Neutron-mapping polymer flow: Scattering, flow visualization, and molecular theory

Flows of complex fluids need to be understood at both macroscopic and molecular scales, because it is the macroscopic response that controls the fluid behavior, but the molecular scale that ultimately gives rise to rheological and solid-state properties. Here the flow field of an entangled polymer melt through an extended contraction, typical of many polymer processes, is imaged optically and by small-angle neutron scattering. The dual-probe technique samples both the macroscopic stress field in the flow and the microscopic configuration of the polymer molecules at selected points. The results are compared with a recent tube model molecular theory of entangled melt flow that is able to calculate both the stress and the single-chain structure factor from first principles. The combined action of the three fundamental entangled processes of reptation, contour length fluctuation, and convective constraint release is essential to account quantitatively for the rich rheological behavior. The multiscale approach unearths a new feature: Orientation at the length scale of the entire chain decays considerably more slowly than at the smaller entanglement length.

Molecular dynamics simulation of the structural and dynamic properties of dioctadecyldimethyl ammoniums in organoclays

The structural and dynamic properties of dioctadecyldimethylammoniums (DODDMA) intercalated into 2:1 layered clays are investigated using isothermal-isobaric (NPT) molecular dynamics (MD) simulation. The simulated results are in reasonably good agreement with the available experimental measurements, such as X-ray diffraction (XRD), atom force microscopy (AFM), Fourier transform infrared (FTIR), and nuclear magnetic resonance (NMR) spectroscopies. The nitrogen atoms are found to be located mainly within two layers close to the clay surface whereas methylene groups form a pseudoquadrilayer structure. The results of tilt angle and order parameter show that interior two-bond segments of alkyl chains prefer an arrangement parallel to the clay surface, whereas the segments toward end groups adopt a random orientation. In addition, the alkyl chains within the layer structure lie almost parallel to the clay surface whereas those out of the layer structure are essentially perpendicular to the surface. The trans conformations are predominant in all cases although extensive gauche conformations are observed, which is in agreement with previous simulations on n-butane. Moreover, an odd-even effect in conformation distributions is observed mainly along the chains close to the head and tail groups. The diffusion constants of both nitrogen atoms and methylene groups in these nanoconfined alkyl chains increase with the temperature and methelene position toward the tail groups.

Molecular recognition of sub-micromolar inhibitors by the epinephrine-synthesizing enzyme phenylethanolamine N-methyltransferase

The crystal structures of human phenylethanolamine N-methyltransferase in complex with S-adenosyl-L-homocysteine (7, AdoHcy) and either 7-iodo-1,2,3,4-tetrahydroisoquinoline (2) or 8,9-dichloro-2,3,4,5-tetrahydro-1H-2-benzazepine (3, LY134046) were determined and compared with the structure of the enzyme complex with 7 and 7-aminosulfonyl-1,2,3,4-tetrahydroisoquinoline (1, SK&F 29661). The enzyme is able to accommodate a variety of chemically disparate functional groups on the aromatic ring of the inhibitors through adaptation of the binding pocket for this substituent and by subtle adjustments of the orientation of the inhibitors within the relatively planar binding site. In addition, the interactions formed by the amine nitrogen of all three inhibitors reinforce the hypothesis that this functional group mimics the beta-hydroxyl of norepinephrine rather than the amine. These studies provide further clues for the development of improved inhibitors for use as pharmacological probes.

Studies of molecular interactions using physical techniques

The investigations described in this thesis concern the molecular interactions between polar solute molecules and various aromatic compounds in solution. Three different physical methods were employed. Nuclear magnetic resonance (n.m.r.) spectroscopy was used to determine the nature and strength of the interactions and the geometry of the transient complexes formed. Cryoscopic studies were used to provide information on the stoichiometry of the complexes. Dielectric constant studies were conducted in an attempt to confirm and supplement the spectroscopic investigations. The systems studied were those between nitromethane, chloroform, acetonitrile (solutes) and various methyl substituted benzenes. In the n.m.r. work the dependence of the solute chemical shift upon the compositions of the solutions was determined. From this the equilibrium quotients (K) for the formation of each complex and the shift induced in the solute proton by the aromatic in the complex were evaluated. The thermodynamic parameters for the interactions were obtained from the determination of K at several temperatures. The stoichiometries of the complexes obtained from cryoscopic studies were found to agree with those deduced from spectroscopic investigations. For most systems it is suggested that only one type of complex, of 1:1 stiochiometry, predominates except that for the acetonitrile-benzene system a 1:2 complex is formed. Two sets of dielectric studies were conducted, the first to show that the nature of the interaction is dipole-induced dipole and the second to calculate K. The equilibrium quotients obtained from spectroscopic and dielectric studies are compared. Time-averaged geometries of the complexes are proposed. The orientation of solute, with respect to the aromatic for the 1:1 complexes, appears to be the one in which the solute lies symmetrically about the aromatic six-fold axis whereas for the 1:2 complex, a sandwich structure is proposed. It is suggested that the complexes are formed through a dipole-induced dipole interaction and steric factors play some part in the complex formation.

