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• 451. Lindner, Manfred
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Particle Physics.
Soft L-e - L-mu - L-tau flavour symmetry breaking and sterile neutrino keV Dark Matter2011In: Journal of Cosmology and Astroparticle Physics, ISSN 1475-7516, E-ISSN 1475-7516, Vol. 2011, no 01, p. 034-Article in journal (Refereed)

We discuss how a L-e - L-mu - L-tau flavour symmetry that is softly broken leads to keV sterile neutrinos, which are a prime candidate for Warm Dark Matter. This is to our knowledge the first model where flavour symmetries are applied simultaneously to active and sterile neutrinos explaining at the same time active neutrino properties and this peculiar Dark Matter scenario. The essential point is that different scales of the symmetry breaking and the symmetry preserving entries in the mass matrix lead to one right- handed neutrino which is nearly massless compared to the other two. Furthermore, we naturally predict vanishing theta(13) and maximal theta(23), while the correct value of theta(12) must come from the mixing of the charged leptons. We can furthermore predict an exact mass spectrum for the light neutrinos, which will be testable in the very near future.

• 452.
KTH, School of Engineering Sciences (SCI), Theoretical Physics.
Decay times in turnover statistics of single enzymes2008In: Physical review E, ISSN 1539-3755, Vol. 78, no 1, p. 010901-1-010901-4Article in journal (Refereed)

The first passage times for enzymatic turnovers in nonequilibrium steady state display a statistical symmetry property related to nonequilibrium fluctuation theorems, which makes it possible to extract the chemical driving force from single molecule trajectories in nonequilibrium steady state. Below, we show that the number of decay constants needed to describe the first passage time distribution of this system is not equal to the number of states in the first passage problem, as one would generally expect. Instead, the structure of the kinetic mechanism makes half of the decay times vanish identically from the turnover time distribution. The terms that cancel out correspond to the eigenvalues of a certain submatrix of the master equation matrix for the first exit time problem. We discuss how these results make modeling and data analysis easier for such systems, and how the turnovers can be measured.

• 453.
KTH, School of Engineering Sciences (SCI), Theoretical Physics.
Stochastic modeling of motor proteins2008Doctoral thesis, comprehensive summary (Other scientific)

Motor proteins are microscopic biological machines that convert chemical energy into mechanical motion and work. They power a diverse range of biological processes, for example the swimming and crawling motion of bacteria, intracellular transport, and muscle contraction. Understanding the physical basis of these processes is interesting in its own right, but also has an interesting potential for applications in medicine and nanotechnology.

The ongoing rapid developments in single molecule experimental techniques make it possible to probe these systems on the single molecule level, with increasing temporal and spatial resolution. The work presented in this thesis is concerned with physical modeling of motor proteins on the molecular scale, and with theoretical challenges in the interpretation of single molecule experiments.

First, we have investigated how a small groups of elastically coupled motors collaborate, or fail to do so, when producing strong forces. Using a simple model inspired by the motor protein PilT, we ﬁnd that the motors counteract each other if the density becomes higher than a certain threshold, which depends on the asymmetry of the system.

Second, we have contributed to the interpretation of experiments in which the stepwise motion of a motor protein is followed in real time. Such data is naturally interpreted in terms of ﬁrst passage processes. Our main conclusions are (1) Contrary to some earlier suggestions, the stepping events do not correspond to the cycle completion events associated with the work of Hill and co-workers. We have given a correct formulation. (2) Simple kinetic models predict a generic mechanism that gives rise to correlations in step directions and waiting times. Analysis of stepping data from a chimaeric ﬂagellar motor was consistent with this prediction. (3) In the special case of a reversible motor, the chemical driving force can be extracted from statistical analysis of stepping trajectories.

