A molecular dynamics study of the microscopic properties of simple dense fluids

The microscopic properties of a two-dimensional model dense fluid of Lennard-Jones disks have been studied using the so-called "molecular dynamics" method. Analyses of the computer-generated simulation data in terms of "conventional" thermodynamic and distribution functions verify the physical validity of the model and the simulation technique.

The radial distribution functions g(r) computed from the simulation data exhibit several subsidiary features rather similar to those appearing in some of the g(r) functions obtained by X-ray and thermal neutron diffraction measurements on real simple liquids. In the case of the model fluid, these "anomalous" features are thought to reflect the existence of two or more alternative configurations for local ordering.

Graphical display techniques have been used extensively to provide some intuitive insight into the various microscopic phenomena occurring in the model. For example, "snapshots" of the instantaneous system configurations for different times show that the "excess" area allotted to the fluid is collected into relatively large, irregular, and surprisingly persistent "holes". Plots of the particle trajectories over intervals of 2.0 to 6.0 x 10^-12 sec indicate that the mechanism for diffusion in the dense model fluid is "cooperative" in nature, and that extensive diffusive migration is generally restricted to groups of particles in the vicinity of a hole.

A quantitative analysis of diffusion in the model fluid shows that the cooperative mechanism is not inconsistent with the statistical predictions of existing theories of singlet, or self-diffusion in liquids. The relative diffusion of proximate particles is, however, found to be retarded by short-range dynamic correlations associated with the cooperative mechanism--a result of some importance from the standpoint of bimolecular reaction kinetics in solution.

A new, semi-empirical treatment for relative diffusion in liquids is developed, and is shown to reproduce the relative diffusion phenomena observed in the model fluid quite accurately. When incorporated into the standard Smoluchowski theory of diffusion-controlled reaction kinetics, the more exact treatment of relative diffusion is found to lower the predicted rate of reaction appreciably.

Finally, an entirely new approach to an understanding of the liquid state is suggested. Our experience in dealing with the simulation data--and especially, graphical displays of the simulation data--has led us to conclude that many of the more frustrating scientific problems involving the liquid state would be simplified considerably, were it possible to describe the microscopic structures characteristic of liquids in a concise and precise manner. To this end, we propose that the development of a formal language of partially-ordered structures be investigated.

I. A study of the dynamics of triplet excitons in molecular crystals. II. An investigation of delayed light emission from Chlorella pyrenoidosa

I. PREAMBLE AND SCOPE

Brief introductory remarks, together with a definition of the scope of the material discussed in the thesis, are given.

II. A STUDY OF THE DYNAMICS OF TRIPLET EXCITONS IN MOLECULAR CRYSTALS

Phosphorescence spectra of pure crystalline naphthalene at room temperature and at 77˚ K are presented. The lifetime of the lowest triplet ³B_1u state of the crystal is determined from measurements of the time-dependence of the phosphorescence decay after termination of the excitation light. The fact that this lifetime is considerably shorter in the pure crystal at room temperature than in isotopic mixed crystals at 4.2˚ K is discussed, with special importance being attached to the mobility of triplet excitons in the pure crystal.

Excitation spectra of the delayed fluorescence and phosphorescence from crystalline naphthalene and anthracene are also presented. The equation governing the time- and spatial-dependence of the triplet exciton concentration in the crystal is discussed, along with several approximate equations obtained from the general equation under certain simplifying assumptions. The influence of triplet exciton diffusion on the observed excitation spectra and the possibility of using the latter to investigate the former is also considered. Calculations of the delayed fluorescence and phosphorescence excitation spectra of crystalline naphthalene are described.

