Thesis advisor: Udayan Mohanty / The stabilization of particular conformations of protein and nucleic acid structure is believed to play an important role in many important biological functions. In chapter one, the α -helical conformation and structural stability of single and double stapled all- hydrocarbon cross-linked p53 peptides when bound and unbound to MDM2 are investigated. Our study provides a comprehensive rationalization of the relationship between peptide stapling strategy, the secondary structural stability, and the binding affinity of p53-MDM2 complex. In chapter two, we study counterion-mediated collapse of a strongly charged model polyelectrolyte chain by Group-II divalent metal cations using coarse-grained Brownian dynamics simulations. Polyelectrolyte effects govern the association of counterions with the chain. Large ions are less effective in counterion condensation than small ions. However, upon counterion condensation, the reduction of the backbone charge is independent of size of the metal cations. Above a threshold value of Coulomb strength parameter, counterion release entropy drives the formation of counterion-induced compact states. In chapter three, the nature of surface tension in the random first order theory of supercooled liquid is analyzed within the framework of Landau-Lifshitz fluctuation theory. We show that the surface tension of a droplet satisfies the differential equation 4πr2(dσ)+ 8πrσ(r)− Br1/2 = 0 , where B/ T = 12πkBcv , T is temperature, kB is dr Boltzmann constant, and cv is heat capacity. A consequence is that the slope of the relaxation time at the glass transition temperature, i.e., the fragility index, is expressed as the square of the ratio of heat capacity and configurational entropy of the supercooled liquid. When backbone extended nucleosides are incorporated into a double helix, a unique helical structure is formed. In chapter four, we find that the predicted stability of modified backbone DNA strands in aqueous solution is in good agreement with experimental melting temperature data. The incorporation of extended backbone nucleosides into a duplex results in elongation of the end-to-end chain distance due to the distortion of the B-DNA conformation at the mutated base-pair insertion. We also find that the modified backbone helical twist is approximately 40 degrees, larger than B-DNA helical twist and closer to the twist angle predicted for D-form DNA. The folding of RNA tertiary structure has been described as an equilibrium between partially folded I (intermediate) states, and the fully folded native conformation, or N state. RNA is highly sensitive to the ionic environment due to its negative charge, and tertiary structures tend to be strongly stabilized by Mg2+. There is a need for models capable of describing the ion atmosphere surrounding RNA with quantitative accuracy. In chapter 5, we present a generalized Manning condensation model of RNA electrostatics for studying the Mg2+-induced RNA folding of the 58mer ribosomal fragment. / Thesis (PhD) — Boston College, 2016. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

It has been reported that the Zr-based amorphous alloys exhibit high corrosion resistance, good mechanical properties, better thermal stability and good glass-forming ability. The thermal properties of the Zr-Al-Cu-Ni amorphous alloys could be improved by adding boron and silicon that also has been reported. Therefore, the Zr-Al-Cu-Ni amorphous alloys are chosen as the base materials for investigating the effect of the thermal properties by adding boron and silicon at the same time. According to the results of the experiment, the Zr60Al7.5Cu17.5Ni10B1Si4 amorphous alloy ribbons with the highest GFA index (g value) and the value is 0.42; the maximum supercooled liquid region (DTx) is about 85 K for the Zr60Al7.5Cu17.5Ni10B1Si4 amorphous alloy ribbons. For the isothermal analysis or non-isothermal analysis, the Avrami index (n value) is not constant, and the Zr60Al7.5Cu17.5Ni10B1Si4 amorphous alloy ribbons with the largest activation energy which was more than 300 kJ/mol. When the Zr60Al7.5Cu17.5Ni10B1Si4 amorphous alloy ribbons were heated to 721 K and held for 4000 seconds, the crystallized phases were ZrO2 with orthorhombic structure and Zr2Ni with tetragonal structure. When the Zr62Al7.5Cu17.5Ni10B2Si1 amorphous alloy ribbons were heated to 724 K and held for 4000 seconds, besides the ZrO2 phase with orthorhombic structure and the Zr2Ni phase with tetragonal structure, a Zr2Ni crystallized phase with cubic structure is also included. According to the observation of the TEM image for heating Zr62Al7.5Cu17.5Ni10B2Si1 amorphous alloy ribbons to 694 K and held for 4000 seconds, there are many grains distribute in the amorphous matrix, and the grain size is about 20 ~40 nm.

