Phospholipid bilayers constitute the primary structural element of biological membranes, and as such, they play a central role in biochemical and biophysical processes at the cellular level, including cell protection, intercellular interactions, trans-membrane transport, cell morphology, and protein function, to name a few. The properties of phospholipid bilayers are thus of great interest from both experimental and theoretical standpoints. Although experiments have provided much of the macroscopic functions and properties of biological membranes, insight into specific mechanisms at the molecular level are seldom accessible by conventional methods. To obtain a better understanding of biochemical and biophysical processes at the molecular level involving phospholipid bilayers, we apply molecular simulation methods to investigate the complexity of the membrane matrix using atomistic models. Here, we discuss three specific biological processes that are associated with biological membranes: 1) membrane stabilization, 2) membrane phase behavior, and 3) fatty acid-induced toxicity in cell membranes. For membrane stabilization, molecular dynamics studies were performed for mixed phospholipid bilayers containing two of the most prevalent phospholipids (phosphatidylcholine and phosphatidylethanolamime) in biological membranes. We presented structural and dynamics properties of these systems, as well as the effect of stabilizing agents, such as trehalose, on their properties. Furthermore, we performed a comprehensive analysis of the phase transition of lipid bilayers and investigated the interactions of stabilizing agents (glucose or trehalose) with lipid bilayers under dehydrated conditions to understand the mechanisms for preservation of cellular systems. For membrane phase behavior, a comprehensive study of the structural properties of saturated and monounsaturated lipid bilayers near the main phase transition were investigated using molecular dynamics simulations. In this study, we demonstrated that atomistic simulations are capable of capturing the phase transformation process of lipid bilayers, providing a valuable set of molecular and structural information at and near its transition state. Lastly, the third study investigated the mechanism for fatty acid-induced toxicity by integrating in vitro and in silico experiments to reveal the biophysical interactions of saturated fatty acid (palmitate) with the cellular membranes and the role of trehalose and unsaturated fatty acids (oleate and linoleate) in preventing changes to the membrane structure. Knowledge gained from this study is essential in the prevention and treatment of obesity-associated cirrhosis diseases. / Ph. D.

A lattice gas with equal numbers of oppositely charged particles, diffusing under the influence of a uniform electric field and an excluded volume condition undergoes an order-disorder phase transition, controlled by the particle density and the field strength. This transition may be continuous (second order) or continuous (first order). Results from previous discrete simulations are shown, and a theoretical continuum model is developed. As this is a nonequilibrium system, there is no associated free energy to determine the location of a first order transition. Instead, the model equations for this system are evolved in time numerically, and the locus of this transition is determined via the presence of a stable state with coexisting regions of order and disorder. The Crank-Nicholson, nonlinear Gauss-Seidel, and GMRES algorithms used to solve the model equations are discussed. Performance enhancements and limits on convergence are considered. / Master of Science

No description available.