• 454.
KTH, School of Engineering Sciences (SCI), Theoretical Physics.
KTH, School of Engineering Sciences (SCI), Applied Physics. Department of Medical Biochemistry and Microbiology, Uppsala Biomedical Center, Uppsala University. KTH, School of Engineering Sciences (SCI), Theoretical Physics, Statistical Physics.
Force generation in small ensembles of Brownian motors2006In: Physical Review E, ISSN 1539-3755, Vol. 74, no 2, p. 021908-1-021908-8Article in journal (Refereed)

The motility of certain gram-negative bacteria is mediated by retraction of type IV pili surface filaments, which are essential for infectivity. The retraction is powered by a strong molecular motor protein, PilT, producing very high forces that can exceed 150 pN. The molecular details of the motor mechanism are still largely unknown, while other features have been identified, such as the ring-shaped protein structure of the PilT motor. The surprisingly high forces generated by the PilT system motivate a model investigation of the generation of large forces in molecular motors. We propose a simple model, involving a small ensemble of motor subunits interacting through the deformations on a circular backbone with finite stiffness. The model describes the motor subunits in terms of diffusing particles in an asymmetric, time-dependent binding potential (flashing ratchet potential), roughly corresponding to the ATP hydrolysis cycle. We compute force-velocity relations in a subset of the parameter space and explore how the maximum force (stall force) is determined by stiffness, binding strength, ensemble size, and degree of asymmetry. We identify two qualitatively different regimes of operation depending on the relation between ensemble size and asymmetry. In the transition between these two regimes, the stall force depends nonlinearly on the number of motor subunits. Compared to its constituents without interactions, we find higher efficiency and qualitatively different force-velocity relations. The model captures several of the qualitative features obtained in experiments on pilus retraction forces, such as roughly constant velocity at low applied forces and insensitivity in the stall force to changes in the ATP concentration.

• 455.
KTH, School of Engineering Sciences (SCI), Theoretical Physics.
KTH, School of Engineering Sciences (SCI), Theoretical Physics.
Dwell Time Symmetry in Random Walks and Molecular Motors2007In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 92, no 11, p. 3804-3816Article in journal (Refereed)

The statistics of steps and dwell times in reversible molecular motors differ from those of cycle completion in enzyme kinetics. The reason is that a step is only one of several transitions in the mechanochemical cycle. As a result, theoretical results for cycle completion in enzyme kinetics do not apply to stepping data. To allow correct parameter estimation, and to guide data analysis and experiment design, a theoretical treatment is needed that takes this observation into account. In this article, we model the distribution of dwell times and number of forward and backward steps using first passage processes, based on the assumption that forward and backward steps correspond to different directions of the same transition. We extend recent results for systems with a single cycle and consider the full dwell time distributions as well as models with multiple pathways, detectable substeps, and detachments. Our main results are a symmetry relation for the dwell time distributions in reversible motors, and a relation between certain relative step frequencies and the free energy per cycle. We demonstrate our results by analyzing recent stepping data for a bacterial flagellar motor, and discuss the implications for the efficiency and reversibility of the force-generating subunits.

• 456.
KTH, School of Engineering Sciences (SCI), Theoretical Physics.
KTH, School of Engineering Sciences (SCI), Theoretical Physics.
Graphene – A Two-Dimensional Dirac Material2014Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis

Graphene is a two-dimensional material, whose popularity has soared in both condensedmatter

physics and material science the past decade. Due to its unique properties,

graphene can be used in a vast array of new and interesting applications that could fundamentally

change the material industry. This report reviews the current research and

literature in order to trace the historical development of graphene. Then, in order to

better understand the material, the unique properties of graphene are explained and potential

applications are listed. From a theoretical physics perspective, the tight-binding

approximation is used to calculate the energy bands formed by the

-electrons. Then, the

electrons close to the Fermi energy are shown to satisfy the relativistic Dirac equation of

a massless fermion and additionally, the Landau energy levels of graphene are calculated.

Finally, the band gap structure of graphene is modelled and compared to that of silicon

• 457. Liu, Ji-Yuan
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Particle Physics.
Hybrid textures of Majorana neutrino mass matrix and current experimental tests2013In: Physical Review D, ISSN 1550-7998, E-ISSN 1550-2368, Vol. 87, no 9, p. 093010-Article in journal (Refereed)

