bacteria can survive sub-zero environments by using specialist proteins that inhibit ice growth. There has been a great deal of work into trying to understand and exploit these proteins for use in cryopreservation, but several strategies fail as the protein’s mechanism for ice growth inhibition causes ice to grow into needle-like crystals, which cause mechanical damage to the cryopreserved material. A range of studies have shown that this shaping can be removed, without affecting ice growth inhibition activity. Synthetic mimics exist, the most interesting being the simple polymer, poly(vinyl alcohol), which alone amongst other synthetic macromolecules displays ice growth inhibition behaviour. The scientific principles behind ice growth, and the molecules that can inhibit this, are detailed in Chapter 1. Chapter 2 examines how the molecular weight of poly(vinyl alcohol) affects ice recrystallisation inhibition activity, and the importance of hydroxyl sequence, using post-polymerisation modification and co-polymerisation. Chapter 3 details the preparation of well-defined block co-polymers of poly(vinyl alcohol), and confirms the importance of the hydroxyl sequence. These polymers maintained their ice recrystallisation inhibition activity despite the addition of large non-active blocks. Chapter 4 demonstrates the synthesis and utility of a novel multifunctional chain transfer agent, which is used to prepare star polymers. The resultant star-poly(vinyl alcohol) was highly active, and activity profiles of these polymers provided further evidence that the mechanism of ice recrystallisation inhibition by poly(vinyl alcohol) does not involve direct binding to ice. Chapter 5 uses the techniques and methodologies developed in Chapter 2 and applies them to another lesser-known ability of poly(vinyl alcohol); thermoresponsivity. In summary, controlled radical polymerisation of vinyl acetate was employed in a range of different ways to prepare poly(vinyl alcohol) and its various co-polymers. These polymers were then tested for ice recrystallisation inhibition. Due to their well defined physical properties, and advanced architectures, new insights into the nature and mechanisms of their activity were available. This mechanistic understanding, and the materials developed for this thesis, display a great deal of potential in expanding the field of cryopreservation.

Biomineralization refers to the production of mineralized tissues by organisms. The fine control which organisms can exert over this process produces crystals with morphologies and properties contrasting to that of non-biogenic crystals and specifically altered to suit the required functional need. A key model system of biomineralization are a unicellular marine algae, coccolithophores, which produce calcium carbonate scales known as coccoliths. These coccoliths are comprised of arrangements of single crystals of calcite interlocked to form a plate-shaped structure. Coccoliths are developed intracellularly in a specialised compartment called the coccolith vesicle, before being extruded to the cell surface. In this work, two vital components of the coccolith biomineralization process are investigated - a soluble polysaccharide thought to act as a habit modifier and an insoluble organic scaffold known as a baseplate that provides the surface for nucleation and growth of the crystals. Whilst both these elements are thought to play a key part in the biomineralization process, the role of each is not fully understood. To investigate the effect of coccolith-associated polysaccharides (CAPs) on nucleation and polymorph selection, two systems that promote different polymorphs of calcium carbonate were utilised. In both systems, the intracrystalline polysaccharide fraction extracted from one species, Gephyrocapsa oceanica, was able to promote calcite nucleation in vitro, even under conditions favouring the kinetically-privileged polymorphs of calcium carbonate: vaterite and aragonite. As this property is not observed with CAPs extracted from its 'sister species', Emiliania huxleyi, the in vivo function of CAPs may differ between the two species. Both cryo-transmission electron microscopy (cryoTEM) and scanning electron microscopy (SEM) were used to determine the mechanism of calcite growth in the presence of G. oceanica CAPs, showing its impact on the forming amorphous calcium carbonate (ACC), decreasing the size of the particles and producing irregular, angular particles. Using cryo-electron tomography (cryoET), it was possible to create a 3D representation of the structure of the baseplate from the coccolithophore Pleurochrysis carterae, revealing its two-sided organisation. Examination of several stages of the coccolith growth process demonstrated the interlocking nature of the calcite crystals that make up the coccolith and the progression of the crystal morphologies over time, and the interaction of these crystals with the baseplate rim. Additionally, the effect of inhibiting carbonic anhydrase (CA), an enzyme involved in the regulation of carbonate species, revealed that inhibition of CA can affect coccolithogenesis as well as cell proliferation.

