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Recently, a one-chain monoclinic unit cell for Cellulose IIII having a single glucose in the asymmetric unit was proposed based on high-resolution diffraction patterns. The new work challenged a two-chain structure published 25 years earlier, although it did not provide new three-dimensional coordinates. Our goals were to solve the structure by modeling, find whether modeling would reject the previously determined two-chain unit cell, and compare the model with the anticipated experimental structure. Combinations of the O2, O3, and O6 hydroxyls produced 54 starting structures. Clusters of 13 cellotetraose chains terminated by methyl groups for each of the 54 starting structures were optimized with MM3(96). Hydroxyl groups on 16 of these 54 structures reoriented to give very similar hydrogenbonding schemes in the interiors, along with the lowest energies. The one-chain cell models had much lower energy. The eight best “up” one-chain models agree well with the structure newly determined by experiment.

Carbon Nanotubes (CNTs) hold great promise as an important engineering material for future applications. To fully exploit CNTs to their full potential, it is important to characterize their material response and ascertain their material properties. We have used molecular mechanics (MM) simulations to conduct virtual experiments on single-wall and multi-wall carbon nanotubes (SWNTs and MWNTs respectively) similar to those performed in the mechanics of materials laboratory on a continuum structure. The output (energy and deformation rather than the load and deflection) is used to understand the material response and formulate macroscopic constitutive relations. From results of MM simulations of axial and torsional deformations on SWNTs, Young's modulus, the shear modulus and the wall thickness of an equivalent continuum tube made of a linear elastic isotropic material were found. These values were used to compare the response of the continuum tube, modeled as an Euler-Bernoulli beam, in bending and buckling with those obtained from the MM simulations. MM simulations have been carried out to find energetically favorable double-walled carbon nanotube (DWNT) configurations, and analyze their responses to extensional, torsional, radial expansion/contraction, bending, and buckling deformations. Loads were applied either to one wall or simultaneously to both walls of an open-ended DWNT. These results were compared against SWNT results. It was found that for simple tension and torsional deformations, results for a DWNT can be derived from those for its constituent SWNTs within 3% error. Radial deformations of a SWNT were achieved by considering a DWNT with the SWNT as one of its walls and moving radially through the same distance all atoms of the other wall of the DWNT thereby causing a pseudo-pressure through changes in the cumulative van der Waals forces which deform the desired wall. Results of radial expansion/contraction of a SWNT were used to deduce an expression for the van der Waals forces, and find through-the-thickness elastic moduli (Young's modulus in the radial direction, Er, and Poisson's ratio ?r?) of the SWNT. We have found four out of the five elastic constants of a SWNT taken to be transversely isotropic about a radial line. MWNTs were studied using the same testing procedures as those used SWNTs. Based on the results from those simulations a continuum model is proposed for a MWNT whose response to mechanical deformations is the same as that of the MWNT. The continuum structure is comprised of concentric cylindrical tubes interconnected by truss elements. Young's modulus, Poisson's ratio, the thickness of each concentric tube, and the stiffness of the truss elements are given. The proposed continuum model is validated by studying its bending and buckling deformations and comparing these results to those from MM simulations. The major contributions to the field on nanotubes and the scientific literature is a simple and robust continuum model for nanotubes. This model can be used to study both SWNTs and MWNTs in either global or local responses by applying different analytic techniques. This model was developed using a consistent engineering methodology that mimicked traditional engineering testing, assumptions and constraints. / Ph. D.