Motivated by recent measurements of a relatively large theta(13) in the Daya Bay and RENO reactor neutrino experiments, we carry out a systematic analysis of the hybrid textures of Majorana neutrino mass matrix M-v, which contain one texture zero and two equal nonzero matrix elements. We show that three neutrino masses (m(1).m(2).m(3)) and three leptonic CP-violating phases (delta, rho, sigma) can fully be determined from two neutrino mass-squared differences (delta m(2), Delta m(2)) and three flavor mixing angles (theta(12), theta(23), theta(13)). Out of sixty logically possible patterns of M-v, thirty-nine are found to be compatible with current experimental data at the 3 sigma level. We demonstrate that the texture zero of M-v is stable against one-loop quantum corrections, while the equality between two independent elements not. Phenomenological implications of M-v for the neutrinoless double-beta decay and leptonic CP violation are discussed, and a realization of the texture zero and equality by means of discrete flavor symmetries is illustrated.

• 458. Liu, Xue-Wen
KTH, School of Engineering Sciences (SCI), Theoretical Physics.
Texture zeros for dirac neutrinos and current experimental tests2013In: International Journal of Modern Physics A, ISSN 0217-751X, E-ISSN 1793-656X, Vol. 28, no 12, p. 1350040-Article in journal (Refereed)

The Daya Bay and RENO reactor neutrino experiments have revealed that the smallest neutrino mixing angle is in fact relatively large, i.e. theta(13) approximate to 9 degrees. Motivated by this exciting progress, we perform a systematic study of the neutrino mass matrix M-nu with one or two texture zeros, in the assumption that neutrinos are Dirac particles. Among 15 possible patterns with two texture zeros, only three turn out to be favored by current neutrino oscillation data at the 3 sigma level. Although all the six patterns with one texture zero are compatible with the experimental data at the 3 sigma level, the parameter space of each pattern is strictly constrained. Phenomenological implications of M-nu on the leptonic CP violation and neutrino mass spectrum are explored, and the stability of texture zeros against the radiative corrections is also discussed.

• 459.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Mathematical Physics.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Mathematical Physics.
Yang-Mills action from minimally coupled bosons on R-4 and on the four-dimensional Moyal plane2005In: Journal of Mathematical Physics, ISSN 0022-2488, E-ISSN 1089-7658, Vol. 46, no 3, p. 032301-Article in journal (Refereed)

We consider bosons on (Euclidean) R-4 that are minimally coupled to an external Yang-Mills field. We compute the logarithmically divergent part of the cutoff regularized quantum effective action of this system. We confirm the known result that this term is proportional to the Yang-Mills action. We use pseudodifferential operator methods throughout to prepare the ground for a generalization of our calculation to the noncommutative four-dimensional Moyal plane R-theta(4) We also include a detailed comparison of our cutoff regularization to heat kernel techniques. In the case of the noncommutative space, we complement the usual technique of asymptotic expansion in the momentum variable with operator theoretic arguments in order to keep separated quantum from noncommutativity effects. We show that the result from the commutative space R-4 still holds if one replaces all pointwise products by the noncommutative Moyal product.

• 460.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Particle Physics.
Radiative neutrino models and observational consequences2011Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis

We give a general introduction to physics, in particular the physics of the Standard Model (SM). Next we discuss one of the problems the SM faces, that of accommodating the neutrino masses. We discuss the concept of radiative mechanisms. Then we study three particular such models in depth.

The first is a model due to Ma which introduces three neutrino singlets and one scalar doublet on top of the SM particle content. We discuss the different neutrino masses that this model can hold. It is found that only case of normal hierarchy among the neutrinos is allowed in this model. We also discuss several observable quantities currently being searched for in experiments, and their relation to this model

The second model is due to Zee and Babu, and is commonly known as the Zee–Babu model. This model adds two electrically charged scalar particles to the SM. We find that this model can describe both the inverted hierarchy and normal hierarchy. The previously mentioned observable quantities are once again discussed, but with this model in mind.

Finally we discuss a model which accounts for the neutrino masses by assuming that there exists a fourth generation of leptons. It is found that this framework is insufficient to describe the observed neutrino masses.