A search for absorption of additional light quanta by triplet excitons in naphthalene and anthracene crystals failed to produce any evidence for the phenomenon. This apparent absence of triplet-triplet absorption in pure crystals is attributed to a low steady-state triplet concentration, due to processes like triplet-triplet annihilation, resulting in an absorption too weak to be detected with the apparatus used in the experiments. A comparison of triplet-triplet absorption by naphthalene in a glass at 77˚ K with that by naphthalene-h₈ in naphthalene-d₈ at 4.2˚ K is given. A broad absorption in the isotopic mixed crystal triplet-triplet spectrum has been tentatively interpreted in terms of coupling between the guest ³B_1u state and the conduction band and charge-transfer states of the host crystal.

III. AN INVESTIGATION OF DELAYED LIGHT EMISSION FROM Chlorella Pyrenoidosa

An apparatus capable of measuring emission lifetimes in the range 5 X 10^-9 sec to 6 X 10^-3 sec is described in detail. A cw argon ion laser beam, interrupted periodically by means of an electro-optic shutter, serves as the excitation source. Rapid sampling techniques coupled with signal averaging and digital data acquisition comprise the sensitive detection and readout portion of the apparatus. The capabilities of the equipment are adequately demonstrated by the results of a determination of the fluorescence lifetime of 5, 6, 11, 12-tetraphenyl-naphthacene in benzene solution at room temperature. Details of numerical methods used in the final data reduction are also described.

The results of preliminary measurements of delayed light emission from Chlorella Pyrenoidosa in the range 10^-3 sec to 1 sec are presented. Effects on the emission of an inhibitor and of variations in the excitation light intensity have been investigated. Kinetic analysis of the emission decay curves obtained under these various experimental conditions indicate that in the millisecond-to-second time interval the decay is adequately described by the sum of two first-order decay processes. The values of the time constants of these processes appear to be sensitive both to added inhibitor and to excitation light intensity.

Dynamics of the East Asian Summer Monsoon in Present and Future Climates

This thesis aims at enhancing our fundamental understanding of the East Asian summer monsoon (EASM), and mechanisms implicated in its climatology in present-day and warmer climates. We focus on the most prominent feature of the EASM, i.e., the so-called Meiyu-Baiu (MB), which is characterized by a well-defined, southwest to northeast elongated quasi-stationary rainfall band, spanning from eastern China to Japan and into the northwestern Pacific Ocean in June and July.

We begin with an observational study of the energetics of the MB front in present-day climate. Analyses of the moist static energy (MSE) budget of the MB front indicate that horizontal advection of moist enthalpy, primarily of dry enthalpy, sustains the front in a region of otherwise negative net energy input into the atmospheric column. A decomposition of the horizontal dry enthalpy advection into mean, transient, and stationary eddy fluxes identifies the longitudinal thermal gradient due to zonal asymmetries and the meridional stationary eddy velocity as the most influential factors determining the pattern of horizontal moist enthalpy advection. Numerical simulations in which the Tibetan Plateau (TP) is either retained or removed show that the TP influences the stationary enthalpy flux, and hence the MB front, primarily by changing the meridional stationary eddy velocity, with reinforced southerly wind on the northwestern flank of the north Pacific subtropical high (NPSH) over the MB region and northerly wind to its north. Changes in the longitudinal thermal gradient are mainly confined to the near downstream of the TP, with the resulting changes in zonal warm air advection having a lesser impact on the rainfall in the extended MB region.

Similar mechanisms are shown to be implicated in present climate simulations in the Couple Model Intercomparison Project - Phase 5 (CMIP5) models. We find that the spatial distribution of the EASM precipitation simulated by different models is highly correlated with the meridional stationary eddy velocity. The correlation becomes more robust when energy fluxes into the atmospheric column are considered, consistent with the observational analyses. The spread in the area-averaged rainfall amount can be partially explained by the spread in the simulated globally-averaged precipitation, with the rest primarily due to the lower-level meridional wind convergence. Clear relationships between precipitation and zonal and meridional eddy velocities are observed.