The thesis entitled “In situ crystallography and charge density analysis of phase transitions in complex inorganic sulfates” consists of six chapters. Structural changes exhibited by ferroic and conducting materials are studied as a function of temperature via in situ crystallography on the same single crystal. These unique experiments bring out the changes in the crystal system resulting in subtle changes in the complex polyhedra, distortions in bond lengths and bond angles, rotation of sulfate tetrahedral around metal atoms, phase separations and charge density features. The results provide new insights into the structural changes during the phase transition in terms of coordination changes, variable bond paths and variability in electrostatic potentials while suggesting possible reaction pathways hitherto unexplored. Chapter 1 gives a brief review of the basic features of structural phase transitions in terms of types of phase transitions, their mechanisms and related properties and outlines some of the key characterization techniques employed in structural phase transition studies like single crystal diffraction, thermal analysis, conductivity, dielectric relaxation, Raman spectroscopy and charge density studies. Chapter 2 deals with the group of compounds A3H(SO4)2, where A= Rb, NH4, K, Na which undergoes ferroelastic to paraelastic phase transitions with increase in temperature. Crystal structures of these compounds have been determined to a high degree of accuracy employing the same single crystal at room temperature at 100K and at higher temperatures. The data collection at 100K allows the examination of the ordered and disordered hydrogen atom positions. Rb3H(SO4)2 show two intermediate phases before reaching the paraelastic phase with increase in temperature. However, in case of (NH4)3H(SO4)2 and K3H(SO4)2, the paraelastic phase transition involves a single step. Chapter 3 deals with variable temperature in situ single crystal X-ray diffraction studies on fast super protonic conductors AHSO4, where A= Rb, NH4, K to characterize the structural phase transitions as well as the dehydration mechanism. The structure of KHSO4 at room temperature belongs to an orthorhombic crystal system with the space group symmetry Pbca and on heating to 463K it transforms to a C centered orthorhombic lattice, space group Cmca. The high temperature structure contain two crystallographically independent units of KHSO4 of which one KHSO4 unit is disordered at oxygen and hydrogen sites an shows a remarkable increase of sulfur oxygen bond distance – 1.753(4)Å. On heating to 475K, two units of disordered KHSO4 combine and loose one molecule of water to result in a structure K2S2O7 along with an ordered KHSO4 in a monoclinic system [space group P21/c]. On further heating to 485K two units of ordered KHSO4 combine, again to lose one water molecule to give K2S2O7 in a monoclinic crystal system [space group C2/c]. In the case of RbHSO4, both the high temperature structural phase transition and a serendipitous polymorph have been characterized by single crystal X-ray diffraction. The room temperature structure is monoclinic, P21/n, and on heating the crystal insitu On the diffractometer to 460K the structure changes to an orthorhombic system [space group Pmmn]. On keeping the crystallization temperature at 80°C polymorph crystals of RbHSO4 were grown. In case of NH4HSO4 both the room temperature and high temperature structures are structurally similar to those in RbHSO4, but the transition temperature is found to be 413K. Chapter 4 deals with the crystal structure, ionic conduction, dielectric relaxation, Raman spectroscopy phase transition pf a fast ion conductor Na2Cd(SO4)2. The structure is monoclinic, space group C2/c, and is built up with inter connecting CdO6 octahedra and SO4 tetrahedra resulting in a framework structure. The mobile Na atoms are present in the framework, resulting in a high ionic conductivity. The conductivity measurement shows two phase transitions one at around 280°C, which was confirmed later from DTA, dielectric relaxation, high temperature powder diffraction and Raman spectroscopy. Chapter 5 describes the structure and in situ phase separation in two different bimetallic sulfates Na2Mn1.167(SO4)2S0.33O1.1672H2O and K4Cd3(SO4)5.3H2O. These compounds were synthesized keeping them as mimics of mineral structures. The structure of Na2Mn1.167(SO4)2S0.33O1.1672H2O is trigonal, space group R . The stiochiometry can be viewed as a combination of Na2Mn(SO4)22H2O resembling the mineral Krohnkite with an additional (Mn0.167S0.333O1.167) motif. On heating the parent compound on the diffractometer to 500K and keeping the capillary at this temperature for one hour, a remarkable structural phase separation occurs with one phase showing a single crystal-single crystal transition and the other generating a polycrystalline phase. The resulting single crystal spots can be indexed in a monoclinic C2/c space group and the structure determination unequivocally suggests the formation of Na2Mn(SO4)2, isostructural to Na2Cd(SO4)z. The mechanism follows the symmetry directed pathway from the rhombohedral → monoclinic symmetry with the removal of symmetry subsequent to the loss of the two coordinated water molecules. In case of K4Cd3(SO4)5.3H2O the structure belongs to the space group P21/n at room temperature and on heating to 500K and holding the capillary at this temperature for 60 minutes as before, the CCD images can be indexed in a cubic P213 space group after the phase separation, generating K2Cd2(SO4)3, belonging to the well known Langbeinite family, while the other phase is expected to be the sought after K2Cd(SO4)2. The possible pathways have been discussed. Chapter 6 reports the charge density studies of phase transitions in a type II langbeinite, Rb2Mn2(SO4)3. The structure displays two different phases, cubic at 200K, orthorhombic at 100K respectively. After multiple refinements it is found that there are significant differences in the actual bond path (Rij) and the conventional bond length. In the cubic phase the distortions in sulfate tetrahedral are more than in the orthorhombic phase which could be the expected driving force for the phase transition to occur. Appendix contains reprints of the work done on the structures of the following: a) Rb2Cd3(SO4)3(OH)2.2H2O: structural stability at 500 K b) Structure of (NH4)2Cd3(SO4)4.5H2O c) Structure of Rb2Cd3(SO4)4.5H2O

Thesis (M.S.)--Miami University, Dept. of Physics, 2005. / Title from first page of PDF document. Document formatted into pages; contains [1], vii, 55 p. : ill. Includes bibliographical references (p. 53-55).