• 461.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
Atomistic modeling of materials under extreme pressure2014Licentiate thesis, comprehensive summary (Other academic)

This thesis is dealing with simulation of polycrystalline materials underthe conditions of anisotropic pressure and temperature. Work has been carriedout in three steps: Research of the inuence of point defects and grain boundaries on theprocess of melting. The inuence of defects' concentration, grain sizeand lattice direction mismatch on the superheating temperature wasstudied. Investigation of the boundaries of application of the metadynamics methodto the simple atomic model with Buckingham interaction. The solidsolidphase transition, where one of the phases has temperature inducedstability was conrmed. We found the optimal size of simulation boxto study the solid-solid phase transitions using the metadynamics technique. A model of polycrystalline materials based on macroscopic approximationwas formulated. This model was applied to the model of the polycrystallinematerial using cellular automata. Using this approximationthe eect of anisotropic stress caused by anisotropic heating was studied.

• 462.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
Computer simulation of materialsunder extreme conditions2016Doctoral thesis, comprehensive summary (Other academic)

Extreme conditions allow us to reveal unusual material properties. At the same time an experimental approach is di-cult under such conditions. Capabilities of a theoretical approach based on simplied models are limited. This explainsa wide application of computer simulations at extreme conditions. My thesis is concerned with computer simulations undersuch a conditions. I address such problems as melting, solidsolid phase transitions, shockwave impact on material properties and chemical reactions under extreme conditions. We addressed these problems to facilitate simulations of phase transitions to provide some interpretation of experimental data andexplain enigmatic phenomena in interior of the Earth.

• 463.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory. KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
Impact of crystal lattice defects on crystal melting: A molecular dynamics study2013In: Computational materials science, ISSN 0927-0256, E-ISSN 1879-0801, Vol. 79, p. 95-98Article in journal (Refereed)

An ideal infinite lattice, when subjected to heating does not melt at the thermodynamic melting temperature. Instead, it remains solid metastably up to considerably higher temperatures. This effect is called superheating. We performed a molecular dynamics simulation of Xenon using Lennard-Jonesium potential with several types of defects. We observed a superheating effect on the chosen model for several pressures and found that the presence of grain inclusion or grain interface eliminates the superheating effect.

• 464.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory. KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
Metadynamics study of fcc-bcc phase transition in Xenon at high pressure and temperatureManuscript (preprint) (Other academic)
• 465.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory. KTH, Centres, Nordic Institute for Theoretical Physics NORDITA. KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory. Comenius University in Bratislava, Slovakia . KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
A metadynamics study of the fcc-bcc phase transition in Xenon at high pressure and temperature2015In: Computational materials science, ISSN 0927-0256, E-ISSN 1879-0801, Vol. 107, p. 66-71, article id 6523Article in journal (Refereed)

Abstract To theoretically find a stable solid phase is not a trivial task even at 0 K. The difficulties multiply at high temperature (T) because even more elaborate crystal structure prediction methods fail in the vicinity of the melting transition. Moreover, if the submelting phase is dynamically unstable at low T some methods cannot be applied at all. The method of metadynamics allows finding local minima of Gibbs free energy without additional simplifications. However, so far this method has been mainly used for study of pressure-induced solid-solid phase transitions and not in searching for T-induced ones. Here we study the applicability of the technique to the latter class of problems as well as to the approximate determination of the transition temperature. We apply the metadynamics method to study the solid-solid phase transition in Xe described by the Buckingham potential at high temperature and observe the fcc-bcc phase transition in a pressure-temperature range consistent with earlier results.

• 466.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
Sound velocity in shock compressed molybdenum obtained by ab initio molecular dynamics2015In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 92, no 6, article id 060101Article in journal (Refereed)

The sound velocity of Mo along the Hugoniot adiabat is calculated from first principles using density-functional theory based molecular dynamics. These data are compared to the sound velocity as measured in recent experiments. The theoretical and experimental Hugoniot and sound velocities are in very good agreement up to pressures of 210 GPa and temperatures of 3700 K on the Hugoniot. However, above that point the experiment and theory diverge. This implies that Mo undergoes a phase transition at about the same point. Considering that the melting point of Mo is likely much higher at that pressure, the related change in the sound velocity in experiment can be ascribed to a solid-solid transition.

