533 research outputs found

    Conformations and dynamics of strongly charged biomolecules

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    This Thesis is based on analytical and numerical calculations concerning strongly charged biomolecules. The study concentrates on statistical properties of strongly charged biopolymers in the presence of neutralizing counterions and reservoir salt ions, involving applications on deoxyribonucleic acid (DNA), which is a key molecule in human cells. The Thesis starts from constructing a theory that explains the counter- and coion distributions around an arbitrary strongly charged surface, and moves to applications involving statistical conformations of highly stretched DNA, and dynamics of settling the DNA chain in the presence of a large amount of reservoir salt. Studies on ion-distributions around a charged surface concentrate on finding a theoretical description in the limit where electrostatic interactions between the ions and the charged surface are so strong that they dominate over the translational entropy of the counter- and coions. In particular we explain how the added electrolyte or salt modifies the ion distributions compared to the zero salt case, a topic which is highly relevant for bioapplications that take place under physiological salt concentration. Application on the DNA overstretching transition involves the evaluation of the response of the chain to a strong external stretching force. Here we explain how the force needed to extend the chain depends on the added electrolyte concentration. We concentrate on finding the conformation of the chain over the persistence length of DNA, and the equation of state for DNA as a function of the stretching force. Studies on dynamical properties of DNA concern the sedimentation velocity of a long DNA chain under physiological salt conditions that it is typically described using the self-avoiding walk (SAW) model. Here we show that in the limit of large polymer or Reynolds number, the chain goes through a crossover in its shape, transforming from slightly perturbed SAW chain into an elongated configuration along the direction of sedimentation. We present a model that couples the instant configuration in a non-linear way to the settling velocity of the chain. This way the scaling laws for both the radius of gyration of the chain characterizing its size, and for the diffusion coefficient of the chain characterizing its dynamics, are found to be in agreement with numerical simulations

    Hadron models and related New Energy issues

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    The present book covers a wide-range of issues from alternative hadron models to their likely implications in New Energy research, including alternative interpretation of lowenergy reaction (coldfusion) phenomena. The authors explored some new approaches to describe novel phenomena in particle physics. M Pitkanen introduces his nuclear string hypothesis derived from his Topological Geometrodynamics theory, while E. Goldfain discusses a number of nonlinear dynamics methods, including bifurcation, pattern formation (complex GinzburgLandau equation) to describe elementary particle masses. Fu Yuhua discusses a plausible method for prediction of phenomena related to New Energy development. F. Smarandache discusses his unmatter hypothesis, and A. Yefremov et al. discuss Yang-Mills field from Quaternion Space Geometry. Diego Rapoport discusses theoretical link between Torsion fields and Hadronic Mechanic. A.H. Phillips discusses semiconductor nanodevices, while V. and A. Boju discuss Digital Discrete and Combinatorial methods and their likely implications in New Energy research. Pavel Pintr et al. describe planetary orbit distance from modified Schrödinger equation, and M. Pereira discusses his new Hypergeometrical description of Standard Model of elementary particles. The present volume will be suitable for researchers interested in New Energy issues, in particular their link with alternative hadron models and interpretation

    Geometrodynamics: Spacetime or Space ?

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    This thesis concerns the split of Einstein's field equations (EFE's) with respect to nowhere null hypersurfaces. Areas covered include A) the foundations of relativity, deriving geometrodynamics from relational first principles and showing that this form accommodates a sufficient set of fundamental matter fields to be classically realistic, alternative theories of gravity that arise from similar use of conformal mathematics. B) GR Initial value problem (IVP) methods, the badness of timelike splits of the EFE's and studying braneworlds under guidance from GR IVP and Cauchy problem methods.Comment: Thesis, University of London, Examined in June by Prof Chris Isham and Prof James Vickers. 226 pages including 21 figure

    Examining the Relationship Between Lignocellulosic Biomass Structural Constituents and Its Flow Behavior

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    Lignocellulosic biomass material sourced from plants and herbaceous sources is a promising substrate of inexpensive, abundant, and potentially carbon-neutral energy. One of the leading limitations of using lignocellulosic biomass as a feedstock for bioenergy products is the flow issues encountered during biomass conveyance in biorefineries. In the biorefining process, the biomass feedstock undergoes flow through a variety of conveyance systems. The inherent variability of the feedstock materials, as evidenced by their complex microstructural composition and non-uniform morphology, coupled with the varying flow conditions in the conveyance systems, gives rise to flow issues such as bridging, ratholing, and clogging. These issues slow down the conveyance process, affect machine life, and potentially lead to partial or even complete shutdown of the biorefinery. Hence, we need to improve our fundamental understanding of biomass feedstock flow physics and mechanics to address the flow issues and improve biorefinery economics. This dissertation research examines the fundamental relationship between structural constituents of diverse lignocellulosic biomass materials, i.e., cellulose, hemicellulose, and lignin, their morphology, and the impact of the structural composition and morphology on their flow behavior. First, we prepared and characterized biomass feedstocks of different chemical compositions and morphologies. Then, we conducted our fundamental investigation experimentally, through physical flow characterization tests, and computationally through high-fidelity discrete element modeling. Finally, we statistically analyzed the relative influence of the properties of lignocellulosic biomass assemblies on flow behavior to determine the most critical properties and the optimum values of flow parameters. Our research provides an experimental and computational framework to generalize findings to a wider portfolio of biomass materials. It will help the bioenergy community to design more efficient biorefining machinery and equipment, reduce the risk of failure, and improve the overall commercial viability of the bioenergy industry

    Cosmological consequences of Quantum Gravity proposals

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    In this thesis, we study the implications of Quantum Gravity models for the dynamics of spacetime and the ensuing departures from classical General Relativity. The main focus is on cosmological applications, particularly the impact of quantum gravitational effects on the dynamics of a homogenous and isotropic cosmological background. Our interest lies in the consequences for the evolution of the early universe and singularity resolution, as well as in the possibility of providing an alternative explanation for dark matter and dark energy in the late universe. The thesis is divided into two main parts, dedicated to alternative (and complementary) ways of tackling the problem of Quantum Gravity. The first part is concerned with cosmological applications of background independent approaches to Quantum Gravity, both in the context of loop quantisation and in quantum geometrodynamics. Particularly relevant in this work is the Group Field Theory approach, which we use to study the effective dynamics of the emergent universe from a full theory of Quantum Gravity (i.e. without symmetry reduction). In the second part, modified gravity theories are introduced as tools to provide an effective description of quantum gravitational effects, e.g. by introducing new degrees of freedom and symmetries. Particularly relevant in this respect is local conformal invariance, which finds a natural realisation in the framework of Weyl geometry. We build a modified theory of gravity based on such symmetry principle, and argue that new fields in the extended gravitational sector may play the role of dark matter. New degrees of freedom are also natural in models with varying fundamental `constants', which we examine critically. Finally, we discuss prospects for future work and point at directions for the derivation of realistic cosmological models from Quantum Gravity candidates.Comment: PhD thesis, King's College London (supervisor: Mairi Sakellariadou), 282 pages, 20 figures; submitted in September 201
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