Le travail presente dans ce memoire decrit la premiere synthese totale d'une helice macrocyclique polypyridinique possedant 15 cycles adjacents. Dans le chapitre i, qui constitue la partie bibliographique, nous presentons l'utilisation des molecules polypyridiniques en temps que recepteurs supramoleculaires et en temps que ligands pour les metaux de transition. Nous presentons ensuite les methodes couramment utilisees pour synthetiser le noyau pyridine. Dans le chapitre ii, apres avoir analyse les resultats de tentatives infructueuses, nous presentons une autre strategie de synthese basee sur un synthon de type 1,2,3,4,5,6,7,8- octahydro acridine. Plusieurs voies de synthese sont envisagees qui conduisent a differents composes correspondant a la structure que nous recherchons. Nous presentons ensuite, l'acces au synthon clef, une 1,2,3,4,5,6,7,8-octahydro acridine substituee en position 9 par une chaine hydrocarbonee susceptible d'etre rallongee en fin de synthese pour conduire aux proprietes mesogenes souhaitees. Cette brique elementaire a subit de nombreux amenagements fonctionnels pour introduire des fonctions cetone, exomethylene cetone et exoalkylidene cetone en position 2 par rapport au cycle pyridinique. Pour cela, deux nouvelles methodes synthetiques ont ete utilisees: la conduite du rearrangement de boekelheide a l'aide d'anhydride trifluoroacetique et l'alkylation des enoneamines par les organomagnesiens. Les memes amenagements fonctionnels ont ete realises sur les squelettes 5,6,7,8-tetrahydro quinoleine et cyclohexanone. A cette occasion, nous decrivons un synthon cyclohexyle hautement fonctionnel. Partant de ces briques elementaires, nous decrivons les syntheses de polypyridines que nous avons realisees, parmi lesquelles, deux cas sont a distinguer. La reaction de cetones et d'exomethylene cetones dans la pyridine en presence d'acetate d'ammonium conduit au compose pyridinique issu de l'addition de michael (addition 1,4). Tandis que dans les memes conditions, les cetones et les exoalkylidenes cetones donnent un autre type de composes pyridiniques apres addition non conjuguee (addition 1,2). Dans les deux cas les regioselectivites observees sont tres elevees et les rendements bons. L'utilisation des deux types de condensation a permis d'obtenir des composes polycycliques polypyridiniques. La fonctionnalisation suivie de la condensation de ceux resultant de l'addition de michael nous a permis d'isoler deux composes macrocycliques: un compose pentapyridinique a 11 cycles adjacents ainsi qu'un compose heptapyridinique a 15 cycles adjacents qui lui est, incontestablement, helicoidal

Coding and decoding information into and from (bio)macromolecules is of pivotal importance for most processes in nature. A simple readout methodology constitutes a key challenge for data-storage in artificial molecules. The determination of the comonomer-order in synthetic sequence-defined macromolecules, however, requires elaborate analytical techniques. The herein presented work focuses on the synthesis of sequence-defined macromolecules via photochemical ligation reactions, and ultimately the development of a novel fluorescence-based readout of the comonomer-order. The synthesis of rigid multifluorophore sequence-defined macromolecules employing an iterative exponential growth strategy additionally resulted in the development of novel, highly efficient photochemical transformations.

In soft materials entropic and enthalpic contributions are of similar magnitude and balance each other. Therefore, the macroscopic mechanical and rheological properties and the phase changes are determined to a high degree by thermal motion of the atoms and molecules. Most of the relevant dynamics takes place on mesoscopic length and time scales in between the picosecond atomic scale and the macroscopic frame. Allowing for the proper space time observation window, neutron spin echo (NSE) spectroscopy uniquely allows to address these motions. Here we briefly present some key experimental results on the mesoscopic dynamics of polymer systems, starting from the standard model of polymer motion - the Rouse model. We briefly touch the role of topological confinement as expressed in the reptation model and discuss in some more detail processes limiting the confinement. In the second part we touch on some new developments relating to large scale internal dynamics of proteins by neutron spin echo. We will report results of some pioneering studies which show the feasibility of such experiments on large scale protein motion which will most likely initiate further studies.