• 467.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Biological Physics.
Dispersion Corrections at Planar Surfaces2016Licentiate thesis, comprehensive summary (Other academic)

When simulating a molecular system, a cutoff distance for interactions is often used to speed up the simulations. This is made at the cost of neglecting some interactions which will lead to inaccurate results for energy, pressure components and surface tension (for systems with surfaces). To compensate for the neglected long-range interactions, continuum corrections can be added to the surface tension, system energies and pressures. For a homogenous isotropic system this is straight-forward but for a system with a surface it is more complicated. In this work we have derived expressions for the corrections to the surface tension, system energies and pressures that are more general than previous results. When these corrections are added to multi-component systems with a surface (or single-component systems with vacuum) they compensate for the change in surface tension, system energy and pressures due to the finite cutoff. When simulating systems with no Coulomb-interactions, the structure of the system may change significantly if the cutoffs are too short. If this is the case then these corrections alone will not be enough. The solution is to add corrections to the force acting on each molecule added during the simulation, which we derive in this work. This solves the structural problem at low cutoffs and makes it possible to calculate an accurate surface tension independent of cutoff.

• 468.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Biological Physics.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Biological Physics.
Dispersion Corrections to Forces at Planar SurfacesManuscript (preprint) (Other academic)

It is known that a cutoff on the van der Waals interactions in molecular dy- namics simulations of systems containing a surface (gas/liquid for instance) may cause substantial changes in the densities of the different parts of the system. In order to make the density independent of the cutoff, we have calculated forces from continuum integrations and added them to the forces calculated in a molecular dynamics program. These corrections compensate for the lack of long range interactions and exert a pressure on the system that may be several hundred bars. We show here that inclusion of such corrections makes the density profile independent of the cutoff. This makes it possible to calculate a surface tension that is independent of the cutoff.

• 469.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Biological Physics.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Biological Physics.
Dispersion Corrections to the Surface Tension at Planar Surfaces2016In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 12, no 8, p. 4025-4032Article in journal (Refereed)

Molecular dynamics simulations are usually performed using cutoffs (r(c)) for the short-ranged dispersion interactions (r(-6)). For isotropic systems, long-range interactions are often added in a continuum approximation. This usually leads to excellent results that are independent of the cutoff length down to about 1 nm. For systems with interfaces or other anisotropic systems the situation is more complicated. We study here planar interfaces, focusing on the surface tension, which is sensitive to cutoffs. Previous analytic results giving the long-range correction to the surface tension of a liquid-vapor interface as a two- or three-dimensional integral are revisited. They are generalized by introducing a dispersion density profile which makes it possible to handle multicomponent systems. For the simple but common hyperbolic tangent profile the integral may be Taylor-expanded in the dimensionless parameter obtained by dividing the profile width with the cutoff length. This parameter is usually small, and excellent agreement with numerical calculations of the integral is obtained by keeping two terms in the expansion. The results are compared to simulations with different lengths of the cutoff for some simple systems. The surface tension in the simulations varies linearly in r(c)(-2), although a small r(c)(-4)-term may be added to improve the agreement. The slope of the r(c)(-2)-line could in several cases be predicted from the change in dispersion density at the interface. The disagreements observed in some cases when comparing to theory occur when the finite cutoff used in the simulations causes structural differences compared to long-range cutoffs or Ewald summation for the r(-6)-interactions.

• 470.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Biological Physics.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Biological Physics.
Dispersion Corrections to the Surface Tension at Planar SurfacesManuscript (preprint) (Other academic)

Molecular dynamics simulations are usually performed using cutoffs (rc) for the short-ranged dispersion interactions (r−6). For isotropic systems, long-range interactions are often added in a continuum approximation. This usually leads to excellent results that are independent of the cutoff length down to about 1 nm. For systems with interfaces or other anisotropic systems the situation is more complicated. We study here planar interfaces, focusing on the surface tension, which is sensitive to cutoffs. Previous analytic results giving the long-range correction to the surface tension of a liquid-vapor interface as a two- or three-dimensional integral are revisited. They are generalized by introducing a dispersion density profile which makes it possible to handle multi-component systems. For the simple but common hyperbolic tangent profile the integral may be Taylor-expanded in the dimensionless parameter obtained by dividing the profile width with the cutoff length. This parameter is usually small and excellent agreement with numerical calculations of the integral is obtained by keeping two terms in the expansion. The results are compared to simulations with different lengths of the cutoff for some simple systems. The surface tension in the simulations varies linearly in rc−2, although a small rc−4-term may be added to improve the agreement. The slope of the rc−2-line could in several cases be predicted from the change in dispersion density at the interface. The disagreements observed in some cases when comparing to theory, occur when the finite cutoff used in the simulations causes structural differences compared to long-range cutoffs or Ewald summation for the r−6-interactions.

