ISM simulations: an overview of models

Until recently the dynamical evolution of the interstellar medium (ISM) was simu- lated using collisional ionization equilibrium (CIE) conditions. However, the ISM is a dynamical system, in which the plasma is naturally driven out of equilibrium due to atomic and dynamic processes operating on different timescales. A step forward in the field comprises a multi-fluid approach taking into account the joint thermal and dynamical evolutions of the ISM gas.

Numerical simulations of the spine for patient-specific models of severe scoliosis

In silico methods, such as musculoskeletal modelling, may aid the selection of the optimal surgical treatment for highly complex pathologies such as scoliosis. Many musculoskeletal models use a generic, simplified representation of the intervertebral joints, which are fundamental to the flexibility of the spine. Therefore, to model and simulate the spine, a suitable representation of the intervertebral joint is crucial. The aim of this PhD was to characterise specimen-specific models of the intervertebral joint for multi-body models from experimental datasets. First, the project investigated the characterisation of a specimen-specific lumped parameter model of the intervertebral joint from an experimental dataset of a four-vertebra lumbar spine segment. Specimen-specific stiffnesses were determined with an optimisation method. The sensitivity of the parameters to the joint pose was investigate. Results showed the stiffnesses and predicted motions were highly depended on both the joint pose. Following the first study, the method was reapplied to another dataset that included six complete lumbar spine segments under three different loading conditions. Specimen-specific uniform stiffnesses across joint levels and level-dependent stiffnesses were calculated by optimisation. Specimen-specific stiffness show high inter-specimen variability and were also specific to the loading condition. Level-dependent stiffnesses are necessary for accurate kinematic predictions and should be determined independently of one another. Secondly, a framework to create subject-specific musculoskeletal models of individuals with severe scoliosis was developed. This resulted in a robust codified pipeline for creating subject-specific, severely scoliotic spine models from CT data. In conclusion, this thesis showed that specimen-specific intervertebral joint stiffnesses were highly sensitive to joint pose definition and the importance of level-dependent optimisation. Further, an open-source codified pipeline to create patient-specific scoliotic spine models from CT data was released. These studies and this pipeline can facilitate the specimen-specific characterisation of the scoliotic intervertebral joint and its incorporation into scoliotic musculoskeletal spine models.

Finite group lattice gauge theories for quantum simulation

The present manuscript focuses on Lattice Gauge Theories based on finite groups. For the purpose of Quantum Simulation, the Hamiltonian approach is considered, while the finite group serves as a discretization scheme for the degrees of freedom of the gauge fields. Several aspects of these models are studied. First, we investigate dualities in Abelian models with a restricted geometry, using a systematic approach. This leads to a rich phase diagram dependent on the super-selection sectors. Second, we construct a family of lattice Hamiltonians for gauge theories with a finite group, either Abelian or non-Abelian. We show that is possible to express the electric term as a natural graph Laplacian, and that the physical Hilbert space can be explicitly built using spin network states. In both cases we perform numerical simulations in order to establish the correctness of the theoretical results and further investigate the models.

Quantum information and quantum communication theory in relation to black hole idealized mechanical models

Oggigiorno il concetto di informazione è diventato cruciale in fisica, pertanto, siccome la migliore teoria che abbiamo per compiere predizioni riguardo l'universo è la meccanica quantistica, assume una particolare importanza lo sviluppo di una versione quantistica della teoria dell'informazione. Questa centralità è confermata dal fatto che i buchi neri hanno entropia. Per questo motivo, in questo lavoro sono presentati elementi di teoria dell'informazione quantistica e della comunicazione quantistica e alcuni sono illustrati riferendosi a modelli quantistici altamente idealizzati della meccanica di buco nero. In particolare, nel primo capitolo sono forniti tutti gli strumenti quanto-meccanici per la teoria dell'informazione e della comunicazione quantistica. Successivamente, viene affrontata la teoria dell'informazione quantistica e viene trovato il limite di Bekenstein alla quantità di informazione chiudibile entro una qualunque regione spaziale. Tale questione viene trattata utilizzando un modello quantistico idealizzato della meccanica di buco nero supportato dalla termodinamica. Nell'ultimo capitolo, viene esaminato il problema di trovare un tasso raggiungibile per la comunicazione quantistica facendo nuovamente uso di un modello quantistico idealizzato di un buco nero, al fine di illustrare elementi della teoria. Infine, un breve sommario della fisica dei buchi neri è fornito in appendice.

