Browsing by discipline "Teoreettinen fysiikka"

Fibroblast growth factor 2 (FGF2) is a protein conserved in mammals with multiple established functions in human biology. It acts as a mitogen promoting cell division and is also a known angiogenic factor. FGF2 has been linked with tumor cell proliferation due to its pro-angiogenic capability. However, in order to perform these functions FGF2 needs to be secreted outside the cell membrane. Secretion of proteins usually happens through the Golgi apparatus as a signal peptide-dependent process. FGF2 has been shown not to have a signal peptide needed for the secretion. Recently, a signal peptide-independent secretion pathway for FGF2 was suggested. The hypothesis is that FGF2 monomers bind to the intracellular leaflet of the cell membrane via interactions with phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) lipids. On the membrane surface, FGF2 monomers are then assumed to aggregate and form larger oligomers. These oligomers are thought to form a pore through which other FGF2 monomers can secrete into the extracellular space. As to FGF2-FGF2 binding needed in oligomerization, currently only one stable dimerization interface is known. In this interface, the key interaction is a disulfide bridge between cysteines C95-C95 stabilizing the complex. In this thesis, I studied the first two steps of the hypothesized secretion pathway using molecular dynamics (MD) and Monte Carlo (MC) simulations. First, I studied FGF2 binding to a cell membrane through umbrella sampling simulations and determined free energies for the membrane binding of FGF2 with different membrane concentrations of cholesterol and PI(4,5)P2 . The free energy was shown to inversely correlate with both quantities. Second, I investigated FGF2 dimerization to find new candidates for the monomer-monomer interfaces needed for FGF2 oligomerization. The dimerization was studied using atomistic MC simulations and coarse-grained MD simulations. Two new promising interfaces were identified, which could play a key role in the higher order oligomerization of FGF2 monomers.

Mirror mode waves arise from the antiphase, low frequency fluctuations of the magnetic field and plasma density when the energy is conserved and a sufficient temperature anisotropy is present in the plasma. These waves are linearly polarized and they are frequently observed in heliospheric plasma, in particular in different sheath structures. They are the most widely studied in the planetary magnetosheaths, but also found in cometosheaths and in the heliosheath. In addition, mirror mode waves are reported to also occur in CME-driven sheaths. The knowledge of mirror modes in CME-driven sheaths is, however, very limited despite of the fact that they might contribute to regulating the CME sheath plasma on a global scale, and also a ect the geoeffectivity of CME-driven sheaths as well as the modulation and acceleration of energetic particles. As of yet, no statistical studies of mirror modes in CME-driven sheaths exist. In this thesis, a background to the basic physical plasma phenomena and structures in the heliosphere is given by briegly discussing the solar wind, interplanetary shocks and sheath regions. The central focus of this thesis is however on CME-driven sheath regions and the mirror mode wave occurrence in them. CME-driven sheaths are turbulent plasma regions between the CME ejecta and its preceding interplanetary shock. This thesis discusses the differences between CME-driven sheaths and other heliospheric sheaths. In addition, mirror modes are considered in detail by presenting the theory of mirror instability in both fluid and kinetic descriptions and by discussing the fundamental features of mirror modes in other heliospheric sheaths regions. The previous studies of mirror modes and the methods applied in them are also widely presented. A program that identifies mirror mode structures from the magnetic field data of a spacecraft is constructed for this thesis. In the identification process, the program applies the linear polarization of mirror modes and the knowledge of the angular change of the magnetic field direction across a mirror mode structure. This new, almost fully automatic program combines previous mirror mode identification methods in a novel way, thus creating a new method for detecting and studying mirror modes in CME-driven sheath regions, as well as in other sheath regions. In this thesis, the constructed program is applied to perform a statistical study of mirror mode waves in CME-driven sheaths. Mirror modes were discovered to be common structures, but similar to the planetary magnetosheaths. They occupy only a relatively small part of the CME sheath. The results show that in CME-driven sheaths mirror modes are generally low amplitude structures that typically occur as trains of two or three mirror mode waves. In addition, the sheath plasma was noted to have notable temperature anisotropies, being generally mirror unstable when mirror modes were detected. The properties of the preceding shock of a CME-driven sheath were deduced to a ect mirror mode occurrence and the shock compression was concluded to provide a source of free energy.