• 471.
KTH, School of Engineering Sciences (SCI), Theoretical Physics. KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, Centres, SeRC - Swedish e-Science Research Centre.
KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC. KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, Centres, SeRC - Swedish e-Science Research Centre.
An Efficient and Extensible Format, Library, and API for Binary Trajectory Data from Molecular Simulations2014In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 35, no 3, p. 260-269Article in journal (Refereed)

Molecular dynamics simulations is an important application in theoretical chemistry, and with the large high-performance computing resources available today the programs also generate huge amounts of output data. In particular in life sciences, with complex biomolecules such as proteins, simulation projects regularly deal with several terabytes of data. Apart from the need for more cost-efficient storage, it is increasingly important to be able to archive data, secure the integrity against disk or file transfer errors, to provide rapid access, and facilitate exchange of data through open interfaces. There is already a whole range of different formats used, but few if any of them (including our previous ones) fulfill all these goals. To address these shortcomings, we present Trajectory Next Generation (TNG)a flexible but highly optimized and efficient file format designed with interoperability in mind. TNG both provides state-of-the-art multiframe compression as well as a container framework that will make it possible to extend it with new compression algorithms without modifications in programs using it. TNG will be the new file format in the next major release of the GROMACS package, but it has been implemented as a separate library and API with liberal licensing to enable wide adoption both in academic and commercial codes.

• 472.
KTH, School of Engineering Sciences (SCI), Theoretical Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre. Center for Biomembrane Research, Stockholm University, Sweden .
Automatic GROMACS Topology Generation and Comparisons of Force Fields for Solvation Free Energy Calculations2015In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 119, no 3, p. 810-823Article in journal (Refereed)

Free energy calculation has long been an important goal for molecular dynamics simulation and force field development, but historically it has been challenged by limited performance, accuracy, and creation of topologies for arbitrary small molecules. This has made it difficult to systematically compare different sets of parameters to improve existing force fields, but in the past few years several authors have developed increasingly automated procedures to generate parameters for force fields such as Amber, CHARMM, and OPLS. Here, we present a new framework that enables fully automated generation of GROMACS topologies for any of these force fields and an automated setup for parallel adaptive optimization of high-throughput free energy calculation by adjusting lambda point placement on the fly. As a small example of this automated pipeline, we have calculated solvation free energies of 50 different small molecules using the GAFF, OPLS-AA, and CGenFF force fields and four different water models, and by including the often neglected polarization costs, we show that the common charge models are somewhat underpolarized.

• 473. Lundh, E.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Statistical Physics.
Ratchet effect for cold atoms in an optical lattice2005In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 94, no 11Article in journal (Refereed)

The possibility of realizing a directed current for a quantum particle in a flashing asymmetric potential is investigated. It is found that quantum resonances, where the value of the effective Planck constant is equal to an integer or half-integer multiple of pi, give rise to a directed current. The effect should be readily observable in experiments.

• 474. Lundin, U
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
Theory of strongly correlated electron systems: II. Including correlation effects into electronic structure calculations2005In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 102, no 6, p. 1046-1055Article in journal (Refereed)

We have previously shown that a division of the f-shell into two subsystems gives a better understanding of the cohesive properties as well the general behavior of lanthanide systems. In this article, we present numerical computations, using the suggested method. We show that the picture is consistent with most experimental data, e.g., the equilibrium volume and electronic structure in general. Compared with standard energy band calculations and calculations based on the self-interaction correction and LIDA + U, the f-(non-f)-mixing interaction is decreased by spectral weights of the many-body states of the f-ion.