Les perovskites hybrides organique-halogénure de plomb représentent une classe de matériaux émergents, proposés en tant qu'absorbeur de lumière dans le cadre d'une nouvelle génération de cellules solaires. La formule chimique de ces composés est APbX3, où A est un cation organique, X représente un anion halogénure (normalement Cl-, Br-, ou l-, ou alors un alliage composé par ces éléments). Les perovskite hybrides combinent d'excellentes propriétés d'absorption avec une grande longueur de diffusion et de longues durées de vie des porteurs de charge, ce qui permet d'atteindre des efficacités de conversion de photons de 22%. Un autre avantage réside dans leur bas coût de fabrication. Par conséquent, avec le développement de cette classe de matériaux, le photovoltaïque basé sur les perovskites sera potentiellement capable de fortement améliorer les performances de la technologie photovoltaïque actuelle, basée sur le silicium. Dans cette thèse, nous utilisons des méthodes optiques afin d'étudier les propriétés électroniques de base et la morphologie de couches minces de plusieurs représentants des perovskites. Nous étudions notamment des composés ayant le methylammonium et le formamidinium en tant que cations organiques ainsi que les iodures et les bromures à large bande interdite et nous montrons de quelle manière la composition chimique influence les paramètres étudiés. Par magnéto-transmission, nous déterminons directement l'énergie de liaison de l'exciton et sa masse réduite. Nous avons trouvé que les énergies de liaison à T = 2K sont comprises de 14 à 25 meV, plus petites ou comparables à l'énergie thermique moyenne à la température ambiante (25meV). De plus, ces valeurs diminuent à T=160K jusqu'à 10-24meV. Suite à ces résultats, nous concluons que les porteurs photocréés dans les perovksites peuvent être considérés ionisés thermiquement à la température ambiante. Les valeurs de masse effective sont comprises entre 0.09-0.13 fois la masse de l'électron libre. Nous montrons également que l'énergie de liaison de l'exciton ainsi que la masse effective dépendent linéairement de la valeur de la bande interdite. Nos résultats permettent donc d'estimer la valeur des paramètres de ces nouveaux composés perovksites. Nous avons étudié la morphologie de couches minces de perovskite par photoluminescence résolue spatialement avec une résolution micrométrique. Cette technique nous a permis d'observer des grains cristallins uniques. Nous démontrons que la transition de la phase tétragonale à orthorhombique à basse température est incomplète dans tous les matériaux étudiés, comme montré par les résidus de phase tétragonale trouvés à T =4K. En étudiant structurellement certaines régions endommagées et photo-recuites, nous montrons que la présence de la phase tétragonale à basse température augmente, causée par une déplétion de l'halogène. / The hybrid organo-lead halide perovskites are an emerging class of materials, proposed for use as light absorbers in a new generation of photovoltaic solar cells. The chemical formula for these materials is APbX3, where A is an organic cation and X represents halide anions (most commonly Br-, Cl- or I-, or alloyed combination of these). The hybrid perovskies combine excellent absorption properties with large diffusion lengths and long lifetime of the carriers, resulting in photon conversion efficiencies as high as 22%. Another advantage is the inexpensiveness of the fabrication process. Therefore, with the rapid development of this class of materials, the perovskite photovoltaics has perspectives to outperform the well-established silicon technology. Here, we use optical methods to investigate the basic electronic properties and morphology in the thin films of several representatives of the hybrid perovskites. We study the compounds based on Methylammonium and Formamidinium organic cations; the iodides and wide band-gap bromides, showing how the chemical composition influences the investigated parameters. Using magneto-transmission, we directly determine the values of exciton binding energy and reduced mass. We find that the exciton binding energies at T = 2 K, varying from 14 to 25 meV, are smaller or comparable to the average thermal energy at room temperature (˜25 meV). Moreover, these values fall further at T = 160 K, to 10-24 meV. Based on that we conclude that the carriers photocreated in a perovskite material can be considered to be thermally ionized at room temperature. The measured reduced masses are in the range of 0.09-0.13 of the electron rest mass. We also show that both exciton binding energy and reduced mass depend linearly on the band gap energy. Therefore, the values of these parameters can be easily estimated for the synthesis of new perovskite compounds. With the spatially resolved photoluminescence, we probe the morphology of perovskite films with micrometer resolution, which enables us to observe single crystalline grains. The resulting maps show that all investigated thin films are composed from the dark and bright crystalline grains. We demonstrate that the low temperature phase transition from tetragonal to orthorhombic phase is incomplete in all studied materials, as the remains of the tetragonal phase are found even at T = 4 K. By investigating structurally damaged and photo annealed regions, where the occurrence of the tetragonal phase at low temperatures is enhanced, we attribute its presence to the depleted halide content.