Stress-induced platelet formation in silicon:a molecular dynamics study

The effect of stress on vacancy cluster configurations in silicon is examined using molecular dynamics. At zero pressure, the shape and stability of the vacancy clusters agrees with previous atomistic results. When stress is applied the orientation of small planar clusters changes to reduce the strain energy. The preferred orientation for the vacancy clusters under stress agrees with the experimentally observed orientations of hydrogen platelets in the high stress regions of hydrogen implanted silicon. These results suggest a theory for hydrogen platelet formation. © 2005 The American Physical Society.

Water network dynamics at the critical moment of a peptide's ß-turn formation:a molecular dynamics study

All-atom molecular dynamics simulations for a single molecule of Leu-Enkephalin in aqueous solution have been used to study the role of the water network during the formation of ß-turns. We give a detailed account of the intramolecular hydrogen bonding, the water-peptide hydrogen bonding, and the orientation and residence times of water molecules focusing on the short critical periods of transition to the stable ß-turns. These studies suggest that, when intramolecular hydrogen bonding between the first and fourth residue of the ß-turn is not present, the disruption of the water network and the establishment of water bridges constitute decisive factors in the formation and stability of the ß-turn. Finally, we provide possible explanations and mechanisms for the formations of different kinds of ß-turns.

Resonance Energy Transfer-Based Molecular Switch Designed Using a Systematic Design Process Based on Monte Carlo Methods and Markov Chains

A RET network consists of a network of photo-active molecules called chromophores that can participate in inter-molecular energy transfer called resonance energy transfer (RET). RET networks are used in a variety of applications including cryptographic devices, storage systems, light harvesting complexes, biological sensors, and molecular rulers. In this dissertation, we focus on creating a RET device called closed-diffusive exciton valve (C-DEV) in which the input to output transfer function is controlled by an external energy source, similar to a semiconductor transistor like the MOSFET. Due to their biocompatibility, molecular devices like the C-DEVs can be used to introduce computing power in biological, organic, and aqueous environments such as living cells. Furthermore, the underlying physics in RET devices are stochastic in nature, making them suitable for stochastic computing in which true random distribution generation is critical.

In order to determine a valid configuration of chromophores for the C-DEV, we developed a systematic process based on user-guided design space pruning techniques and built-in simulation tools. We show that our C-DEV is 15x better than C-DEVs designed using ad hoc methods that rely on limited data from prior experiments. We also show ways in which the C-DEV can be improved further and how different varieties of C-DEVs can be combined to form more complex logic circuits. Moreover, the systematic design process can be used to search for valid chromophore network configurations for a variety of RET applications.

We also describe a feasibility study for a technique used to control the orientation of chromophores attached to DNA. Being able to control the orientation can expand the design space for RET networks because it provides another parameter to tune their collective behavior. While results showed limited control over orientation, the analysis required the development of a mathematical model that can be used to determine the distribution of dipoles in a given sample of chromophore constructs. The model can be used to evaluate the feasibility of other potential orientation control techniques.