In soft materials entropic and enthalpic contributions are of similar magnitude and balance each other. Therefore, the macroscopic mechanical and rheological properties and the phase changes are determined to a high degree by thermal motion of the atoms and molecules. Most of the relevant dynamics takes place on mesoscopic length and time scales in between the picosecond atomic scale and the macroscopic frame. Allowing for the proper space time observation window, neutron spin echo (NSE) spectroscopy uniquely allows to address these motions. Here we briefly present some key experimental results on the mesoscopic dynamics of polymer systems, starting from the standard model of polymer motion - the Rouse model. We briefly touch the role of topological confinement as expressed in the reptation model and discuss in some more detail processes limiting the confinement. In the second part we touch on some new developments relating to large scale internal dynamics of proteins by neutron spin echo. We will report results of some pioneering studies which show the feasibility of such experiments on large scale protein motion which will most likely initiate further studies.

Coumarin and cinnamate derivatives were positioned as either polymer chain ends or side groups to synthesize photoactive macromolecules and gain the ability to reversibly control molecular weight and crosslink density using UV light. The cinnamates and coumarins were reacted onto the polymers via multiple reaction pathways. Polymers were functionalized with coumarin or cinnamate groups via an esterification reaction between hydroxyl functionalities and an acid chloride derivatized coumarin group. In addition to the esterification reaction, cinnamates were also coupled to polymers via a ring opening reaction between a hydroxyl functionalized cinnamate derivative and a maleic anhydride repeat unit copolymerized into the polymer. Both functional groups undergo a [2p + 2p] photodimerization reaction (coumarin groups in the UVA and cinnamate groups in the UVB), which was utilized to crosslink and chain-extend macromolecules. Coumarin dimers possess the additional ability to photocleave and thus reverse when irradiated at 254 nm. The coumarin reversible photodimerization reaction was utilized to reversibly increase the molecular weight and molecular weight distribution of coumarin-functionalized PEG monols and diols. For example, the number average molecular weight of the coumarin-functionalized PEG diol doubled and the molecular weight distribution increased from 1.08 to 2.75 when exposed to 110 J cm-2 of UVA irradiation. Subsequent photocleavage (UVC irradiation, 2 J cm-2) of the chain-extended PEGs, cleaved coumarin dimers decreasing the molecular weight and molecular weight distribution to their original values. A number of poly(alkyl acrylate) and poly(methyl acrylate) systems were functionalized with coumarin groups to study the effect of the glass transition temperature and alkyl ester side group composition on the photodimerization reaction and subsequent crosslinking. The glass transition temperature (Tg) acted as an on/off switch for the photodimerization reaction. While the absolute difference between Tg and irradiance temperature did not affect the rate or extent of photodimerization reaction, polymers with a Tg greater than the irradiance temperature displayed less reaction than those with a Tg lower than the irradiance temperature. The final extent of conversion was controlled by a complex combination of factors including alkyl ester side chain steric bulkiness. Coumarin-functionalized alkyl acrylates based on ethylhexyl acrylate were tested as detachable PSAs. A 98% decrease in the adhesive peel strength was observed after exposure to UVA irradiation. Cinnamate groups were utilized in the design and synthesis of UV-curable hot melt pressure sensitive adhesives (PSAs). The cinnamate groups were attached to the PSAs to provide a method to increase molecular weight and add a small amount of crosslinking leading to an increase the adhesive strength of the PSAs. Broadband UV irradiation from a laboratory scale industrial lamp increased the peel strength of the adhesives. Postcure of the irradiated cinnamate-functionalized UV-curable hot melt PSAs was reduced compared to photoinitiated free-radical photocurable UV-curable hot melt PSAs.
Ph. D.

Chemistry
Ph.D.
The use of femtosecond (fs) laser pulses in laser-induced breakdown spectroscopy (LIBS) and for chemical analysis using mass spectrometry is explored. A comparison of fs-LIBS and remote filament-induced breakdown spectroscopy (R-FIBS) in the analysis of graphite composites yielded more accurate results with filaments due to intensity clamping within the filament. The investigation of fs-LIBS and R-FIBS in the detection of explosives led to the discovery of femtosecond vaporization of intact molecules under ambient conditions. This knowledge was then used in the development of a new ambient laser-based mass analysis technique. The combination of nonresonant femtosecond laser vaporization with electrospray post-ionization called laser electrospray mass spectrometry (LEMS) was investigated as a universal detection method of pharmaceuticals, biological macromolecules and plant tissues. We show the capability of femtosecond lasers to desorb sample without any sample preparation or resonant transition in the sample or substrate. Ambient mass spectral imaging and tissue type classification is also demonstrated.