No description available.

The Kibble-Zurek mechanism (KZM) primarily characterizes scaling in the formation of topological defects when a system crosses a continuous phase transition. The KZM was first used to study the evolution of the early universe, describing the topology of cosmic domains and strings as the symmetry-breaking phase transitions acted on the vacuum fields during the initial cooling. A ferromagnetic spin-1 $^{87}$Rb Bose-Einstein condensate (BEC) exhibits a second-order gapless quantum phase transition due to a competition between the magnetic and collisional spin interaction energies. Unlike extended systems where the KZM is illustrated by topological defects, we focus our study on the temporal evolution of the spin populations and observe how the scaling of the spin dynamics depend on how fast the system is driven through the critical point. In our case, the excitations are manifest in the temporal evolution of the spin populations illustrating a Kibble-Zurek type scaling, where the dynamics of slow quenches through the critical point are predicted to exhibit universal scaling as a function of quench speed. The KZM has been studied theoretically and experimentally in a large variety of systems. There has also been a tremendous interest in the KZM in the cold atoms community in recent years. It has been observed not only in ion chains and in atomic gases in optical lattices, but also in Bose gases through the formation of vortices or solitons. The KZM in the context of crossing the quantum phase transition in a ferromagnetic BEC has been theoretically studied, but this thesis is the first experimental investigation of this phenomenon.