Finally, the response of the EASM to greenhouse gas forcing is investigated at different time scales in CMIP5 model simulations. The reduction of radiative cooling and the increase in continental surface temperature occur much more rapidly than changes in sea surface temperatures (SSTs). Without changes in SSTs, the rainfall in the monsoon region decreases (increases) over ocean (land) in most models. On longer time scales, as SSTs increase, rainfall changes are opposite. The total response to atmospheric CO^2 forcing and subsequent SST warming is a large (modest) increase in rainfall over ocean (land) in the EASM region. Dynamic changes, in spite of significant contributions from the thermodynamic component, play an important role in setting up the spatial pattern of precipitation changes. Rainfall anomalies over East China are a direct consequence of local land-sea contrast, while changes in the larger-scale oceanic rainfall band are closely associated with the displacement of the larger-scale NPSH. Numerical simulations show that topography and SST patterns play an important role in rainfall changes in the EASM region.

Robust Control of Evolutionary Dynamics

The application of principles from evolutionary biology has long been used to gain new insights into the progression and clinical control of both infectious diseases and neoplasms. This iterative evolutionary process consists of expansion, diversification and selection within an adaptive landscape - species are subject to random genetic or epigenetic alterations that result in variations; genetic information is inherited through asexual reproduction and strong selective pressures such as therapeutic intervention can lead to the adaptation and expansion of resistant variants. These principles lie at the center of modern evolutionary synthesis and constitute the primary reasons for the development of resistance and therapeutic failure, but also provide a framework that allows for more effective control.

A model system for studying the evolution of resistance and control of therapeutic failure is the treatment of chronic HIV-1 infection by broadly neutralizing antibody (bNAb) therapy. A relatively recent discovery is that a minority of HIV-infected individuals can produce broadly neutralizing antibodies, that is, antibodies that inhibit infection by many strains of HIV. Passive transfer of human antibodies for the prevention and treatment of HIV-1 infection is increasingly being considered as an alternative to a conventional vaccine. However, recent evolution studies have uncovered that antibody treatment can exert selective pressure on virus that results in the rapid evolution of resistance. In certain cases, complete resistance to an antibody is conferred with a single amino acid substitution on the viral envelope of HIV.

The challenges in uncovering resistance mechanisms and designing effective combination strategies to control evolutionary processes and prevent therapeutic failure apply more broadly. We are motivated by two questions: Can we predict the evolution to resistance by characterizing genetic alterations that contribute to modified phenotypic fitness? Given an evolutionary landscape and a set of candidate therapies, can we computationally synthesize treatment strategies that control evolution to resistance?

To address the first question, we propose a mathematical framework to reason about evolutionary dynamics of HIV from computationally derived Gibbs energy fitness landscapes -- expanding the theoretical concept of an evolutionary landscape originally conceived by Sewall Wright to a computable, quantifiable, multidimensional, structurally defined fitness surface upon which to study complex HIV evolutionary outcomes.

To design combination treatment strategies that control evolution to resistance, we propose a methodology that solves for optimal combinations and concentrations of candidate therapies, and allows for the ability to quantifiably explore tradeoffs in treatment design, such as limiting the number of candidate therapies in the combination, dosage constraints and robustness to error. Our algorithm is based on the application of recent results in optimal control to an HIV evolutionary dynamics model and is constructed from experimentally derived antibody resistant phenotypes and their single antibody pharmacodynamics. This method represents a first step towards integrating principled engineering techniques with an experimentally based mathematical model in the rational design of combination treatment strategies and offers predictive understanding of the effects of combination therapies of evolutionary dynamics and resistance of HIV. Preliminary in vitro studies suggest that the combination antibody therapies predicted by our algorithm can neutralize heterogeneous viral populations despite containing resistant mutations.