On The Consistency Of Monte Carlo Track Structure Dna Damage Simulations.

Monte Carlo track structures (MCTS) simulations have been recognized as useful tools for radiobiological modeling. However, the authors noticed several issues regarding the consistency of reported data. Therefore, in this work, they analyze the impact of various user defined parameters on simulated direct DNA damage yields. In addition, they draw attention to discrepancies in published literature in DNA strand break (SB) yields and selected methodologies. The MCTS code Geant4-DNA was used to compare radial dose profiles in a nanometer-scale region of interest (ROI) for photon sources of varying sizes and energies. Then, electron tracks of 0.28 keV-220 keV were superimposed on a geometric DNA model composed of 2.7 × 10(6) nucleosomes, and SBs were simulated according to four definitions based on energy deposits or energy transfers in DNA strand targets compared to a threshold energy ETH. The SB frequencies and complexities in nucleosomes as a function of incident electron energies were obtained. SBs were classified into higher order clusters such as single and double strand breaks (SSBs and DSBs) based on inter-SB distances and on the number of affected strands. Comparisons of different nonuniform dose distributions lacking charged particle equilibrium may lead to erroneous conclusions regarding the effect of energy on relative biological effectiveness. The energy transfer-based SB definitions give similar SB yields as the one based on energy deposit when ETH ≈ 10.79 eV, but deviate significantly for higher ETH values. Between 30 and 40 nucleosomes/Gy show at least one SB in the ROI. The number of nucleosomes that present a complex damage pattern of more than 2 SBs and the degree of complexity of the damage in these nucleosomes diminish as the incident electron energy increases. DNA damage classification into SSB and DSB is highly dependent on the definitions of these higher order structures and their implementations. The authors' show that, for the four studied models, different yields are expected by up to 54% for SSBs and by up to 32% for DSBs, as a function of the incident electrons energy and of the models being compared. MCTS simulations allow to compare direct DNA damage types and complexities induced by ionizing radiation. However, simulation results depend to a large degree on user-defined parameters, definitions, and algorithms such as: DNA model, dose distribution, SB definition, and the DNA damage clustering algorithm. These interdependencies should be well controlled during the simulations and explicitly reported when comparing results to experiments or calculations.

Interplay Of Weak Interactions In The Atom-by-atom Condensation Of Xenon Within Quantum Boxes.

Condensation processes are of key importance in nature and play a fundamental role in chemistry and physics. Owing to size effects at the nanoscale, it is conceptually desired to experimentally probe the dependence of condensate structure on the number of constituents one by one. Here we present an approach to study a condensation process atom-by-atom with the scanning tunnelling microscope, which provides a direct real-space access with atomic precision to the aggregates formed in atomically defined 'quantum boxes'. Our analysis reveals the subtle interplay of competing directional and nondirectional interactions in the emergence of structure and provides unprecedented input for the structural comparison with quantum mechanical models. This approach focuses on-but is not limited to-the model case of xenon condensation and goes significantly beyond the well-established statistical size analysis of clusters in atomic or molecular beams by mass spectrometry.

Turbulence in collisionless plasmas: statistical analysis from numerical simulations with pressure anisotropy