Thesis (MScMedSc)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: Background Individuals who are latently infected with Mycobacterium tuberculosis (M.tb) are able to quell the infection by balancing the innate and adaptive immune responses. Glucocorticoids (GCs) can affect this balance and can increase the risk of reactivation of TB. The three month injectable contraceptive medroxyprogesterone acetate (MPA) is widely used by women in developing countries, where TB is rife. MPA, unlike the two monthly contraceptive norethisterone enanthate (NET), possesses selective glucocorticoid activity, and could therefore alter immune responses to TB. Aims The aim of my investigation was to elucidate the immune modulatory effects of the synthetic progestins, MPA and NET, compared to the endogenous hormones, cortisol and progesterone, in Mycobacterium bovis Bacillus Calmette–Guérin (BCG) or anti-CD3 stimulated peripheral blood mononuclear cells (PBMC). I aim to determine the effects of MPA, NET, cortisol and progesterone on the receptor expression of glucocorticoid and various progesterone receptors. I investigate the effect of the above mentioned hormones on the downstream signalling cascades in the presence or absence of either BCG or anti-CD3. The overall immune modulation will be determined with regard to the cytokine production in PBMCs. Methods The presence of receptors for these steroid hormones in PBMCs was verified and BCG, anti-CD3 and hormone induced changes in receptor expression determined through RT-PCR. The impact of cortisol, MPA, NET and progesterone on BCG or anti-CD3 mediated activation of downstream signalling molecules were determined by Western blot as well as Luminex analysis. Results and Conclusion My results show that BCG and anti-CD3 mediated activation of the T cell receptor associated signalling molecules, Lck, ZAP-70, LAT was inhibited by the steroid hormones. Similarly several kinases including JNK, ERK and p38 and transcription factors including STAT3, STAT5 and CREB were differentially affected by the hormones. The inhibition of phosphorylation seen in the different signalling molecules indicated an inhibition of activation of downstream signalling cascades. To investigate the impact of the hormone induced changes in the signalling cascades on the expression of inflammatory and anti-inflammatory cytokines Luminex analysis was performed on the supernatant of the BCG and anti-CD3 stimulated PBMC cultures. Cortisol and MPA, but not NET and progesterone, significantly inhibited the secretion of IL-1α, IL-1β, IL-6, IL-10, TNF-α, IL-12 and IL-13. These results suggest that the immune suppressive effects of MPA are likely mediated through a combination of direct genomic GR action as well as through direct or indirect inhibition of several signalling molecules. The inhibition of the IFN-γ, IL-12, IL-1and IL-6 secretion by MPA could potentially increase the risk of susceptibility to TB in women using this contraceptive. Therefore the absence of glucocorticoid activity seen with NET could make this contraceptive a better choice for women in TB endemic areas. / AFRIKAANSE OPSOMMING: Agtergrond Individue wat latent met Mikobakterium tuberkulose (M.tb) geïnfekteer is, is in staat om die infeksie te onderdruk deur die ingebore en aanpasbare immuunrespons te balanseer. Glukokortikoïede (GCs) kan hierdie balans beïnvloed en kan die risiko van heraktivering van tuberkulose (TB) verhoog. Die drie maande inspuitbare voorbehoedmiddel medroksiprogestroon-asetaat (MPA) word algemeen gebruik deur vroue in ontwikkelende lande, waar TB volop is. MPA, in teenstelling met die twee maandelikse voorbehoedmiddel noretisteroon enantaat (NET), beskik selektiewe glukokortikoïed aktiwiteit, en kan dus die immuunrespons teenoor TB verander. Doelwitte Die doel van my studie was om die immuunregulerende effekte van die sintetiese progestiene, MPA en NET, toe te lig , in vergelyking met die endogene hormone, kortisol en progesteroon, in Mycobacterium bovis Bacillus Calmette - Guerin (BCG) of anti- CD3 gestimuleerde perifere bloed mononukleêre selle (PBMSe). Ek het beoog om die gevolge van MPA, NET, kortisol en progesteroon op die reseptor uitdrukking van glukokortikoïede en verskeie progesteroon reseptore te bepaal. Ek het ondersoek ingestel op die effek van die bogenoemde hormone op die sein transduksie in die teenwoordigheid of afwesigheid van óf BCG of anti-CD3. Die algehele immuun -modulasie sal bepaal word met betrekking tot die produksie van sitokiene in PBMSe . Metodes Die teenwoordigheid van reseptore vir die steroïedhormone in PBMSe is geverifieer en BCG en anti-CD3 en die veranderinge deurdie hormone in verband met die reseptor uitdrukking bepaal deur RT -PCR. Die impak van kortisol, MPA, NET en progesteroon op BCG of anti- CD3 aktivering van sein transduksie molekules is bepaal deur ‘Western blot’ asook Luminex analise. Resultate en gevolgtrekking My resultate toon dat BCG en anti-CD3 die aktivering van die T-sel reseptor wat verband hou met sein molekules , LCK , ZAP -70 , en LAT word geïnhibeer deur die steroïedhormone . Van die kinases insluitend JNK , ERK en p38 en transkripsie faktore, insluitend STAT3 , STAT5 en CREB is beïnvloed deur die hormone. Die inhibisie van fosforilering gesien in die verskillende sein molekules dui daarop aan dat 'n inhibisie van aktivering van sein transduksie. Die impak van die hormoon veroorsaak veranderinge in die sein transduksie met betrekking tot die uitdrukking van inflammatoriese en anti -inflammatoriese sitokiene Luminex analise is uitgevoer op die supernatant van die BCG en anti-CD3 gestimuleerde PBMS kulture. Kortisol en MPA, maar nie NET en progesteroon , het aansienlik die produksie van IL-1α , IL-1β , IL-6 , IL-10 , TNF-α , IL-12 en IL-13 geïnhibeer. Hierdie resultate dui daarop dat die immuunstelsel se onderdrukkende effekte van MPA is waarskynlik bemiddel deur 'n kombinasie van direkte genomiese GR interaksie sowel as deur direkte of indirekte inhibisie van verskeie sein molekules . Die inhibisie van die IFN-γ, IL-12, IL-1 en IL-6 sekresie deur MPA kan potensieel die risiko verhoog van vatbaarheid vir TB in vroue wat hierdie voorbehoedmiddel gebruik. Daarom oor die afwesigheid van glukokortikoïede aktiwiteit wat gesien is met NET, kan maak laat hierdie voorbehoedmiddel 'n beter keuse vir vroue in TB endemiese gebiede.