Dynamics of non-Abelian Aharonov-Bohm systems

This thesis examines several examples of systems in which non-Abelian magnetic flux and non-Abelian forms of the Aharonov-Bohm effect play a role. We consider the dynamical consequences in these systems of some of the exotic phenomena associated with non-Abelian flux, such as Cheshire charge holonomy interactions and non-Abelian braid statistics. First, we use a mean-field approximation to study a model of U(2) non-Abelian anyons near its free-fermion limit. Some self-consistent states are constructed which show a small SU(2)-breaking charge density that vanishes in the fermionic limit. This is contrasted with the bosonic limit where the SU(2) asymmetry of the ground state can be maximal. Second, a global analogue of Chesire charge is described, raising the possibility of observing Cheshire charge in condensedmatter systems. A potential realization in superfluid He-3 is discussed. Finally, we describe in some detail a method for numerically simulating the evolution of a network of non-Abelian (S₃) cosmic strings, keeping careful track of all magnetic fluxes and taking full account of their non-commutative nature. I present some preliminary results from this simulation, which is still in progress. The early results are suggestive of a qualitatively new, non-scaling behavior.

Microwave dynamics of quasiparticles and critical fields in superconducting films

The microwave response of the superconducting state in equilibrium and non-equilibrium configurations was examined experimentally and analytically. Thin film superconductors were mostly studied in order to explore spatial effects. The response parameter measured was the surface impedance.

For small microwave intensity the surface impedance at 10 GHz was measured for a variety of samples (mostly Sn) over a wide range of sample thickness and temperature. A detailed analysis based on the BCS theory was developed for calculating the surface impedance for general thickness and other experimental parameters. Experiment and theory agreed with each other to within the experimental accuracy. Thus it was established that the samples, thin films as well as bulk, were well characterised at low microwave powers (near equilibrium).

Thin films were perturbed by a small dc supercurrent and the effect on the superconducting order parameter and the quasiparticle response determined by measuring changes in the surface resistance (still at low microwave intensity and independent of it) due to the induced current. The use of fully superconducting resonators enabled the measurement of very small changes in the surface resistance (< 10^-9 Ω/sq.). These experiments yield information regarding the dynamics of the order parameter and quasiparticle systems. For all the films studied the results could be described at temperatures near T_c by the thermodynamic depression of the order parameter due to the static current leading to a quadratic increase of the surface resistance with current.

For the thinnest films the low temperature results were surprising in that the surface resistance decreased with increasing current. An explanation is proposed according to which this decrease occurs due to an additional high frequency quasiparticle current caused by the combined presence of both static and high frequency fields. For frequencies larger than the inverse of the quasiparticle relaxation time this additional current is out of phase (by π) with the microwave electric field and is observed as a decrease of surface resistance. Calculations agree quantitatively with experimental results. This is the first observation and explanation of this non-equilibrium quasiparticle effect.

For thicker films of Sn, the low temperature surface resistance was found to increase with applied static current. It is proposed that due to the spatial non-uniformity of the induced current distribution across the thicker films, the above purely temporal analysis of the local quasiparticle response needs to be generalised to include space and time non-equilibrium effects.

The nonlinear interaction of microwaves arid superconducting films was also examined in a third set of experiments. The surface impedance of thin films was measured as a function of the incident microwave magnetic field. The experiments exploit the ability to measure the absorbed microwave power and applied microwave magnetic field absolutely. It was found that the applied surface microwave field could not be raised above a certain threshold level at which the absorption increased abruptly. This critical field level represents a dynamic critical field and was found to be associated with the penetration of the app1ied field into the film at values well below the thermodynamic critical field for the configuration of a field applied to one side of the film. The penetration occurs despite the thermal stability of the film which was unequivocally demonstrated by experiment. A new mechanism for such penetration via the formation of a vortex-antivortex pair is proposed. The experimental results for the thinnest films agreed with the calculated values of this pair generation field. The observations of increased transmission at the critical field level and suppression of the process by a metallic ground plane further support the proposed model.