Thesis advisor: John T. Fourkas / One can extract a tremendous amount of information about the organizational and dynamic states of molecules, in situ and in real-time, through highly sensitive and noninvasive single particle optical probing. The highly efficient, multi-photon excited luminescence from stabilized metal nanoclusters renders these species useful as optical probes that can be used in detecting single particle and molecular dynamics. We generate stable, and monodisperse samples of Ag nanoclusters as small as 1 nm in diameter, and find that through substitution of various stabilizer molecules we can precisely tune the size of the clusters over a 1-6 nm range of diameters, ensuring monodispersity and stability at every stage. These clusters also exhibit highly efficient, polarized luminescence upon two photon excitation at 800 nm and remain highly photostable, not exhibiting the deleterious blinking that occurs with many single-molecule fluorophores. In order to demonstrate the utility of these clusters as single-molecule probes, we track their emission polarization over long periods in deeply supercooled liquids such as 4'(octahydro-4,7-methano-5H-inden-5-yliden) bisphenol dimethyl ether (ODE). Our results suggest that these clusters can detect nanoscale dynamics with high sensitivity. / Thesis (BS) — Boston College, 2004. / Submitted to: Boston College. College of Arts and Sciences. / Discipline: Chemistry. / Discipline: College Honors Program.

The study of supercooled liquids and glasses remains one of the most divisive and divided fields in modern physics. Despite a vast amount of effort and research time invested in this topic, the answers to many central questions remain disputed and incomplete. However, the link between the behaviour of supercooled liquids and their energy landscapes is well established and widely accepted. Understanding this link would be a key step towards resolving many of the mysteries and controversies surrounding the glass transition. Therefore the study of glassy energy landscapes is an important area of research. In this thesis, I report some of the most detailed computational studies of glassy potential energy landscapes ever performed. Using geometry optimisation techniques, I have sampled the local minima and saddle points of the landscapes for several supercooled liquids to analyse their dynamics and thermodynamics. Some of my analysis follows previous work on the binary Lennard-Jones fluid (BLJ), a model atomic liquid. BLJ is a fragile glass former, meaning that its transport coefficients have super-Arrhenius temperature dependence, rather than the more usual Arrhenius behaviour exhibited by strong liquids. The difference in behaviour between these two classes of liquid has previously been attributed to differing degrees of structure in the relevant energy landscapes. I have studied models for both fragile and strong glass formers: the molecular liquid ortho-terphenyl (OTP) and viscous silica (SiO$_{2}$) respectively. My results for OTP agree closely with trends observed for BLJ, suggesting that the same diffusion mechanism is applicable to fragile molecular liquids as well as to atomic. However, the dynamics and energy landscape of OTP are made complicated by the molecular orientational degrees of freedom, making the analysis more challenging for this system. Dynamics of BLJ, OTP and silica are all dominated by cage-breaking events: structural rearrangements in which atoms change their nearest neighbours. I propose a robust and general method to identify cage breaks for small rigid molecules, and compare some properties of cage breaks between strong and fragile systems. The energy landscapes of BLJ and OTP both display hierarchical ordering of potential energy minima into metabasins. These metabasins can be detected by the cage-breaking method. It has previously been suggested that metabasins are responsible for super-Arrhenius behaviour, and are absent from the landscapes of strong liquids such as SiO2. My results indicate that metabasins are present on the silica landscape, but that they each contain fewer minima than metabasins in BLJ or OTP. Metabasins are associated with anticorrelated particle motion, mediated by reversed transitions between minima of the potential energy landscape. I show that accounting for time-correlation of particle displacement vectors is essential to describe super-Arrhenius behaviour in BLJ and OTP, but also required to reproduce strong behaviour in silica. I hypothesise that the difference between strong and fragile liquids arises from a longer correlation timescale in the latter case, and I suggest a number of ways in which this proposition could be tested. I have investigated the effect on the landscape of freezing the positions of some particles in a BLJ fluid. This “pinning” procedure induces a dynamical crossover that has been described as an equilibrium “pinning transition”, related to the hypothetical ideal glass transition. I show that the pinning transition is related to (and probably caused by) a dramatic change in the potential energy landscape. Pinning a large fraction of the particles in a supercooled liquid causes its energy landscape to acquire global structure and hence structure-seeking behaviour, very different from the landscape of a typical supercooled liquid. I provide a detailed description of this change in structure, and investigate the mechanism underlying it. I introduce a new algorithm for identifying hierarchical organisation of a landsape, which uses concepts related to the pinning transition but is applicable to unpinned liquids as well. This definition is complementary to metabasins, but the two methods often identify the same higher-order structures. The new “packings” algorithm offers a route to test thermodynamic theories of the glass transition in the context of the potential energy landscape. Over the course of this thesis, I discuss several different terms and methods to identify higher-order structures in the landscapes of model glass formers, and investigate how this organisation varies between different systems. Although little variation is immediately apparent between most glassy landscapes, deeper analysis reveals a surprising diversity, which has important implications for dynamical behaviour in the vicinity of the glass transition.