Temple University--Theses

The investigation of real-time dynamics of charged and neutral quantum excitation propagating through macromolecular systems is receiving growing attention due to its potentially countless applications in nano-scale (opto-)electronics and in biophysics. Several key issues have not been fully clarified yet, including the role played by molecular thermal fluctuations and the possible correlations between the degree of quantum coherence and the efficiency of the transport process. In order to gain some insight, we developed a rigorous and systematic framework describing quantum transport, based on a field-theoretic formalism.

The investigation of real-time dynamics of charged and neutral quantum excitation propagating through macromolecular systems is receiving growing attention due to its potentially countless applications in nano-scale (opto-)electronics and in biophysics. Several key issues have not been fully clarified yet, including the role played by molecular thermal fluctuations and the possible correlations between the degree of quantum coherence and the efficiency of the transport process. In order to gain some insight, we developed a rigorous and systematic framework describing quantum transport, based on a field-theoretic formalism.

Cement-based materials, such as concrete or mortars, are usually considered materials with low technological level. Although they are the most employed human made materials in the world, others such as wood, plastics, metals and even stones are usually more valued in the everyday life: probably the fact that cement is cheap, readily available, common, and has been employed successfully for centuries, contributes to its low technology perception. However, this vision is far from the reality: the cement paste is a complex multicomponent and heterogeneous composite system, with different structural features at different length scales. The mechanism in which the clinker in contact with water becomes a hardened paste comprises hundreds of chemical reactions and physical processes. Understanding the molecular details of cement hydration processes is of fundamental importance due to the technological and economical impact of these materials. Several aspects need to be considered, and a realistic approach should be limited to a few specific features. Many efforts have been devoted over the last 40 years to develop mathematical models for understanding and predicting highly complex cement hydration kinetics, microstructure development and the implications of these for the changing physical-chemical properties of cement paste and concrete. An accurate hydration simulation approach would enable scientists and engineers not only to predict the performance of concrete, but also to design new cementitious materials. Despite significant effort and progress, the ability to perform such a complete simulation has not yet been developed, mainly because cement hydration is one of the more complex phenomena in engineering/materials science. The main objective of this PhD thesis is to analyse the influence of superplasticizers on the microevolution of cement suspensions during early hydration based of Molecular Dynamics (MD) approaches. To this purpose we implemented a MD protocol for the study of the behavior of polycarboxylate-ether-based superplasticizers (PCEs) in the presence of selected cement surfaces, tricalcium aluminate (C3A) and tricalcium silicate (C3S), water molecules and calcium hydroxide. The final goal of the project, which was carried in collaboration with the group of Prof. G. Artioli - Università degli Studi di Padova, Dipartimento di Geoscienze, was to clarify structure-properties relationships, in order to design new products with enhanced properties. In fact, the rheology of cement pastes can be controlled by the use of superplasticizers that, by adsorbing on the surfaces of cement particles, enhance their workability. The protocol was made up of the following steps: i) building of the cement surfaces, ii) parameterization of force field, iii) setting of the simulation and evaluation of physical observables. Some methodological knowledges acquired were employed on side-applications, for example the evaluation of electrostatic interactions of other organic molecules, in particular partial charges of amino acids (AA) and nonstandard amino acids (Non-AA), present in the human Connexin protein. To be precise, following the earlier approach of Bayly et al [Bayly1993], we obtained the charge set by fitting to the electrostatic