On the Dynamics of the Adenylate Energy System: Homeorhesis vs Homeostasis

Biochemical energy is the fundamental element that maintains both the adequate turnover of the biomolecular structures and the functional metabolic viability of unicellular organisms. The levels of ATP, ADP and AMP reflect roughly the energetic status of the cell, and a precise ratio relating them was proposed by Atkinson as the adenylate energy charge (AEC). Under growth-phase conditions, cells maintain the AEC within narrow physiological values, despite extremely large fluctuations in the adenine nucleotides concentration. Intensive experimental studies have shown that these AEC values are preserved in a wide variety of organisms, both eukaryotes and prokaryotes. Here, to understand some of the functional elements involved in the cellular energy status, we present a computational model conformed by some key essential parts of the adenylate energy system. Specifically, we have considered (I) the main synthesis process of ATP from ADP, (II) the main catalyzed phosphotransfer reaction for interconversion of ATP, ADP and AMP, (III) the enzymatic hydrolysis of ATP yielding ADP, and (IV) the enzymatic hydrolysis of ATP providing AMP. This leads to a dynamic metabolic model (with the form of a delayed differential system) in which the enzymatic rate equations and all the physiological kinetic parameters have been explicitly considered and experimentally tested in vitro. Our central hypothesis is that cells are characterized by changing energy dynamics (homeorhesis). The results show that the AEC presents stable transitions between steady states and periodic oscillations and, in agreement with experimental data these oscillations range within the narrow AEC window. Furthermore, the model shows sustained oscillations in the Gibbs free energy and in the total nucleotide pool. The present study provides a step forward towards the understanding of the fundamental principles and quantitative laws governing the adenylate energy system, which is a fundamental element for unveiling the dynamics of cellular life.

The importance of interaction strength for food web dynamics and ecosystem functioning

Global biodiversity is eroding at an alarming rate, through a combination of anthropogenic disturbance and environmental change. Ecological communities are bewildering in their complexity. Experimental ecologists strive to understand the mechanisms that drive the stability and structure of these complex communities in a bid to inform nature conservation and management. Two fields of research have had high profile success at developing theories related to these stabilising structures and testing them through controlled experimentation. Biodiversity-ecosystem functioning (BEF) research has explored the likely consequences of biodiversity loss on the functioning of natural systems and the provision of important ecosystem services. Empirical tests of BEF theory often consist of simplified laboratory and field experiments, carried out on subsets of ecological communities. Such experiments often overlook key information relating to patterns of interactions, important relationships, and fundamental ecosystem properties. The study of multi-species predator-prey interactions has also contributed much to our understanding of how complex systems are structured, particularly through the importance of indirect effects and predator suppression of prey populations. A growing number of studies describe these complex interactions in detailed food webs, which encompass all the interactions in a community. This has led to recent calls for an integration of BEF research with the comprehensive study of food web properties and patterns, to help elucidate the mechanisms that allow complex communities to persist in nature. This thesis adopts such an approach, through experimentation at Lough Hyne marine reserve, in southwest Ireland. Complex communities were allowed to develop naturally in exclusion cages, with only the diversity of top trophic levels controlled. Species removals were carried out and the resulting changes to predator-prey interactions, ecosystem functioning, food web properties, and stability were studied in detail. The findings of these experiments contribute greatly to our understanding of the stability and structure of complex natural communities.

The East Asian Collection at Duke University: Dynamics of Change.

Traces the history of Duke's East Asian Studies program and associated library collections from the beginning of the twentieth century to the present. Describes the strengths of the Japanese, Chinese and Korean collections, materials in special collections and cooperation with the University of North Carolina.