In recent years, we have experienced increasing interest in the understanding of the physical properties of collisionless plasmas, mostly because of the large number of astrophysical environments (e. g. the intracluster medium (ICM)) containing magnetic fields that are strong enough to be coupled with the ionized gas and characterized by densities sufficiently low to prevent the pressure isotropization with respect to the magnetic line direction. Under these conditions, a new class of kinetic instabilities arises, such as firehose and mirror instabilities, which have been studied extensively in the literature. Their role in the turbulence evolution and cascade process in the presence of pressure anisotropy, however, is still unclear. In this work, we present the first statistical analysis of turbulence in collisionless plasmas using three-dimensional numerical simulations and solving double-isothermal magnetohydrodynamic equations with the Chew-Goldberger-Low laws closure (CGL-MHD). We study models with different initial conditions to account for the firehose and mirror instabilities and to obtain different turbulent regimes. We found that the CGL-MHD subsonic and supersonic turbulences show small differences compared to the MHD models in most cases. However, in the regimes of strong kinetic instabilities, the statistics, i.e. the probability distribution functions (PDFs) of density and velocity, are very different. In subsonic models, the instabilities cause an increase in the dispersion of density, while the dispersion of velocity is increased by a large factor in some cases. Moreover, the spectra of density and velocity show increased power at small scales explained by the high growth rate of the instabilities. Finally, we calculated the structure functions of velocity and density fluctuations in the local reference frame defined by the direction of magnetic lines. The results indicate that in some cases the instabilities significantly increase the anisotropy of fluctuations. These results, even though preliminary and restricted to very specific conditions, show that the physical properties of turbulence in collisionless plasmas, as those found in the ICM, may be very different from what has been largely believed.

Dynamic polarizability, Cauchy moments, and the optical absorption spectrum of liquid water: A sequential molecular dynamics/quantum mechanical approach

The dynamic polarizability and optical absorption spectrum of liquid water in the 6-15 eV energy range are investigated by a sequential molecular dynamics (MD)/quantum mechanical approach. The MD simulations are based on a polarizable model for liquid water. Calculation of electronic properties relies on time-dependent density functional and equation-of-motion coupled-cluster theories. Results for the dynamic polarizability, Cauchy moments, S(-2), S(-4), S(-6), and dielectric properties of liquid water are reported. The theoretical predictions for the optical absorption spectrum of liquid water are in good agreement with experimental information.

Combined Monte Carlo and quantum mechanics study of the solvatochromism of phenol in water. The origin of the blue shift of the lowest pi-pi* transition

A combined and sequential use of Monte Carlo simulations and quantum mechanical calculations is made to analyze the spectral shift of the lowest pi-pi* transition of phenol in water. The solute polarization is included using electrostatic embedded calculations at the MP2/aug-cc-pVDZ level giving a dipole moment of 2.25 D, corresponding to an increase of 76% compared to the calculated gas-phase value. Using statistically uncorrelated configurations sampled from the MC simulation,first-principle size-extensive calculations are performed to obtain the solvatochromic shift. Analysis is then made of the origin of the blue shift. Results both at the optimized geometry and in room-temperature liquid water show that hydrogen bonds of water with phenol promote a red shift when phenol is the proton-donor and a blue shift when phenol is the proton-acceptor. In the case of the optimized clusters the calculated shifts are in very good agreement with results obtained from mass-selected free jet expansion experiments. In the liquid case the contribution of the solute-solvent hydrogen bonds partially cancels and the total shift obtained is dominated by the contribution of the outer solvent water molecules. Our best result, including both inner and outer water molecules, is 570 +/- 35 cm(-1), in very good agreement with the small experimental shift of 460 cm(-1) for the absorption maximum.

The isotropic nuclear magnetic shielding constants of acetone in supercritical water: A sequential Monte Carlo/quantum mechanics study including solute polarization

The nuclear isotropic shielding constants sigma((17)O) and sigma((13)C) of the carbonyl bond of acetone in water at supercritical (P=340.2 atm and T=673 K) and normal water conditions have been studied theoretically using Monte Carlo simulation and quantum mechanics calculations based on the B3LYP/6-311++G(2d,2p) method. Statistically uncorrelated configurations have been obtained from Monte Carlo simulations with unpolarized and in-solution polarized solute. The results show that solvent effects on the shielding constants have a significant contribution of the electrostatic interactions and that quantitative estimates for solvent shifts of shielding constants can be obtained modeling the water molecules by point charges (electrostatic embedding). In supercritical water, there is a decrease in the magnitude of sigma((13)C) but a sizable increase in the magnitude of sigma((17)O) when compared with the results obtained in normal water. It is found that the influence of the solute polarization is mild in the supercritical regime but it is particularly important for sigma((17)O) in normal water and its shielding effect reflects the increase in the average number of hydrogen bonds between acetone and water. Changing the solvent environment from normal to supercritical water condition, the B3LYP/6-311++G(2d,2p) calculations on the statistically uncorrelated configurations sampled from the Monte Carlo simulation give a (13)C chemical shift of 11.7 +/- 0.6 ppm for polarized acetone in good agreement with the experimentally inferred result of 9-11 ppm. (C) 2008 American Institute of Physics.