Surface growth by using nanocluster deposition has attracted a lot of attention in recent years due to possibilities to affect electronic properties of the resulting thin films. Industry is interested in this method because with cluster deposition it is possible to manufacture thin films much faster than by using single atom deposition. In some cases, nanocluster deposition is the only method by which thin films have been able to be deposited successfully. I have studied Si20 cluster deposition on the Si(0 0 1) surface. I used molecular dynamics simulations to simulate epitaxial silicon growth at temperatures 300 K, 500 K, 700 K, 1000 K, 1300 K and 1600 K. I used two potential models to do this, the Tersoff and the Stillinger-Weber potentials. This work focuses on the differences in the results of these potential models at various temperatures. All the atoms in the cluster had 1 eV of energy. I observed that the growth is stronger with the Stillinger-Weber potential almost at every temperature. At 300 K no epitaxial growth was seen and at 1600 K the substrate melted. I observed almost complete epitaxial growth with the Stillinger-Weber potential, whereas with the Tersoff potential there was an amorphous layer on top of the crystalline region. The epitaxial growth didn't originate from the diffusion as much as from the rearrangement of atoms at the amorphous-crystalline interface.

This thesis reviews the multiscale entanglement renormalisation ansatz or MERA, a numerical tool for the study of quantum many-body systems and a discrete realisation of the AdS/CFT duality. The thesis covers an introduction to the necessary background concepts of entanglement, entanglement entropy and tensor network states, the structure and main features of MERA and its applications in condensed matter theory and holography. Also covered are details on the algorithmic implementation of MERA and some of its generalisations and extensions. MERA belongs to a class of variational ansatze for quantum many-body states known as tensor network states. It is especially well-suited for the study of scale invariant critical points. MERA is based on a real-space renormalisation group procedure called entanglement renormalisation, designed to systematically handle entanglement at different length scales along the coarse-graining flow. Entanglement renormalisation has be used for example to efficiently describe Kitaev states of the toric code, the prime example of topological order, and numerically study the ground state of the highly frustrated spin-1/2 Heisenberg model on a kagome lattice and various other one- and two-dimensional lattice models. The geometric and causal structure of MERA, which underlies its effectiveness as a numerical tool, also makes it a discrete version of the AdS/CFT duality. This duality describes a conformal field theory by a gravity theory in a higher dimensional space, and vice versa. The duality is manifest in the scaling of entanglement entropy in MERA, which is governed by a law highly analogous to the Ryu-Takayanagi formula for holographic entanglement entropy, in the connection between thermal states and a black-hole-like MERA and in the connection between correlation functions and holographic geodesics in a scale invariant MERA. The aim of this thesis is to lead the reader to an understanding of what MERA is, how it works and how it can be used. MERA's core features and uses are presented in a comprehensive and explicit way, and a broad view of possible applications and further directions is given. Plenty of references are also offered to direct the reader to further research on how MERA may relate to his/her interests.

In this work the connection between neutrino mass mechanisms and leptonic CP violation at collider experiments is studied. These subjects are connected on a fundamental level: the neutrino mass models dictate the form of the neutrino mass matrix; leptonic CP violation is expressed in the neutrino mass matrix by the Dirac and Majorana phases. The mass of neutrinos has been a subject of intensive study since the discovery of neutrino oscillation in the 1990s. This was the first, and still the only, observation that could not be explained by the standard model of particle physics. Neutrino mass mechanisms provide a way to extend the symmetry group of the standard model so that the neutrino masses are included. In addition to the tree-level seesaw mechanisms, four higher energy models, namely the minimal left-right symmetric model, the Littlest Higgs model, an SU(5) with an adjoint fermion, and the Altarelli-Feruglio model are reviewed. The first three extend the symmetry group of the standard model by a continuous symmetry, whereas the last extends it with a discrete flavor symmetry. It is possible that the seesaw mediators responsible for neutrino masses are within the energy reach of the LHC. Then the parameters of the neutrino mass matrix could be probed at collider experiments. One could determine the existence of the Dirac and Majorana phases by studying their effects on observable quantities of the channels including the seesaw mediators. These effects are reviewed in this work. The non-zero values of the phases would still not determine the existence of leptonic CP violation: generally, a CP odd phase can lead into CP even processes. It is concluded that the discovery potential of the Majorana phases is quite promising at the studied processes. For the Dirac phase, the effects are more subtle and its value will probably be determined at other experiments.

At the moment, neutrons stars are some of the few objects in the Universe which allow us to study the physics of cold dense matter. This matter is denser than atomic nuclei and the thermal energy of its particles is much smaller than their Fermi energy. This kind of research is possible because the mass-radius behavior of the neutron star population depends strongly on the equation of state of neutron star matter. Unfortunately, precise enough radius measurements have not been available until very recently when simultaneous mass-radius measurements were developed. Since this development is still going on, no-one has yet combined these new kinds of measurements with perturbative Quantum Chromodynamics (pQCD) calculations, for example. This thesis has two main functions: Firstly, we want to present the current knowledge about neutron stars and cold dense matter. Secondly, we want to introduce a Bayesian method which connects astronomical observations and current pQCD results by using polytropes. In this fashion, it should be possible to further restrict the behavior of the equation of state of cold dense matter at neutron star densities. Nevertheless, a detailed examination of this approach is left to future studies.