Preliminary studies on the effect of the increased biodiversity on the population dynamics of Caliroa cerasi L. (Hymenoptera: Tenthredinidae), and its natural enemy Trichogramma minutum R. (Hymenoptera: Trichogrammatidae) in a sweet cherry (Prunus avium L.) orchard in Virch (Southern Patagonia Argentina)

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Preliminary studies on the effect of the increased biodiversity on the population dynamics of Caliroa cerasi L. (Hymenoptera: Tenthredinidae), and its natural enemy Trichogramma minutum R. (Hymenoptera: Trichogrammatidae) in a sweet cherry (Prunus avium L.) orchard in Virch (Southern Patagonia Argentina)

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Computational fluid dynamics: advancements in technology for modeling iron and steelmaking processes

Computational fluid dynamics (CFD) software technology has formed the basis of many investigations into the behavior and optimization of primary iron and steelmaking processes for the last 25+ years. The objective of this contribution is to review the progress in CFD technologies over the last decade or so and how this can be brought to bear in advancing the process analysis capability of primary ferrous operations. In particular, progress on key challenges such as compute performance, fluid-structure transformation and interaction, and increasingly complex geometries are highlighted.

Molecular dynamics studies of the STAT3 homodimer:DNA complex: relationships between STAT3 mutations and protein-DNA recognition.

Signal Transducers and Activators of Transcription (STAT) proteins are a group of latent cytoplasmic transcription factors involved in cytokine signaling. STAT3 is a member of the STAT family and is expressed at elevated levels in a large number of diverse human cancers and is now a validated target for anticancer drug discovery.. Understanding the dynamics of the STAT3 dimer interface, accounting for both protein-DNA and protein-protein interactions, with respect to the dynamics of the latent unphosphorylated STAT3 monomer, is important for designing potential small-molecule inhibitors of the activated dimer. Molecular dynamics (MD) simulations have been used to study the activated STAT3 homodimer:DNA complex and the latent unphosphorylated STAT3 monomer in an explicit water environment. Analysis of the data obtained from MD simulations over a 50 ns time frame has suggested how the transcription factor interacts with DNA, the nature of the conformational changes, and ways in which function may be affected. Examination of the dimer interface, focusing on the protein-DNA interactions, including involvement of water molecules, has revealed the key residues contributing to the recognition events involved in STAT3 protein-DNA interactions. This has shown that the majority of mutations in the DNA-binding domain are found at the protein-DNA interface. These mutations have been mapped in detail and related to specific protein-DNA contacts. Their structural stability is described, together with an analysis of the model as a starting-point for the discovery of novel small-molecule STAT3 inhibitors.

Icewine fermentation by Saccharomyces cervisiae : fundamental stress responses and comparative fermentation dynamics

Please consult the paper edition of this thesis to read. It is available on the 5th Floor of the Library at Call Number: Z 9999.5 B63 P54 2007

How predation and landscape fragmentation affect vole population dynamics

Background: Microtine species in Fennoscandia display a distinct north-south gradient from regular cycles to stable populations. The gradient has often been attributed to changes in the interactions between microtines and their predators. Although the spatial structure of the environment is known to influence predator-prey dynamics of a wide range of species, it has scarcely been considered in relation to the Fennoscandian gradient. Furthermore, the length of microtine breeding season also displays a north-south gradient. However, little consideration has been given to its role in shaping or generating population cycles. Because these factors covary along the gradient it is difficult to distinguish their effects experimentally in the field. The distinction is here attempted using realistic agent-based modelling. Methodology/Principal Findings: By using a spatially explicit computer simulation model based on behavioural and ecological data from the field vole (Microtus agrestis), we generated a number of repeated time series of vole densities whose mean population size and amplitude were measured. Subsequently, these time series were subjected to statistical autoregressive modelling, to investigate the effects on vole population dynamics of making predators more specialised, of altering the breeding season, and increasing the level of habitat fragmentation. We found that fragmentation as well as the presence of specialist predators are necessary for the occurrence of population cycles. Habitat fragmentation and predator assembly jointly determined cycle length and amplitude. Length of vole breeding season had little impact on the oscillations. Significance: There is good agreement between our results and the experimental work from Fennoscandia, but our results allow distinction of causation that is hard to unravel in field experiments. We hope our results will help understand the reasons for cycle gradients observed in other areas. Our results clearly demonstrate the importance of landscape fragmentation for population cycling and we recommend that the degree of fragmentation be more fully considered in future analyses of vole dynamics.