potentials of Non-AA calculated using ab-initio methods. This effort was carried out in collaboration with the group of F. Mammano - Università degli Studi di Padova, Dipartimento di Fisica e Astronomia [Zonta2014]. Finally, in a joint effort with Dott.ssa L. Orian, Dott. M. Torsello and P. Calligari, of my research group, simulate complete simulation was carried out of the Connexin 26 hemichannel (Cx26) behaviour in the presence of post-translational modifications (PTMs) and Ca2+. The contribution to this joint project described in this thesis, was aimed to i) the analysis of the structure of the channel and ii) the preservation of salt bridges between Glu47, Arg75 and gamma-Glu47, Arg75 in the presence/asbsence of Ca2+. Lastly, preliminary results based on a collaboration with Stazione Sperimentale del Vetro (SSV) of Murano (Ve) for the project: "Computational methods for the modeling of equilibrium properties of glassy materials", is presented. The goal of this work was the elaboration, optimization and validation of a model of the type of ideal solutions for the thermodynamic properties of glasses and the inclusion in integrated software platforms. This work is organised as follows. In chapter 1, a brief overview is presented of the atomistic simulation methods used during the Thesis, because several levels of theory were selected depending on their capabilities to solve punctual problems: ab initio, Molecular Mechanics, and Molecular Dynamics. In chapter 2, an introduction to cement chemistry and the necessary basis is given in order to follow the results and discussions of the systems presented in this Thesis. It covers a description of clinker phases, superplasticizers, the hydration process, the cement paste structure and computational methods applied in cement research. In chapter 3, the results of four MD simulations are discussed for a system consisting of PCE-(23-7-1), a comb-shaped polymer unit model superplasticizer of methyl-polyethylene glycole methacrylate and methacrylic acids (seven back bone units, one side-chain unit and twenty three polyethylene-oxide units in the side chain), the C3A and C3S surfaces, explicit molecules of water, Ca2+ and OH- ions (pore solution): from the MD trajectories were calculated conformational properties. In chapter 4, the results are discussed of partial charges parametrization of Non-AA, the structural channel analysis and salt-bridges analysis of Cx26 protein. In chapter 5, the thermodynamic model is presented for calculating the composition of glasses, the interpolation for temperature dependence of thermodynamic properties and the validation of model with a simple binary oxide system Na2O-SiO2.
Il cemento e i suoi derivati, come calcestruzzo e malte, sono generalmente considerati materiali a basso livello tecnologico. Pur essendo il materiale più prodotto e utilizzato al mondo, altri, come legno, plastica, metalli e anche le pietre sono considerati più importanti nella vita di tutti i giorni: probabilmente il fatto che il cemento è economico, comune, facilmente disponibile ed è stato impiegato con successo per secoli, contribuisce alla sua bassa percezione tecnologia. Tuttavia, questa visione è lontana dalla realtà: la pasta di cemento è un sistema composito multicomponente eterogeneo e complesso; il meccanismo con cui clinker in contatto con l'acqua diventa una pasta indurita comprende centinaia di processi chimici e fisici. La comprensione dei dettagli molecolari nel processo d'idratazione del cemento è di fondamentale importanza per l'impatto tecnologico ed economico di questi materiali. Molti aspetti devono essere considerati e un approccio realistico dovrebbe essere limitato a poche caratteristiche specifiche. Molti sforzi sono stati fatti negli ultimi quarant'anni per sviluppare modelli matematici che consentono la comprensione e la previsione della complessa cinetica d'idratazione, lo sviluppo di microstrutture e le implicazioni nelle proprietà fisico-chimiche del calcestruzzo. Un approccio accurato nella simulazione del processo d'idratazione consentirebbe a scienziati e ingegneri non solo di prevedere le prestazioni del calcestruzzo, ma anche per progettare nuovi materiali cementizi. Nonostante i notevoli sforzi fatti e i progressi ottenuti, la capacità di effettuare una simulazione così completa non è stata ancora sviluppata, perchè il processo d'idratazione è uno dei fenomeni più complessi nell'ingegneria/scienza dei materiali. L'obiettivo principale della mia Tesi di Dottorato è l'analisi dell'influenza dei superfluidificanti