Thesis (MSc)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: Organic molecular salts have a wide range of physical properties which can be chemically tailored by minor variations of their substituents. These characteristics include high degrees of anisotropy, electrical conductivity ranging from superconducting to insulating, and structural changes in the crystal lattice during first order phase transitions brought about by minimal changes in temperature, effective pressure, and in some cases even light. Hence, these materials are particularly interesting for the development of molecular electronics and also as study materials in solid state physics. The family of copper-dimethyl-dicyanoquinone-diimine (Cu(DMe-DCNQI)2) salts forms part of the radical anion salt subclass of organic molecular crystals and is of particular interest due to its extraordinarily high conductivity compared to other quasi one-dimensional organic conductors. Its metal-to-insulator phase transition is characterised by conductivity jumps across several orders of magnitude within a few kelvin. Over the past three decades the metallic and insulating phases, as well as the transition behaviour have been investigated extensively utilising a broad spectrum of methods amongst others electrical conductivity, electron spin resonance, and re ectivity measurements, x-ray photoelectron and infrared spectroscopy, x-ray diffraction, and dilatometry. Fast light-switching between phases has been observed in partially deuterated forms of Cu(DCNQI)2 on sub-100-ps time scales. Furthermore, the phase transition is believed to be induced by a deformation of the crystalline lattice and a charge density wave formation which are detectable in diffraction images. Therefore we want to investigate this metal-to-insulator phase transition structurally and temporally via ultrafast electron diffraction. The technique of ultrafast electron diffraction employs the fundamentals of pump-probe spectroscopy: One of the two femtosecond pulsed laser beams excites the thin, crystalline sample, while the other - after being converted into a pulsed electron beam via the photoelectric effect - forms a diffraction image of the sample's lattice structure. The arrival time of the two pulses at the sample can be varied by a few femtoseconds with respect to each other enabling the resolution of ultrafast structural dynamics of the crystal's atomic lattice via electron diffraction. During the work presented in this thesis the sample preparation and characterisation leading to a successful introduction of Cu(DCNQI)2 into our ultrafast electron diffraction setup is presented. A diffraction pattern of comparable quality to that of a commercially available transmission electron microscope was recorded of the metallic state of partially deuterated d6 Cu(DCNQI)2. Subsequent analysis of the obtained diffraction data and further studies of the low temperature state { including simulations as well as experiments { have narrowed down the factors still making the diffraction pattern evasive. Possible solutions to experimental challenges are proposed to make the documentation of structural ultrafast dynamics in these organic molecular salts an attainable goal in the future. / AFRIKAANSE OPSOMMING: Organiese molekulêre soute het `n wye verskeidenheid van fisiese eienskappe wat chemies verander kan word deur geringe variasie in die samestelling van die sout. Hierdie eienskappe sluit in `n hoë graad van anisotropie, elektriese geleidingsvermoë wat strek van supergeleiding tot elektriese isolasie, en strukturele veranderinge in die kristalstruktuur tydens eerste orde fase-oorgange wat veroorsaak word deur geringe veranderinge in temperature, effektiewe druk en in sommige gevalle selfs lig. Gevolglik is hierdie material besonder interessant vir die ontwikkeling van molekulêre elektronika en ook as studiemateriaal in vastetoestandfisika. Die familie van koperdimetieldisianokinoondiimien (Cu(DMe-DCNQI)2) soute vorm `n deel van die radikaal-anioon-sout subklas van organiese molekulêre kristalle en is van besondere belang as gevolg van hulle buitengewone hoë elektriese geleidingsvermoë in vergelyking met ander kwasi-eendimensionele organiese geleiers. Die metaal-na-isolator fase-oorgang van hierdie kristal word gekenmerk deur die verandering van die geleidingsvermoë met verskeie ordegroottes binne `n paar kelvin. Gedurende die laaste drie dekades is die metaal en isolator fases, asook die oorgangsgedrag deeglik ondersoek met behulp van `n wye verskeidenheid van metodes wat onder andere elektriese geleidingsvermoë, elektron-spin resonans en reeksiemetings, x-straal fotoelektron en infrarooi spektroskopie, x-straal diffraksie en dilatometrie insluit. Vinnige skakeling tussen fases is waargeneem in gedeeltelik gedeuteerde vorms van Cu(DCNQI)2 op `n sub-100-ps tydskaal. Daar word verder geglo dat die fase-oorgang geïnduseer word deur `n deformasie van die kristalstruktuur en die vorming van `n ladingsdigtheidgolf wat meetbaar is in elektrondiffraksiebeelde. Om hierdie rede wil ons die metaal-na-isolator fase-oorgang se struktuur- en tydafhanklikheid ondersoek deur gebruik te maak van ultra-vinnige elektron diffraksie. Die tegniek van ultra-vinnige elektron diffraksie maak gebruik van die beginsels van pomp-toets spektroskopie: Een van die twee femtosekonde laserpulse wek die dun kristallyne monster op, terwyl die ander na omskakeling in `n elektronpuls via die foto-elektriese effek `n diffraksiebeeld van die monster se kristalstruktuur vorm. Die aankomtyd van die twee pulse by die monster kan met `n paar femtosekondes ten opsigte van mekaar verander word om die tydresolusie van die ultra-vinnige strukturele dinamika van die kristal se atoomstruktuur deur elektrondiffraksie moontlik te maak. In hierdie tesis word die monstervoorbereiding en karakterisering wat gelei het tot suksesvolle eksperimente op Cu(DCNQI)2 in ons ultra-vinnige elektron diffraksie opstelling behandel. `n Diffraksie patroon waarvan die kwaliteit vergelykbaar is met die van `n kommersiëel beskikbare transmissie elektron mikroskoop is gemeet vir die metaalfase van gedeeltelik gedeuteerde d6 Cu(DCNQI)2. Daaropvolgende analiese van die gemete diffraksiedata en verdere studies van die lae temperatuur toestand wat simulasies sowel as eksperimente insluit het `n klein aantal faktore uitgewys wat steeds die deteksie van die isolatorfase se ladingsdigtheidgolf se kenmerkende diffraksiepatroon verhoed. Moontlike oplossings tot eksperimentele uitdagings word voorgestel om die dokumentering van strukturele ultra-vinnige dinamika in hierdie organiese molekulêre soute `n haalbare toekomstige doelwit te maak.

We investigate phase transitions in holographic models of QCD. In chapter I, we explore the effect of constant external U(1) fields on the physics of chiral symmetry breaking, as realized in the D3/D7 model. We discover that this model exhibits the phenomenon of magnetic catalysis, which is what one would expect from a weakly coupled field theory intuition. In chapter II, we continue exploring the effect of external U(1) fields but now on the backreacted D3/D7 model, where the backreaction is obtained via a smearing procedure. We again find the magnetic catalysis effect, however the results differ from the previous case depending on the backreaction parameters. In chapter III, we investigate lattices of instantons in the D4/D8 model of chiral symmetry breaking. These instanton lattices can change dimensionality, and in particular we investigate the 1D [right arrow] 2D transition as a simpler case of the more complicated 3D [right arrow] 4D transition which is conjectured to be holographically dual to the baryonic to quarkyonic phase transition. Besides this interpretation, one could also view this as a hypothetical condensed matter system. We have a lattice of instantons dominated by two-body forces, whose interactions depend not only on their mutual distance in physical space but also on their relative orientations in the internal isospace. We obtain a rich variety of instanton crystals whose description could serve to be useful beyond holography. / text