The aim of the study was to investigate the crystallization kinetics and solidification behaviour of Fe60Co8Mo5Zr10W2B15 bulk glass forming alloy. The solidification behaviour in near-equilibrium and non-equilibrium cooling conditions was studied. The eutectic and peritectic reactions were found to exist in the solidification sequence of the alloy. The bulk metallic glass formation was achieved by using two methods: quenching from the liquid state and quenching from the semi-state. Scanning electron microscopy, x-ray diffraction and thermal analysis techniques were utilized in the characterization of the samples produced throughout the study. The choice of the starting material and the alloy preparation method was found to be effective in the amorphous phase formation. The critical cooling rate was calculated as 5.35 K/s by using the so-called Barandiaran and Colmenero method which was found to be comparable to the best glass former known to date. The isothermal crystallization kinetics of the alloy was studied at temperatures chosen in the supercooled liquid region and above the first crystallization temperature. The activation energies for glass transition and crystallization events were determined by using different analytical methods such as Kissinger and Ozawa methods. The magnetic properties of the alloy in the annealed, amorphous and as-cast states were characterized by using a vibrating sample magnetometer. The alloy was found to have soft magnetic properties in all states, however the annealed specimen was found to have less magnetic energy loss as compared to the others.

No description available.

L'énigme de la transition vitreuse réside en grande partie dans le fait que lorsqu'un matériau entre dans l'état dit surfondu, sa dynamique ralentit de façon spectaculaire, donnant l'impression d'une transition vers un état solide, sans que pour autant on ne parvienne à constater de transition thermodynamique par les expériences usuelles.Autrement dit, on ne parvient pas à expliquer le ralentissement spectaculaire de la dynamique par la croissance d'une longueur mesurable expérimentalement.Ceci conduit à la prolifération de théories souvent contradictoires quant à l'origine de la dynamique vitreuse.Durant la dernière décennie une piste prometteuse de mise en évidence d'une telle longueur a été proposée : il s'agit de la mesure des réponses diélectriques non linéaires d'ordre 3 du matériau ainsi que de leur évolution en température. En effet, les réponses non linéaires reflètent les effets collectifs caractéristiques de l'ordre amorphe, qui ne se traduisent que dans les fonctions de corrélations d'ordre élevé.Durant cette thèse nous avons construit sur ces bases expérimentales et théoriques, une expérience de mesure des réponses non linéaires d'ordre 5. En exploitant ces résultats sur la réponse diélectrique d'ordre 5 et des résultats précédents sur la réponse d'ordre 3, nous sommes parvenus, en collaboration avec une équipe d'expérimentateurs et de théoriciens, à fournir des indices forts de l'existence d'un point critique thermodynamique dans le Glycérol et le Propylène Carbonate. Ceci constitue une avancée significative dans la compréhension des matériaux vitreux.En particulier, cette découverte permet de poser des contraintes fortes sur les théories existantes et contribue à clore certains débats théoriques ayant eu cours sur plusieurs décennies. / The puzzle of the glass transition mainly resides in the fact that a supercooled liquid undergoes when cooled down, a spectacular dynamics slow down, while no evidence of any kind of thermodynamic transition has been measured through usual means.The absence of any known growth of a length scale that could explain the glassy dynamics leads to a wide range of competing models and theories trying to explain the origins of this dynamics.In the last decade, a promising lead has been put forward, that could allow the community to experimentally access such a growing length scale, through third order non-linear dielectric response measurements, and more in particular this response's temperature dependence. Indeed, non-linear response measurements reflect the collective effects that characterize the amorphous order and translate into high order correlation functions.During this PhD, we have built upon this experimental and theoretical background to design a fifth order non-linear dielectric response measurement experiment. In collaboration with a team of experimentalists and theoreticians, we have used these results in conjunction with third order response measurement results to make a very strong case advocating the existence of a thermodynamic critical point in Glycerol and Propylene Carbonate. This is a very significant advance in the understanding of the behaviour of glassy materials.This ground breaking discovery puts very strong constraints on existing theories and will contribute to end some decades-long theoretical debates within the glassy community.