sulla microevoluzione di sospensioni cementizie durante l'idratazione, usando metodi di Dinamica Molecolare (MD): abbiamo implementato un protocollo MD per studiare il comportamento dei superfluidificanti a base di eteri policarbossilati (PCEs), in presenza di superfici selezionate di cemento, alluminato tricalcico (C3A) e silicato tricalcico (C3S), molecole d'acqua e idrossido di calcio. L'obiettivo finale del progetto, realizzato in collaborazione con il gruppo del Prof. G. Artioli - Università degli Studi di Padova, Dipartimento di Geoscienze, era quello di chiarire le relazioni struttura - proprietà per riuscire a progettare nuovi prodotti con caratteristiche avanzate: infatti, la reologia di paste di cemento puà essere controllata mediante l'uso dei superfluidificanti che, legandosi sulle superfici delle particelle di cemento, ne migliorano la lavorabilità. Il protocollo è costituito dalle seguenti fasi: i) costruzione delle superfici cementizie, ii) parametrizzazione del campo di forza, iii) impostazione della simulazione e valutazione delle osservabili fisiche. Alcune conoscenze metodologiche acquisite sono impiegate con laterali applicazioni, per esempio la valutazione delle interazioni elettrostatiche di altre molecole organiche, in particolare le cariche parziali di amminoacidi (AA) e amminoacidi non standard (non-AA), presenti nella proteina umana Connessina: per essere precisi, seguendo l'approccio di Bayly [Bayly1993], abbiamo ottenuto il set di cariche dal fitting dei potenziali elettrostatici di Non-AA calcolati con metodi ab-initio. Questo lavoro è stato realizzato in collaborazione con il gruppo di F. Mammano - Università degli Studi di Padova, Dipartimento di Fisica e Astronomia [Zonta2014]. In collaborazione con la Dott.ssa L. Orian, Dott. M. Torsello e P. Calligari, del mio gruppo di ricerca, mediante Dinamica Molecolare abbiamo simulato la Connessina 26 emicanale (Cx26) in presenza di modificazioni post-traduzionali (PTM) e Ca2+: il mio contributo, in sostanza, aveva lo scopo di analizzare i) la struttura del canale e ii) la conservazione dei ponti salini tra Glu47, Arg75 e gamma-Glu47, Arg75 in presenza/assenza di Ca2+ all'interno del canale. Infine, ho iniziato una collaborazione con la Stazione Sperimentale del Vetro (SSV) di Murano (Ve) in questo progetto: "Metodi computazionali per la modellazione di proprietà d'equilibrio dei materiali vetrosi". L'obiettivo di questo lavoro è stato l'elaborazione, l'ottimizzazione e validazione di un modello del tipo soluzioni ideali per il calcolo di proprietà termodinamiche del vetro e l'inclusione in piattaforme software integrate. Fino ad ora, abbiamo ottenuto il calcolo della composizione dei vetri silicati considerando la dipendenza dalla temperatura della , termodinamicamente coerente, di ossidi elementari e misti all'interno del vetro; adesso ci stiamo occupando del calcolo della viscosità, dilatazione termica, proprietà ottiche, ecc. La tesi è organizzata nel seguente modo. Nel capitolo 1, una breve panoramica dei metodi di simulazione atomistica utilizzati durante la Tesi, perchè diversi livelli di teoria sono stati selezionati in base alle loro capacità di risolvere specifici problemi: ab-initio, Meccanica Molecolare e Dinamica Molecolare. Nel capitolo 2, un'introduzione alla chimica del cemento e i presupposti necessari per comprendere i risultati e discussioni dei sistemi analizzati in questa Tesi: una descrizione delle fasi clinker, dei superfluidificanti, il processo di idratazione, la struttura della pasta di cemento e i metodi computazionali più comuni nello studio dei materiali cementizi. Nel capitolo 3, i risultati di quattro simulazioni MD di un sistema costituito da PCE-(23-7-1), un polimero superfluidificante modello, a forma di pettine, costituito da metil-polietilen-glicole metacrilato e acido metacrilico (sette unità nel backbone, una catena laterale e ventitrè‚ unità poli-etilen-ossido in catena laterale), le superfici C3A e C3S, le molecole di H2O e gli ioni Ca2+ e OH- (pore solution): dalle traiettorie MD sono state calcolate le proprietà conformazionali del PCE. Nel capitolo 4, i risultati della parametrizzazione delle cariche parziali di amminoacidi non naturali, dell'analisi strutturale del canale e dei ponti salini della proteina Cx26. Nel capitolo 5, il modello fisico-matematico per il calcolo della composizione dei vetri, l'interpolazione per la dipendenza dalla temperatura delle propriet… termodinamiche e la convalida del modello con un semplice vetro costituito da un ossido misto Na2O-SiO2.