Charged polysaccharides as model polyelectrolytes : computational studies of transport and conformational properties : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Physics at Massey University, Palmerston North, New Zealand

Homogalacturonans (HGs) are polysaccharide co-polymers of galacturonic acid and its methylesterified counterpart, that play a crucial role in the mechanobiology of the cell walls of all land plants. When extracted, in solution, at pH values above the pKa, the carboxyl groups carried by the unmethylesterified residues endow the polymer chains with charge, making these systems interesting polyelectrolytes. The interand intra-molecular distributions of the non-charged methylesterified residues and their charged methylesterified counterparts are vital behaviour-determining characteristics of a sample's structure. Previous work has led to the development of techniques for the control of the amount and distribution of charges, and with these tools and samples available in dfiferent degrees of polymerisation, including small oligomers, the system offers a flexible test-bed for studying the behaviour of biological polyelectrolytes. This thesis is rooted in exploring the use of computational approaches, in particular molecular dynamics, to calculate the conformation of such polyelectrolytes in solution and to describe their transport properties in electric fields. The results of simulations are, in all cases, compared with the results of experimental work in order to ground the simulations. First, in chapter 2, these simulations are applied to calculate the free solution electrophoretic mobilities of galacturonides, charged oligosaccharides derived from digests of partially methylesterified HGs. The simulations are compared with experiment and were found to correctly predict the loss of resolution of electrophoretic mobilities for fully-charged species above a critical degree of polymerisation (DP), and the ionic strength dependence of the electrophoretic mobilities of different partially charged oligosaccharides. Next, in chapter 3, molecular dynamics (MD) simulations are used to calculate the electrophoretic mobilities of HGs that have different amounts and distributions of charges placed along the backbone. The simulations are shown to capture experimental results well even for samples that possess high charge densities. In addition they illuminate the role that local counterion condensation can play in the determination of the electrophoretic mobility of heterogeneous blocky polyelectrolytes that cannot be adequately described by a single chain-averaged charge spacing. Finally, in chapter 4, the last part of the research focusses on the configurations of these polyelelectrolyes in dilute solution, and on how the interactions between several chains can lead to the spatially heterogenous nature of polyelectrolyte solutions. Such questions are of long standing interest in the polyelectrolyte field and the results are compared with results from Small Angle X-Ray Scattering(SAXS). Overall the work demonstrates how state of the art MD approaches can provide insights into experimental results obtained from fundamentally interesting and biologically relevent polyelectrolytes

Metallic phase of disordered graphene superlattices with long-range correlations

Using the transfer matrix method, we study the conductance of the chiral particles through a monolayer graphene superlattice with long-range correlated disorder distributed on the potential of the barriers. Even though the transmission of the particles through graphene superlattice with white noise potentials is suppressed, the transmission is revived in a wide range of angles when the potential heights are long-range correlated with a power spectrum $S(k)\sim1/k^{\beta}$. As a result, the conductance increases with increasing the correlation exponent values gives rise a metallic phase. We obtain a phase transition diagram in which a critical correlation exponent depends strongly on disorder strength and slightly on the energy of the incident particles. The phase transition, on the other hand, appears in all ranges of the energy from propagating to evanescent mode regimes.Comment: 8 pages, 11 figure

Nodular Fasciitis of the Auricle: A Case Report

Introduction: Nodular fasciitis is described as a benign reactive proliferation of myofibroblasts. Due to its rapid-growing nature, a precise clinical diagnosis is difficult and the condition is frequently misdiagnosed as malignant lesions.   Case Report: In this study, we present the case of a young woman with an auricular nodular fasciitis as an example of one of the rarest sites of this tumor. The patient underwent an excision of the lesion under general anesthesia. The literature choices for treatment include complete excision, partial excision, or intralesional injection of steroids. Due to its associated local discomfort, and in order to exclude other differential diagnosis, we recommend a complete surgical excision.   Conclusion:  Auricular nodular fasciitis is a rare lesion. Due to its associated local discomfort, and in order to exclude other differential diagnosis, we recommend a complete surgical excision

An analysis of the landscape structure changes as an ecological approach to achieve sustainable regional planning (Case Study: Latian Dam Watershed)

The formation of modifications or conception in the landscape could possibly, be a procedure relative to its natural and non-disturbance process; and it could be hastened by the occurrence of disturbance regimes. The objective of this research is to survey the changes in a landscape structure, over a period of 30 years, to attain information, as to the current conditions of land use, utilizing landscape metrics in the watershed area of the Latian Dam, so as to analyze the results and the voids present, towards obtaining a specified sustainable regional planning for the abovementioned watershed. Land use was identified and reviewed by means of four Landsat satellite images for 1987, 1998, 2007, and 2017; and in this watershed, it was classified into four classes, (a) build-up areas, (b) vegetated areas, (c) bare lands and (d) water bodies. Subsequently, by taking advantage of 7 metrics at the landscape level and 8 metrics at the class level, the landscape structure in this watershed was quantified by utilizing the Fragstats 4.2 Software. The survey results illustrated an increment in the number of patches (NP), decrementing the mean area of the patches (AREA-MN), and increasing the Interspersion & Juxtaposition Index (IJI) signifies amplified fragmentation at the landscape level in this watershed. Similarly, the NP has also incremented at the class level, and thus, the fragmentation of patches and fragmentation in the entire three classes of land use, namely, build-up areas, bare lands, and vegetated areas has occurred. The amount of patchiness for the build-up class, with due attention to the increment in the mean area of patches (AREA-MIN), which demonstrates the fact that, this class is inclined and has a tendency towards a coarse-grained structure and a metric decrement in the AREA-MIN in the vegetated areas, illustrates that this class is prone to the fine-grained structure

Resolving solution conformations of the model semi-flexible polyelectrolyte homogalacturonan using molecular dynamics simulations and small-angle x-ray scattering

The conformation of polyelectrolytes in the solution state has long been of interest in polymer science. Herein we utilize all atom molecular dynamics simulations (MD) and small-angle x-ray scattering experiments (SAXS) to elucidate the molecular structure of the model polyelectrolyte homogalacturonan. Several degrees of polymerization were studied and in addition partial methylesterification of the otherwise charge-carrying carboxyl groups was used in order to generate samples with varying intra-chain charge distributions. It is shown that at length scales above around 1nm the conformation of isolated chains has surprisingly little dependence on the charge distribution or the concentration of attendant monovalent salts, reflective of the intrinsic stiffness of the saccharide rings and the dynamical constraints of the glycosidic linkage. Indeed the conformation of isolated chains over all accessible length scales is well described by the atomic coordinates available from fibre diffraction studies. Furthermore, in more concentrated systems it is shown that, after careful analysis of the SAXS data, the form of the inter-particle effects heralded by the emergence of a so-called polyelectrolyte peak, can be extracted, and that this phenomena can be reproduced by multiple chain MD simulations