No description available.

Lorsqu’un liquide est refroidit suffisamment vite, la cristallisation peut être évitée. On a alors un liquide surfondu dont le temps de relaxation augmente fortement quand la température diminue vers la température de transition vitreuse Tg. En-dessous de Tg, le systèmeest dans l’état vitreux. Il vieillit : son temps de relaxation augmente au cours du temps. L’existence d’une longueur de corrélation croissante associée au ralentissement de la dynamique des liquides surfondus (ou des verres) est une des grandes questions toujours ouvertes dans la physique de la transition vitreuse. Des arguments théoriques très généraux ont montré que la mesure de la susceptibilité alternative non linéaire d’ordre trois des liquides surfondus (ou des verres) donnait directement accès à la longueur de corrélation dynamique. Nous avons mis au point une expérience à haute sensibilité permettant d’accéder à deux susceptibilités diélectriques non linéaires d’ordre trois près de Tg. Nos résultats obtenus sur du glycrol surfondu sont quantitativement en très bon accord avec les prédictions théoriques. Ils montrent que la longueur de corrélation dynamique augmente lorsque T diminue vers Tg. En dessous de Tg, l’étude du vieillissement d’une des susceptibilités non linéaires nous a permis de mettre en évidence que la longueur de corrélation dynamique augmente au cours du temps. Ces résultats renforcent le scénario selon lequel la transition vitreuse serait liée à un point critique sous-jacent, ce qui expliquerait l’ubiquité du comportement vitreux dans la nature. / Upon fast enough cooling, a liquid avoids crystallization and enters in a supercooled state. The relaxation time of this supercooled liquid increases extremely fast when the temperature decreases towards the glass transition temperature Tg. Below Tg, the system is in the glassy state. It ages : the relaxation time increases with time. The existence of a growing correlation length associated to the slowing down of supercooled liquids (or of glasses) is one of the main open issues in the physics of the glass transition. On very general theoretical arguments, it has been shown that the third order a.c. nonlinear susceptibility around Tg gives direct access to the dynamical correlation length. We have developped a high sensibility experiment to measure, close to Tg, two nonlinear dielectric susceptibilities of the third order. Our results performed on supercooled glycerol are quantitatively in very good agreement with theoretical predictions. They show that the dynamical correlation length increases when T decreases towards Tg. Below Tg, aging experiments of one of the nonlinear susceptibilities reveal that the dynamical correlation length increases with time. These results clearly evidence the collective character of glassy dynamics and reinforce the picture of an underlying critical point, which would explain the ubiquity of the glass transition in Nature.