Emergent and reentrant fractional quantum Hall effect in trilayer systems in a tilted magnetic field

Magnetotransport measurements in triple-layer electron systems with high carrier density reveal fractional quantum Hall effect at total filling factors nu>2. With an in-plane magnetic field we are able to control the suppression of interlayer tunneling which causes a collapse of the integer quantum Hall plateaus at nu=2 and nu=4, and an emergence of fractional quantum Hall states with increasing tilt angles. The nu=4 state is replaced by three fractional quantum Hall states with denominator 3. The state nu=7/3 demonstrates reentrant behavior and the emergent state at nu=12/5 has a nonmonotonic behavior with increasing in-plane field. We attribute the observed fractional quantum Hall plateaus to correlated states in a trilayer system.

Magnetoconfined levels in a parabolic quantum dot: An analytical solution of a three-dimensional Fock-Darwin problem in a tilted magnetic field

The energy spectrum of an electron confined in a quantum dot (QD) with a three-dimensional anisotropic parabolic potential in a tilted magnetic field was found analytically. The theory describes exactly the mixing of in-plane and out-of-plane motions of an electron caused by a tilted magnetic field, which could be seen, for example, in the level anticrossing. For charged QDs in a tilted magnetic field we predict three strong resonant lines in the far-infrared-absorption spectra.

Anomalous dephasing scattering rate of two-dimensional electrons in double quantum well structures

The results on the measurement of electrical conductivity and magnetoconductivity of a GaAs double quantum well between 0.5 and 1.1 K are reported. The zero magnetic-field conductivity is well described from the point of view of contributions made by both the weak localization and electron-electron interaction. At low field and low temperature, the magnetoconductivity is dominated by the weak localization effect only. Using the weak localization method, we have determined the electron dephasing times tau(phi) and tunneling times tau(t). Concerning tunneling, we concluded that tau(t) presents a minimum around the balance point; concerning dephasing, we observed an anomalous dependence on temperature and conductivity (or elastic mean free path) of tau(phi). This anomalous behavior cannot be explained in terms of the prevailing concepts for the electron-electron interaction in high-mobility two-dimensional electron systems.

Precise determination of quantum critical points by the violation of the entropic area law

Finite-size scaling analysis turns out to be a powerful tool to calculate the phase diagram as well as the critical properties of two-dimensional classical statistical mechanics models and quantum Hamiltonians in one dimension. The most used method to locate quantum critical points is the so-called crossing method, where the estimates are obtained by comparing the mass gaps of two distinct lattice sizes. The success of this method is due to its simplicity and the ability to provide accurate results even considering relatively small lattice sizes. In this paper, we introduce an estimator that locates quantum critical points by exploring the known distinct behavior of the entanglement entropy in critical and noncritical systems. As a benchmark test, we use this new estimator to locate the critical point of the quantum Ising chain and the critical line of the spin-1 Blume-Capel quantum chain. The tricritical point of this last model is also obtained. Comparison with the standard crossing method is also presented. The method we propose is simple to implement in practice, particularly in density matrix renormalization group calculations, and provides us, like the crossing method, amazingly accurate results for quite small lattice sizes. Our applications show that the proposed method has several advantages, as compared with the standard crossing method, and we believe it will become popular in future numerical studies.

Atomic scale characterization of Mn doped InAs/GaAs quantum dots

Several growth procedures for doping InAs/GaAs quantum dots (QDs) with manganese (Mn) have been investigated with cross-sectional scanning tunneling microscopy. It is found that expulsion of Mn out of the QDs and subsequent segregation makes it difficult to incorporate Mn in the QDs even at low growth temperatures of T=320 degrees C and high Mn fluxes. Mn atoms in and around QDs have been observed with strain and potential confinement changing the appearance of the Mn features.