Our present-day understanding of fundamental constituents of matter and their interactions is based on the Standard Model of particle physics, which relies on quantum gauge field theories. On the other hand, the large scale dynamical behaviour of spacetime is understood via the general theory of relativity of Einstein. The merging of these two complementary aspects of nature, quantum and gravity, is one of the greatest goals of modern fundamental physics, the achievement of which would help us understand the short-distance structure of spacetime, thus shedding light on the events in the singular states of general relativity, such as black holes and the Big Bang, where our current models of nature break down. The formulation of quantum field theories in noncommutative spacetime is an attempt to realize the idea of nonlocality at short distances, which our present understanding of these different aspects of Nature suggests, and consequently to find testable hints of the underlying quantum behaviour of spacetime. The formulation of noncommutative theories encounters various unprecedented problems, which derive from their peculiar inherent nonlocality. Arguably the most serious of these is the so-called UV/IR mixing, which makes the derivation of observable predictions especially hard by causing new tedious divergencies, to which our previous well-developed renormalization methods for quantum field theories do not apply. In the thesis I review the basic mathematical concepts of noncommutative spacetime, different formulations of quantum field theories in the context, and the theoretical understanding of UV/IR mixing. In particular, I put forward new results to be published, which show that also the theory of quantum electrodynamics in noncommutative spacetime defined via Seiberg-Witten map suffers from UV/IR mixing. Finally, I review some of the most promising ways to overcome the problem. The final solution remains a challenge for the future.

We investigate a dark sector augmentation of the standard model with a keV-scale right-handed sterile neutrino field 𝑁 and a TeV-scale singlet scalar field 𝑆. The ("warm") dark matter candidate of the model is the sterile neutrino, which is produced from decays of singlet scalars. The dark sector is coupled to the standard model via the Higgs portal coupling between the singlet scalar and Higgs 𝐻. The momentum distribution function, which contains the full information about the production process, is obtained for sterile neutrinos by solving a system of Boltzmann equations. For simplicity, we assume the effective number of relativistic degrees of freedom to be constant during the dark matter production. We take into account several constraints from structure formation and cosmology, and find that even this simple model gives rise to a rich phenomenology. In particular, we find that, in addition to offering a realistic dark matter candidate, the sterile neutrino can attain a highly non-thermal momentum distribution in the process. A direct consequence of this is the inability to assess the impact on the structure formation with the usual estimators that require a thermal momentum distribution, such as the free-streaming length. We rely on [72], which uses the linear power spectrum, instead of the free-streaming length, to estimate the impact on structure formation. This method also works for non-thermal momentum spectra. On the side, we discuss the evidence for dark matter, known problems of the ΛCDM, and the basic production mechanisms in the early universe. Also a comprehensive, analytical and numerical, reduction of necessary equations is presented.

Ability to deduce three-dimensional structure of a protein from its one-dimensional amino acid chain is a long-standing challenge in structural biology. Accurate structure prediction has enormous application potential in e.g. drug development and design of novel enzymes. In past this problem has been studied experimentally (X-ray crystallography, nuclear magnetic resonance imaging) and computationally by simulating molecular dynamics of protein folding. However, the latter requires enormous computing resources and the former is expensive and time-consuming. Direct contact analysis (DCA) is an inference method relying on direct correlations measured from multiple sequence alignments (MSA) of protein families to predict contacts between amino acids in the three-dimensional structure of a protein. It solves the 21-state inverse Potts problem of statistical physics, i.e. given the correlations, what are the interactions between the amino acids of a protein. The current state of the art in the DCA approach is the plmDCA-algorithm relying on pseudolikelihood maximization. In this study the performance of the parallelised asymmetric plmDCA-algorithm is tested on a diverse set of more than 100 protein families. It is seen that generally for MSA's with more than approximately 2000 sequences plmDCA is able to predict more than half of the 100 top-scoring contacts correctly with the prediction accuracy increasing almost linearly as a function of the number of sequences. Parallelisation of plmDCA is also observed to make the algorithm tens of times (depending on the number of CPU cores used) faster than the previously described serial plmDCA. Extensions to Potts model taking into account the differences in distributions of gaps and amino acids in MSA's are investigated. An extension incorporating the position-dependant frequencies of gaps of length one to Potts model is found to increase the prediction accuracy for short sequences. Further and more extensive studies are however needed to discover the full potential of this approach.