Orientador: Maurice de Koning / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Fisica Gleb Wataghin / Made available in DSpace on 2018-08-13T12:16:33Z (GMT). No. of bitstreams: 1 CarvajalJara_DiegoAlejandro_M.pdf: 4649880 bytes, checksum: d014cd5c835938e4643e478fa70353be (MD5) Previous issue date: 2009 / Resumo: Recentemente tem sido proposta a existência de uma transição líquido-líquido em substâncias puras com o propósito de explicar alguns comportamentos anômalos como os incrementos de funções resposta (compressibilidade isotérmica, coeficiente de expansão térmica, calor específico) ao diminuir a temperatura de um líquido. A existência deste tipo de transição foi demostrada experimentalmente para o fósforo por dispersão de raios X, e através de simulações atomísticas ou de primeiros princípios para a água, o silício, o carbono, etc. A compreensão detalhada deste tipo de transição está intimamente relacionada à questão fundamental de quais fatores físicos controlam as propriedades de um líquido, e portanto o estudo desta é de grande importância para o desenvolvimento de novas tecnologias, a síntese de novos materiais e o controle de suas propriedades. Neste trabalho realizamos simulações atomísticas sobre um sistema de 1152 partículas de Gálio submetidas a um potencial semi-empírico MEAM, com condições periódicas de contorno. Com estas simulações procuramos uma transição líquido-líquido no Gálio através de um processo de eliminação de três teorias. Inicialmente mostramos que o limite de metaestabilidade do líquido super-aquecido tem um comportamento monótono decrescente no plano de fase P-T. Posteriormente nosso sistema apresenta histerese, uma descontinuidade no volume, estruturas locais diferentes, duas fases que fluem, e um calor latente característico de uma transição de fase de primeira ordem. Por todas estas razões concluímos que o sistema simulado apresenta um transição líquido-líquido de primeira ordem. Adicionalmente foram realizadas compressões e expansões isotérmicas para temperaturas diferentes, observando que estes processos também apresentam histerese e que ela diminui com o aumento da temperatura, indicando assim a possível existência de um segundo ponto crítico e a finalização da transição líquido-líquido. Finalizamos o trabalho com a obtenção e a caracterização de uma possível nova fase cristalina do Gálio cuja estrutura ainda não tem sido obtida experimentalmente. Esta fase foi obtida por casualidade durante o estudo da existência de uma transição líquido-líquido no Gálio ao tencionar o Gálio a -1.6GPa. Sua estrutura é do tipo ortorrômbica com uma simetria Cmcm (grupo espacial 63) e sua principal diferença do Gálio-I é a orientação dos dímeros de Gálio, que nesta nova fase estão dispostos paralelamente. Simulações por DFT mostraram que esta nova fase é metaestável a pressão nula e chega a ser estável a pressões negativas abaixo de ~ 1.5GPa. / Abstract: Recently, the existence of a liquid-liquid transition in pure substances has been proposed as an explanation of anomalous behaviors such as the increase of response functions (isothermal compressibility, coefficient of thermal expansion, specific heat) with decreasing temperature displayed by some liquids. The existence of this type of transition has been demonstrated experimentally for phosphorous by X-ray diÿraction, and through atomistic simulations for water, silicon and carbon. The detailed understanding of this type of transition is closely related to the fundamental question of which physical factors control the properties of a liquid. Therefore, the study of this phenomenon is of great importance for the development of new technologies, the synthesis of new materials and the control of their properties. In this work, we carry out a series of atomistic simulations of a system containing 1152 Gallium atoms described by a semi-empirical Modified Embedded-Atom Model subject to periodic boundary conditions. By means of these simulations we search for a liquid-liquid transition in Gallium by means of a process of elimination of three theories. Initially we show that the limit of metastability of the superheated liquid has a decreasing monotonous behavior in the pressure-temperature phase diagram. Subsequently, our system presents hysteresis, a discontinuity in volume, two phases that have different local atomic structures and display diffusion, and a latent heat, all characteristic of a first-order phase transition. For all these reasons we conclude that the simulated system presents a liquid-liquid phase transition of first-order in the supercooled regime. In addition, we carried out several simulations of isothermal compressions and expansions for different temperatures. These results also show hysteresis although it is found to decrease with increasing temperature, thus indicating the possible existence of a second critical point at which the liquid-liquid transition ends. We finish our studies with the discovery and characterization of a crystalline phase of Gallium whose structure has not been observed experimentally. This phase was obtained by chance during the study of the existence of a liquid-liquid transition in Gallium under tension of -1.6GPa. Its structure is of the orthorhombic type with Cmcm symmetry (space group 63). Its main difference with respect to the Gallium-I phase is that in the new phase the Gallium dimers are disposed in a parallel fashion. Subsequent DFT simulations show that this new phase is metastable at zero pressure and predict it to become stable with respect to Gallium-I arrives at negative pressures below ~1.5GPa. / Mestrado / Física da Matéria Condensada / Mestre em Física