L'orientation et la propriété de mémoire de forme des polymères cristallins liquides à chaînes latérales covalents et supramoléculaires

In many studies of the side-chain liquid crystalline polymers (SCLCPs) bearing azobenzene mesogens as pendant groups, obtaining the orientation of azobenzene mesogens at a macroscopic scale as well as its control is important, because it impacts many properties related to the cooperative motion characteristic of liquid crystals and the trans-cis photoisomerization of the azobenzene molecules. Various means can be used to align the mesogens in the polymers, including rubbed surface, mechanical stretching or shearing, and electric or magnetic field. In the case of azobenzene-containing SCLCPs, another method consists in using linearly polarized light (LPL) to induce orientation of azobenzene mesogens perpendicular to the polarization direction of the excitation light, and such photoinduced orientation has been the subject of numerous studies. In the first study realized in this thesis (Chapter 1), we carried out the first systematic investigation on the interplay of the mechanically and optically induced orientation of azobenzene mesogens as well as the effect of thermal annealing in a SCLCP and a diblock copolymer comprising two SCLCPs bearing azobenzene and biphenyl mesogens, respectively. Using a supporting-film approach previously developed by our group, a given polymer film can be first stretched in either the nematic or smectic phase to yield orientation of azobenzene mesogens either parallel or perpendicular to the strain direction, then exposed to unpolarized UV light to erase the mechanically induced orientation upon the trans–cis isomerization, followed by linearly polarized visible light for photoinduced reorientation as a result of the cis–trans backisomerization, and finally heated to different LC phases for thermal annealing. Using infrared dichroism to monitor the change in orientation degree, the results of this study have unveiled complex and different orientational behavior and coupling effects for the homopolymer of poly{6-[4-(4-methoxyphenylazo)phenoxy]hexyl methacrylate} (PAzMA) and the diblock copolymer of PAzMA-block- poly{6-[4-(4-cyanophenyl) phenoxy]hexyl methacrylate} (PAzMA-PBiPh). Most notably for the homopolymer, the stretching-induced orientation exerts no memory effect on the photoinduced reorientation, the direction of which is determined by the polarization of the visible light regardless of the mechanically induced orientation direction in the stretched film. Moreover, subsequent thermal annealing in the nematic phase leads to parallel orientation independently of the initial mechanically or photoinduced orientation direction. By contrast, the diblock copolymer displays a strong orientation memory effect. Regardless of the condition used, either for photoinduced reorientation or thermal annealing in the liquid crystalline phase, only the initial stretching-induced perpendicular orientation of azobenzene mesogens can be recovered. The reported findings provide new insight into the different orientation mechanisms, and help understand the important issue of orientation induction and control in azobenzene-containing SCLCPs. The second study presented in this thesis (Chapter 2) deals with supramolecular side-chain liquid crystalline polymers (S-SCLCPs), in which side-group mesogens are linked to the chain backbone through non-covalent interactions such as hydrogen bonding. Little is known about the mechanically induced orientation of mesogens in S-SCLCPs. In contrast to covalent SCLCPs, free-standing, solution-cast thin films of a S-SCLCP, built up with 4-(4’-heptylphenyl) azophenol (7PAP) H-bonded to poly(4-vinyl pyridine) (P4VP), display excellent stretchability. Taking advantage of this finding, we investigated the stretching-induced orientation and the viscoelastic behavior of this S-SCLCP, and the results revealed major differences between supramolecular and covalent SCLCPs. For covalent SCLCPs, the strong coupling between chain backbone and side-group mesogens means that the two constituents can mutually influence each other; the lack of chain entanglements is a manifestation of this coupling effect, which accounts for the difficulty in obtaining freestanding and mechanically stretchable films. Upon elongation of a covalent SCLCP film cast on a supporting film, the mechanical force acts on the coupled polymer backbone and mesogenic side groups, and the latter orients cooperatively and efficiently (high orientation degree), which, in turn, imposes an anisotropic conformation of the chain backbone (low orientation degree). In the case of the S-SCLCP of P4VP-7PAP, the coupling between the side-group mesogens and the chain backbone is much weakened owing to the dynamic dissociation/association of the H-bonds linking the two constituents. The consequence of this decoupling is readily observable from the viscoelastic behavior. The average molecular weight between entanglements is basically unchanged in both the smectic and isotropic phase, and is similar to non-liquid crystalline samples. As a result, the S-SCLCP can easily form freestanding and stretchable films. Furthermore, the stretching induced orientation behavior of P4VP-7PAP is totally different. Stretching in the smectic phase results in a very low degree of orientation of the side-group mesogens even at a large strain (500%), while the orientation of the main chain backbone develops steadily with increasing the strain, much the same way as amorphous polymers. The results imply that upon stretching, the mechanical force is mostly coupled to the polymer backbone and leads to its orientation, while the main chain orientation exerts little effect on orienting the H-bonded mesogenic side groups. This surprising finding is explained by the likelihood that during stretching in the smectic phase (at relatively higher temperatures) the dynamic dissociation of the H-bonds allow the side-group mesogens to be decoupled from the chain backbone and relax quickly. In the third project (Chapter 3), we investigated the shape memory properties of a S-SCLCP prepared by tethering two azobenzene mesogens, namely, 7PAP and 4-(4'-ethoxyphenyl) azophenol (2OPAP), to P4VP through H-bonding. The results revealed that, despite the dynamic nature of the linking H-bonds, the supramolecular SCLCP behaves similarly to covalent SCLCP by exhibiting a two-stage thermally triggered shape recovery process governed by both the glass transition and the LC-isotropic phase transition. The ability for the supramolecular SCLCP to store part of the strain energy above T[subscript g] in the LC phase enables the triple-shape memory property. Moreover, thanks to the azobenzene mesogens used, which can undergo trans-cis photoisomerization, exposure the supramolecular SCLCP to UV light can also trigger the shape recovery process, thus enabling the remote activation and the spatiotemporal control of the shape memory. By measuring the generated contractile force and its removal upon turning on and off the UV light, respectively, on an elongated film under constant strain, it seems that the optically triggered shape recovery stems from a combination of a photothermal effect and an effect of photoplasticization or of an order-disorder phase transition resulting from the trans-cis photoisomerization of azobenzene mesogens.

