286 research outputs found

    Hidden in the dark:Seeking the vanished polycylic aromatic hydrocarbons in planet-forming discs

    Get PDF
    The origin of life is closely linked to the formation of planetary systems, and both are fundamental drivers of modern astronomical research. Especially carbon is of interest as it is the building block of life as we know.In the interstellar medium, about 15 % of carbon is locked in the form of polycyclic aromatic hydrocarbons (PAHs). The infrared signals of these complex molecules have been observed in numerous astrophysical environments. Their detection in planet-forming discs is of particular interest, as these are the birth-sites of exoplanets. By understanding the evolution of PAHs during planet formation, it is possible to trace a large fraction of carbon. Additionally, the signals of PAHs can reveal crucial information about planet-forming discs themselves to better understand planet formation.This thesis particularly focuses on the formation of molecular clusters of PAHs bound by van der Walls forces in planet forming discs. We analysed the stability of PAH clusters against stellar UV radiation from young stars and modelled their dissociation rates. Further, we model the evolution of clusters in the presence of dust grains, as they interact through freeze-out. Then, we investigate the depletion of observable gas-phase PAHs which has been observed in many discs. Next, we simulate observations and discuss the amount of retrievable information from spectra. Finally, we investigate the interaction of PAHs with stellar X-rays from T Tauri discs and their influence on the destruction of PAHs and PAH clusters

    Multi-Scale Fluctuations in Non-Equilibrium Systems: Statistical Physics and Biological Application

    Get PDF
    Understanding how fluctuations continuously propagate across spatial scales is fundamental for our understanding of inanimate matter. This is exemplified by self-similar fluctuations in critical phenomena and the propagation of energy fluctuations described by the Kolmogorov-Law in turbulence. Our understanding is based on powerful theoretical frameworks that integrate fluctuations on intermediary scales, as in renormalisation group or coupled mode theory. In striking contrast to typical inanimate systems, living matter is typically organised into a hierarchy of processes on a discrete set of spatial scales: from biochemical processes embedded in dynamic subcellular compartments to cells giving rise to tissues. Therefore, the understanding of living matter requires novel theories that predict the interplay of fluctuations on multiple scales of biological organisation and the ensuing emergent degrees of freedom. In this thesis, we derive a general theory of the multi-scale propagation of fluctuations in non-equilibrium systems and show that such processes underlie the regulation of cellular behaviour. Specifically, we draw on paradigmatic systems comprising stochastic many-particle systems undergoing dynamic compartmentalisation. We first derive a theory for emergent degrees of freedom in open systems, where the total mass is not conserved. We show that the compartment dynamics give rise to the localisation of probability densities in phase space resembling quasi-particle behaviour. This emergent quasi-particle exhibits fundamentally different response kinetics and steady states compared to systems lacking compartment dynamics. In order to investigate a potential biological function of such quasi-particle dynamics, we then apply this theory to the regulation of cell death. We derive a model describing the subcellular processes that regulate cell death and show that the quasi-particle dynamics gives rise to a kinetic low-pass filter which suppresses the response of the cell to fast fluituations in cellular stress signals. We test our predictions experimentally by quantifying cell death in cell cultures subject to stress stimuli varying in strength and duration. In closed systems, where the total mass is conserved, the effect of dynamic compartmentalisation depends on details of the kinetics on the scale of the stochastic many-particle dynamics. Using a second quantisation approach, we derive a commutator relation between the kinetic operators and the change in total entropy. Drawing on this, we show that the compartment dynamics alters the total entropy if the kinetics of the stochastic many-particle dynamics violate detailed balance. We apply this mechanism to the activation of cellular immune responses to RNA-virus infections. We show that dynamic compartmentalisation in closed systems gives rise to giant density fluctuations. This facilitates the emergence of gelation under conditions that violate theoretical gelation criteria in the absence of compartment dynamics. We show that such multi-scale gelation of protein complexes on the membranes of dynamic mitochondria governs the innate immune response. Taken together, we provide a general theory describing the multi-scale propagation of fluctuations in biological systems. Our work pioneers the development of a statistical physics of such systems and highlights emergent degrees of freedom spanning different scales of biological organisation. By demonstrating that cells manipulate how fluctuations propagate across these scales, our work motivates a rethinking of how the behaviour of cells is regulated