Este trabalho visou a análise estrutural de três compostos orgânicos: [A] : (2SR, 8SR)-2-(8-O-borinil-8-fenil)etil piperidina (C17H28NOB), [B] : (1SR, 2SR)-1-p-Bromoanilina-1-fenil-2-metil-3-pentanona -(C18H20NOBr) e [C] : um triterpeno-(C30O3H46) por difração de raio-X e por mecânica molecular. As estruturas no estado sólido foram primeiramente obtidas por difração de raios-x por monocristais, e posteriormente analisadas por mecânica molecular. [A]: monoclínico, grupo espacial C2/c, a=15.259(3)&#197, b=12.574(2)&#197, c=17.413(5)&#197, &#946=94.44&#176, Z=8, Dx=1.089 g/cm3, V=3331.45޵ as estruturas cristalográficas e por mecânica molecular não apresentam grandes desvios. [B]: triclínico, grupo espacial P1&#175, a=8.467(7)&#197, b=8.7361(3)&#197, c=12.468(9)&#197, &#945=82.401(5)&#176, &#946=83.096(6)&#176, &#978=69.026(5)&#176, Z=2, Dx=1.430 g/cm3, V=850.95޵ a principal diferença entre as duas estruturas cristalográfica e por mecânica molecular está no ângulo de torsão C(2)-C(1)-N-C(8) de 59.8&#176. Entre as moléculas relacionadas pelo centro de inversão existe duas pontes de hidrogênio entre os átomos O-N. [C]: ortorrômbico, grupo espacial P212121, a=7.314(7)&#197, b=12.807(3)&#197, c=26.812(5)&#197, Z=4, Dx=1.197 g/cm3, V=2511.49&#1973. Não existem grandes diferenças entre as estruturas cristalográficas e por mecânica molecular. As moléculas estão dimerizadas por uma ponte de hidrogênio entre os átomos (O1) e (O2) das moléculas relacionadas por simetria. / This work aimed the structural analysis of three organic compounds: [A] : (2SR, 8SR)-2-(8-O-borinyl-8-phenyl)ethyl piperidine (C17H28NOB), [B] : (1SR, 2SR)-1-p-Bromoaniline-1-phenyl-2-methyl-3-pentanone -(C18H20NOBr) e [C] : um triterpene-(C30O3H46) using X-ray diffraction and molecular mechanics. The solid state structures were firstly obtained by X-ray diffraction of single crystals, and further analyzes by molecular mechanics. [A]: monoclinic, space group, C2/c, a=15.259(3)&#197, b=12.574(2)&#197, c=17.413(5)&#197, &#946=94.44&#176, Z=8, Dx=1.089 g/cm3, V=3331.45޵ the crystallographic and molecular mechanics structures dont show large differences. [B]: triclinic, space group P1&#175, a=8.467(7)&#197, b=8.7361(3)&#197, c=12.468(9)&#197, &#945=82.401(5)&#176, &#946=83.096(6)&#176, &#978=69.026(5)&#176, Z=2, Dx=1.430 g/cm3, V=850.95޵ the main difference between the crystallographic and the molecular mechanics structures is in the dihedral angle C(2)-C(1)-N-C(8) de 59.8&#176. There are between the molecules related by inversion center two hydrogen bonds between the atoms O-N. [C]: orthorhombic, space group, P212121, a=7.314(7)&#197, b=12.807(3)&#197, c=26.812(5)&#197, Z=4, Dx=1.197 g/cm3, V=2511.49&#1973. There are not large differences between the crystallographic and the molecular mechanics structures. The molecules are dimerized by a hydrogen bond between the atoms (O1) and (O2) from molecules symmetrically related.