Molecular Origins of Higher Harmonics in Large-Amplitude Oscillatory Shear Flow: Shear Stress Response

Recent work has focused on deepening our understanding of the molecular origins of the higher harmonics that arise in the shear stress response of polymeric liquids in large-amplitude oscillatory shear flow. For instance, these higher harmonics have been explained by just considering the orientation distribution of rigid dumbbells suspended in a Newtonian solvent. These dumbbells, when in dilute suspension, form the simplest relevant molecular model of polymer viscoelasticity, and this model specifically neglects interactions between the polymer molecules [R.B. Bird et al., J Chem Phys, 140, 074904 (2014)]. In this paper, we explore these interactions by examining the Curtiss-Bird model, a kinetic molecular theory designed specifically to account for the restricted motions that arise when polymer chains are concentrated, thus interacting and specifically, entangled. We begin our comparison using a heretofore ignored explicit analytical solution [Fan and Bird, JNNFM, 15, 341 (1984)]. For concentrated systems, the chain motion transverse to the chain axis is more restricted than along the axis. This anisotropy is described by the link tension coefficient, ε, for which several special cases arise: ε = 0 corresponds to reptation, ε > 1/8 to rod-climbing, 1/2 ≥ ε ≥ 3/4 to reasonable predictions for shear-thinning in steady simple shear flow, and ε = 1 to the dilute solution without hydrodynamic interaction. In this paper, we examine the shapes of the shear stress versus shear rate loops for the special cases ε = (0,1/8, 3/8,1) , and we compare these with those of rigid dumbbell and reptation model predictions.

Molecular And Biochemical Characterization Of Caffeine Synthase And Purine Alkaloid Concentration In Guarana Fruit.

Guarana seeds have the highest caffeine concentration among plants accumulating purine alkaloids, but in contrast with coffee and tea, practically nothing is known about caffeine metabolism in this Amazonian plant. In this study, the levels of purine alkaloids in tissues of five guarana cultivars were determined. Theobromine was the main alkaloid that accumulated in leaves, stems, inflorescences and pericarps of fruit, while caffeine accumulated in the seeds and reached levels from 3.3% to 5.8%. In all tissues analysed, the alkaloid concentration, whether theobromine or caffeine, was higher in young/immature tissues, then decreasing with plant development/maturation. Caffeine synthase activity was highest in seeds of immature fruit. A nucleotide sequence (PcCS) was assembled with sequences retrieved from the EST database REALGENE using sequences of caffeine synthase from coffee and tea, whose expression was also highest in seeds from immature fruit. The PcCS has 1083bp and the protein sequence has greater similarity and identity with the caffeine synthase from cocoa (BTS1) and tea (TCS1). A recombinant PcCS allowed functional characterization of the enzyme as a bifunctional CS, able to catalyse the methylation of 7-methylxanthine to theobromine (3,7-dimethylxanthine), and theobromine to caffeine (1,3,7-trimethylxanthine), respectively. Among several substrates tested, PcCS showed higher affinity for theobromine, differing from all other caffeine synthases described so far, which have higher affinity for paraxanthine. When compared to previous knowledge on the protein structure of coffee caffeine synthase, the unique substrate affinity of PcCS is probably explained by the amino acid residues found in the active site of the predicted protein.