    Biophysical modelling of bacterial colonisation of urinary catheters

    Get PDF
    I developed the first mathematical model for the infection dynamics of a urinary catheter. Urinary catheters are thin tubes which are inserted into the urethra to drain the bladder. They are commonly used for patients undergoing surgery under anaesthesia, or for elderly patients in long term care facilities. Unfortunately, urinary catheters develop bacterial infections at rates up to 5% per catheter day, with potential complications including catheter blockage, bladder damage, and kidney infections. Attempts to prevent or mitigate infections have been largely ineffective, and through mathematical modelling I seek to understand why. The primary aim of my PhD was to uncover routes by which techniques and approaches from physics can contribute to tackling catheter-associated urinary tract infections (CAUTI). I have provided new clinical insight by developing a novel population dynamics model and applying it to reveal the key factors determining how, why, and when catheters get infected. CAUTI are complex phenomena, involving the host physiology in the urethra and bladder, multiple catheter surfaces, urine flow dynamics within the catheter lumen (the inner channel), and bacterial growth and behaviour. Guided by discussions with clinical collaborators, I considered this system (of catheter, host, and colonising bacteria) as a set of smaller subsystems. I divided the model into 4 subsystems, in which bacteria first grow and colonise the extraluminal surface (the outside of the catheter), before spreading into the bladder. The bacteria grow in the urine in the bladder, and then are swept down through the catheter lumen, where finally some adhere on the intraluminal surface. I then identified suitable mathematical descriptions for the change in the bacterial populations. These descriptions take the form of Fisher, logistic growth, and convection-diffusion equations, which, using insight from clinicians, I coupled together. I implemented this model computationally by developing code (in C++ and Python) to numerically solve the coupled equations, applying this to explore the effects of varying the properties of the catheter, host, and bacteria. I found the rate of urine production by the kidneys to be critical in determining the outcome of bacterial infection, as it governs a transition between a high bacterial density state in the bladder and a ‘washed-out’ state whereby bacteria may grow on the catheter surfaces, but there is no bacteriuria (no bacterial growth in the urine). These results are highly significant for the prevention and mitigation of CAUTI, as they imply that increasing fluid intake may reduce the likelihood of bacteriuria. I also discovered that the urethral length determines the timescale over which infection may occur, giving important insight into observed gendered differences in infection rates in short-term catheterisation. Finally, my model suggests an avenue for future work to investigate the origin of infections, by studying bacterial distributions across the catheter surface, and comparing with modelled distributions to determine the initial conditions. I interpreted the model predictions in the context of clinical data, finding new perspectives on both in vitro and in vivo previous studies. By considering how clinical interventions correspond to changes in model parameters, I classified clinical interventions as postponement, mitigation, or prevention, and discussed the contexts in which those interventions might be effective. I applied the model to predict the outcome of a clinical trial of catheter interventions, showing that the model provides quantitatively better fits to clinical data than previous fits applied in the literature, and successfully qualitatively predicted trial outcomes, including identifying an outcome (reduced incidence of bacteriuria associated with the use of silver-alloy catheters in males) that was present in the study dataset, but not discussed in the original study. My work suggests physical mechanisms that explain clinical observations, demonstrating how from basic assumptions many complex phenomena emerge. Through the development of a population dynamics model with direct clinical implications, I applied physics to make an important contribution to CAUTI research

    Encounter-based approach to target search problems: a review

    Full text link
    In this review, we present the encounter-based approach to target search problems, in which the diffusive dynamics is described by the joint probability of the position of the particle and the number of its encounters with a given target set. The knowledge of the statistics of encounters allows one to implement various mechanisms of reactions on the target set, beyond conventional reaction schemes. We formulate this approach for three relevant settings: discrete random walks, Brownian motion with bulk reactions, and reflected Brownian motion with surface reactions. In all cases, we discuss the advantages of this approach, its recent applications and possible extensions

    Numerical Methods for Wave Turbulence: Isotropic 3-Wave Kinetic Equations

    Get PDF
    Wave turbulence theory has remained an active area of research since its inception in the early part of the last century. In the kinetic regime, the main objects of study are the wave kinetic equations. The breakthrough discovery of constant flux, time independent solutions by Zakharov in the late 1960\u27s has allowed for the theories predictions to be verified both experimentally and computationally in a wide array of physical systems. However, there remain many open questions concerning the time dependent solutions of the wave kinetic equations. In this thesis, we aim to partially address this open area of the wave turbulence theory by providing numerical methods for the time dependent solutions of the isotropic 3-wave kinetic equations. The methods we develop herein are able to confirm previous analysis for time dependent solutions, specifically the behavior of the energy cascade of these solutions

    Understanding the Impact of Physicochemical Modifications on the Cold Gelling Behavior of Micellar Casein Concentrate Dispersions