Protein mechanical responses play a critical role in a wide variety of biological phenomena, impacting events as diverse as muscle contraction and stem cell differentiation. Recent advances in both experimental and computational techniques have provided the opportunity to explore protein constitutive properties at the molecular level. However, despite these advances many questions remain about how proteins respond to applied mechanical forces, particularly as a function of load magnitude. In order to address these questions, relatively simple helical structures were computationally tested to determine the mechanisms and kinetics of unfolding at a range of physiologically relevant load magnitudes. Atomically detailed constant force molecular dynamics simulations combined with the Milestoning kinetic analysis framework revealed that the mean first passage time (MFPT) of the initiation of unfolding of long (~16nm) isolated helical domains was a non-monotonic function of the magnitude of applied tensile load. The unfolding kinetics followed a profile ranging from 2.5ns (0pN) to a peak of 3.75ns (20pN) with a decreasing MFPT beyond 40pN reflected by an MFPT of 1ns for 100pN. The application of the Milestoning framework with a coarse-grained network analysis approach revealed that intermediate loads (15pN-25pN) retarded unfolding by opening additional, slower unfolding pathways through non-native [pi]-helical conformations. Analysis of coiled-coil helical pairs revealed that the presence of the second neighboring helix delayed unfolding initiation by a factor of 20, with calculated MFPTs ranging from 55ns (0pN) to 85ns (25pN per helix) to 20ns (100pN per helix). The stability of the coiled-coil domains relative to the isolated helix was shown to reflect a decreased propensity to break flexibility restraining intra-helix hydrogen bonds, thereby delaying [psi] backbone dihedral angle rotation and unfolding. These results show for the first time a statistically determined profile of unfolding kinetics for an atomically detailed protein that is non-monotonic with respect to load caused by a change in the unfolding mechanism with load. Together, the methods introduced for analyzing the mechanical response of proteins as well as the timescales determined for the initiation of unfolding provide a framework for the determination of the constitutive properties of proteins and non-biological polymers with more complicated geometries. / text

Este trabalho visou a análise estrutural de três compostos orgânicos: [A] : (2SR, 8SR)-2-(8-O-borinil-8-fenil)etil piperidina (C17H28NOB), [B] : (1SR, 2SR)-1-p-Bromoanilina-1-fenil-2-metil-3-pentanona -(C18H20NOBr) e [C] : um triterpeno-(C30O3H46) por difração de raio-X e por mecânica molecular. As estruturas no estado sólido foram primeiramente obtidas por difração de raios-x por monocristais, e posteriormente analisadas por mecânica molecular. [A]: monoclínico, grupo espacial C2/c, a=15.259(3)&#197, b=12.574(2)&#197, c=17.413(5)&#197, &#946=94.44&#176, Z=8, Dx=1.089 g/cm3, V=3331.45޵ as estruturas cristalográficas e por mecânica molecular não apresentam grandes desvios. [B]: triclínico, grupo espacial P1&#175, a=8.467(7)&#197, b=8.7361(3)&#197, c=12.468(9)&#197, &#945=82.401(5)&#176, &#946=83.096(6)&#176, &#978=69.026(5)&#176, Z=2, Dx=1.430 g/cm3, V=850.95޵ a principal diferença entre as duas estruturas cristalográfica e por mecânica molecular está no ângulo de torsão C(2)-C(1)-N-C(8) de 59.8&#176. Entre as moléculas relacionadas pelo centro de inversão existe duas pontes de hidrogênio entre os átomos O-N. [C]: ortorrômbico, grupo espacial P212121, a=7.314(7)&#197, b=12.807(3)&#197, c=26.812(5)&#197, Z=4, Dx=1.197 g/cm3, V=2511.49&#1973. Não existem grandes diferenças entre as estruturas cristalográficas e por mecânica molecular. As moléculas estão dimerizadas por uma ponte de hidrogênio entre os átomos (O1) e (O2) das moléculas relacionadas por simetria. / This work aimed the structural analysis of three organic compounds: [A] : (2SR, 8SR)-2-(8-O-borinyl-8-phenyl)ethyl piperidine (C17H28NOB), [B] : (1SR, 2SR)-1-p-Bromoaniline-1-phenyl-2-methyl-3-pentanone -(C18H20NOBr) e [C] : um triterpene-(C30O3H46) using X-ray diffraction and molecular mechanics. The solid state structures were firstly obtained by X-ray diffraction of single crystals, and further analyzes by molecular mechanics. [A]: monoclinic, space group, C2/c, a=15.259(3)&#197, b=12.574(2)&#197, c=17.413(5)&#197, &#946=94.44&#176, Z=8, Dx=1.089 g/cm3, V=3331.45޵ the crystallographic and molecular mechanics structures dont show large differences. [B]: triclinic, space group P1&#175, a=8.467(7)&#197, b=8.7361(3)&#197, c=12.468(9)&#197, &#945=82.401(5)&#176, &#946=83.096(6)&#176, &#978=69.026(5)&#176, Z=2, Dx=1.430 g/cm3, V=850.95޵ the main difference between the crystallographic and the molecular mechanics structures is in the dihedral angle C(2)-C(1)-N-C(8) de 59.8&#176. There are between the molecules related by inversion center two hydrogen bonds between the atoms O-N. [C]: orthorhombic, space group, P212121, a=7.314(7)&#197, b=12.807(3)&#197, c=26.812(5)&#197, Z=4, Dx=1.197 g/cm3, V=2511.49&#1973. There are not large differences between the crystallographic and the molecular mechanics structures. The molecules are dimerized by a hydrogen bond between the atoms (O1) and (O2) from molecules symmetrically related.

No description available.