On The Distinct Molecular Architectures Of Dipping- And Spray-lbl Films Containing Lipid Vesicles.

The introduction of spraying procedures to fabricate layer-by-layer (LbL) films has brought new possibilities for the control of molecular architectures and for making the LbL technique compliant with industrial processes. In this study we show that significantly distinct architectures are produced for dipping and spray-LbL films of the same components, which included DODAB/DPPG vesicles. The films differed notably in their thickness and stratified nature. The electrical response of the two types of films to aqueous solutions containing erythrosin was also different. With multidimensional projections we showed that the impedance for the DODAB/DPPG spray-LbL film is more sensitive to changes in concentration, being therefore more promising as sensing units. Furthermore, with surface-enhanced Raman scattering (SERS) we could ascribe the high sensitivity of the LbL films to adsorption of erythrosin.

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.

Molecular And Morphological Evidence Reveals A New Species In The Phyllomedusa Hypochondrialis Group (hylidae, Phyllomedusinae) From The Atlantic Forest Of The Highlands Of Southern Brazil.

The taxonomic status of a disjunctive population of Phyllomedusa from southern Brazil was diagnosed using molecular, chromosomal, and morphological approaches, which resulted in the recognition of a new species of the P. hypochondrialis group. Here, we describe P. rustica sp. n. from the Atlantic Forest biome, found in natural highland grassland formations on a plateau in the south of Brazil. Phylogenetic inferences placed P. rustica sp. n. in a subclade that includes P. rhodei + all the highland species of the clade. Chromosomal morphology is conservative, supporting the inference of homologies among the karyotypes of the species of this genus. Phyllomedusa rustica is apparently restricted to its type-locality, and we discuss the potential impact on the strategies applied to the conservation of the natural grassland formations found within the Brazilian Atlantic Forest biome in southern Brazil. We suggest that conservation strategies should be modified to guarantee the preservation of this species.

Effect Of Aloe Vera Application On The Content And Molecular Arrangement Of Glycosaminoglycans During Calcaneal Tendon Healing.

Although several treatments for tendon lesions have been proposed, successful tendon repair remains a great challenge for orthopedics, especially considering the high incidence of re-rupture of injured tendons. Our aim was to evaluate the pharmacological potential of Aloe vera on the content and arrangement of glycosaminoglycans (GAGs) during tendon healing, which was based on the effectiveness of A. vera on collagen organization previously observed by our group. In rats, a partial calcaneal tendon transection was performed with subsequent topical A. vera application at the injury site. The tendons were treated with A. vera ointment for 7 days and excised on the 7(th) , 14(th) , or 21(st) day post-surgery. Control rats received ointment without A. vera. A higher content of GAGs and a lower amount of dermatan sulfate were detected in the A. vera-treated group on the 14(th) day compared with the control. Also at 14 days post-surgery, a lower dichroic ratio in toluidine blue stained sections was observed in A. vera-treated tendons compared with the control. No differences were observed in the chondroitin-6-sulfate and TGF-β1 levels between the groups, and higher amount of non-collagenous proteins was detected in the A. vera-treated group on the 21(st) day, compared with the control group. No differences were observed in the number of fibroblasts, inflammatory cells and blood vessels between the groups. The application of A. vera during tendon healing modified the arrangement of GAGs and increased the content of GAGs and non-collagenous proteins.

Genetic Breeding And Diversity Of The Genus Passiflora: Progress And Perspectives In Molecular And Genetic Studies.

Despite the ecological and economic importance of passion fruit (Passiflora spp.), molecular markers have only recently been utilized in genetic studies of this genus. In addition, both basic genetic researches related to population studies and pre-breeding programs of passion fruit remain scarce for most Passiflora species. Considering the number of Passiflora species and the increasing use of these species as a resource for ornamental, medicinal, and food purposes, the aims of this review are the following: (i) to present the current condition of the passion fruit crop; (ii) to quantify the applications and effects of using molecular markers in studies of Passiflora; (iii) to present the contributions of genetic engineering for passion fruit culture; and (iv) to discuss the progress and perspectives of this research. Thus, the present review aims to summarize and discuss the relationship between historical and current progress on the culture, breeding, and molecular genetics of passion fruit.