    Get PDF
    When skim milk is filtered via microfiltration, the amount of casein (one of the major milk proteins) in solution can be concentrated. When casein content is high enough (\u3e15%), the solution forms a gel at cold temperatures. With growing trends in the food industry towards simplistic ingredient labels, commonly used gums and stabilizers in the dairy industry are becoming less preferred. In the future, there is potential for the gelling properties of micellar casein to be applied to dairy products as a thickener or stabilizer, but the mechanism behind gel formation isn’t understood well. In this study, the gel strength, gelation temperature, and structural changes of casein in response to modifications were studied to understand how they may affect gelation. These modifications included reductions in protein content (from 18.5 to 10%), pH adjustment (from 6.2 to 6.8), addition of a calcium chelating salt (sequesters calcium, a structural component of casein), and addition of a common dairy stabilizer: kappa carrageenan. Protein content was the main determinant of gel strength; reductions from the original protein content of 18.5% to less than 15% resulted in weaker gels that required lower temperatures to form a gel. We found that as the pH increased from 6.2 to 6.8, stronger gels can be formed at a higher temperature. The addition of calcium chelating salts improved these qualities as well but increasing concentrations from moderate (25mM) to high (50mM) resulted in a reduction in gel strength. Microstructure analysis of gels via transmission electron microscopy revealed that with increasing pH, the micellar structure of casein was disintegrating, forming a dispersion of free casein fragments. Calcium chelation at moderate concentrations partially disintegrated the protein structure, but high concentrations led to the formation of large casein aggregates causing a reduction in gel strength. When kappa carrageenan was added, it allowed samples diluted to 10% protein to form a gel which was not previously possible. Kappa carrageenan had minimal interaction with casein, but it was responsible for a stronger gel. Overall, modifications of casein can increase the gel strength and temperature of gelation due to the structural changes in casein

    The interplay of gas, dust, and magnetorotational instability in magnetized protoplanetary disks

    Get PDF
    The rich diversity of exoplanets discovered in various physical environments clearly shows that planet formation is an efficient process with multiple outcomes. To un- derstand the emergence of newborn planets, one can rewind the clock of planetary systems by investigating the formation and evolution of their natal environment, the so-called protoplanetary disks. In the core accretion scenario, rocky planets such as the Earth are thought to be formed from cosmic dust particles that grow into pebbles and planetesimals, the building blocks of planets, later assembling to- gether. An intricate puzzle in this theory is how exactly these building blocks are formed and kept long enough in the natal protoplanetary disk. Protoplanetary disks are weakly magnetized accretion disks that are subject to the magnetorotational instability (MRI). It is to date one of the main candidates for explaining their turbulence and angular momentum transport. The nonideal magnetohydrodynamic effects prevent the MRI from operating everywhere in the protoplanetary disk, leading to MRI active regions with high turbulence and non- MRI regions with low turbulence. It has been hypothesized that these variations in the disk turbulence can lead to pressure maxima where dust particles can be trapped. In these so-called dust traps, dust particles can grow efficiently into peb- bles and potentially planetesimals. Yet, it is still an open question how this MRI- powered mechanism shapes the secular evolution of protoplanetary disks, and how it is involved in the first steps of planet formation. It is because the interplay of gas evolution, dust evolution (dynamics and grain growth processes combined) and MRI-driven turbulence over millions of years has never been investigated. The central goal of this thesis is to bridge the gap in the core accretion scenario of planet formation by building the very first unified disk evolution framework that captures self-consistently this interplay. The unique approach adopted in this thesis leads to an exciting new pathway for the generation of spontaneous dust traps everywhere in the protoplanetary disk, which can be potential birth-sites for planets by forming and keeping their necessary building blocks

    Drug-Loaded Colloidal Systems in Nanomedicine II

    Get PDF
    This reprint highlights high-quality original research and review papers that include innovative colloidal drug delivery systems and cutting-edge characterization techniques that significantly contribute to the area of nanomedicine. The results presented are of high interest for specialists from a broad spectrum of fields, including biomedical, pharmaceutical, industrial, and biotechnological spheres

    Molecules in Superfluid Helium Nanodroplets

    Get PDF
    This open access book covers recent advances in experiments using the ultra-cold, very weakly perturbing superfluid environment provided by helium nanodroplets for high resolution spectroscopic, structural and dynamic studies of molecules and synthetic clusters. The recent infra-red, UV-Vis studies of radicals, molecules, clusters, ions and biomolecules, as well as laser dynamical and laser orientational studies, are reviewed. The Coulomb explosion studies of the uniquely quantum structures of small helium clusters, X-ray imaging of large droplets and electron diffraction of embedded molecules are also described. Particular emphasis is given to the synthesis and detection of new species by mass spectrometry and deposition electron microscopy

    21st Century Nanostructured Materials

    Get PDF
    Nanostructured materials (NMs) are attracting interest as low-dimensional materials in the high-tech era of the 21st century. Recently, nanomaterials have experienced breakthroughs in synthesis and industrial and biomedical applications. This book presents recent achievements related to NMs such as graphene, carbon nanotubes, plasmonic materials, metal nanowires, metal oxides, nanoparticles, metamaterials, nanofibers, and nanocomposites, along with their physical and chemical aspects. Additionally, the book discusses the potential uses of these nanomaterials in photodetectors, transistors, quantum technology, chemical sensors, energy storage, silk fibroin, composites, drug delivery, tissue engineering, and sustainable agriculture and environmental applications
    • …
    corecore