• 475.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
Alternative phenomenological coupling parameter for finite-size analysis of numerical data at criticality2010In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 82, no 2, p. 024414-Article in journal (Refereed)

We introduce a parameter W(beta,L) =(pi (2)/< m(2)>- 2/(pi-2) which like the kurtosis (Binder cumulant) is a phenomenological coupling characteristic of the shape of the distribution p(m) of the order parameter m. To demonstrate the use of the parameter we analyze extensive numerical data obtained from density-of-states measurements on the canonical simple-cubic spin-1/2 Ising ferromagnet, for sizes L=4 to L=256. Using the W parameter accurate estimates are obtained for the critical inverse temperature beta(c)=0.2216541(2), and for the thermal exponent nu=0.6308(4). In this system at least, corrections to finite-size scaling are significantly weaker for the W parameter than for the Binder cumulant.

• 476.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
Critical scaling to infinite temperature2011In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 83, no 18, p. 184408-Article in journal (Refereed)

Three-dimensional Ising model ferromagnets on different lattices with nearest-neighbor interactions, and on simple-cubic lattices with equivalent interactions out to further neighbors, are studied numerically. The susceptibility data for all these systems are analyzed using the critical renormalization-group theory formalism over the entire temperature range above T-c with an appropriate choice of scaling variable and scaling expressions. Representative experimental data on a metallic ferromagnet (Ni) and an elementary fluid (Xe) are interpreted in the same manner so as to estimate effective coordination numbers.

• 477.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
Fortuin-Kasteleyn and damage-spreading transitions in random-bond Ising lattices2012In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 86, no 4, p. 041121-Article in journal (Refereed)

The Fortuin-Kasteleyn and heat-bath damage-spreading temperatures T FK(p) and T DS(p) are studied on random-bond Ising models of dimensions 2-5 and as functions of the ferromagnetic interaction probability p; the conjecture that T DS(p)∼T FK(p) is tested. It follows from a statement by Nishimori that in any such system, exact coordinates can be given for the intersection point between the Fortuin-Kasteleyn T FK(p) transition line and the Nishimori line [p NL,FK, T NL,FK]. There are no finite-size corrections for this intersection point. In dimension 3, at the intersection concentration [p NL,FK], the damage spreading T DS(p) is found to be equal to T FK(p) to within 0.1%. For the other dimensions, however, T DS(p) is observed to be systematically a few percent lower than T FK(p).

• 478.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
Ising ferromagnet in dimension five: Link and spin overlaps2013In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 87, no 2Article in journal (Refereed)

In the simple [hyper]cubic five-dimension, near-neighbor-interaction Ising ferromagnet, extensive simulation measurements are made of the link overlap and the spin overlap distributions. These "two replica" measurements are standard in the spin glass context but are not usually recorded in ferromagnet simulations. The moments and moment ratios of these distributions (the variance, the kurtosis, and the skewness) show clear critical behaviors at the known ordering temperature of the ferromagnet. Analogous overlap effects can be expected quite generally in Ising ferromagnets in any dimension. The link overlap results in particular, with peaks at criticality in the kurtosis and the skewness, also have implications for spin glasses.

• 479.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
Broken-cycle-free subgraphs and the log-concavity conjecture for chromatic polynomials2006In: Experimental Mathematics, ISSN 1058-6458, E-ISSN 1944-950X, Vol. 15, no 3, p. 343-353Article in journal (Refereed)

This paper concerns the coefficients of the chromatic polynomial of a graph. We first report on a computational verification of the strict log-concavity conjecture for chromatic polynomials for all graphs on at most 11 vertices, as well as for certain cubic graphs. In the second part of the paper we give a number of conjectures and theorems regarding the behavior of the coefficients of the chromatic polynomial, in part motivated by our computations. Here our focus is on epsilon(G), the average size of a broken-cycle-free subgraph of the graph G, whose behavior under edge deletion and contraction is studied.

• 480.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
Critical behavior of the Ising model on the four-dimensional cubic lattice2009Article in journal (Refereed)

In this paper we investigate the nature of the singularity of the Ising model of the four-dimensional cubic lattice. It is rigorously known that the specific heat has critical exponent alpha = 0 but a nonrigorous field-theory argument predicts an unbounded specific heat with a logarithmic singularity at T-c. We find that within the given accuracy the canonical ensemble data are consistent both with a logarithmic singularity and a bounded specific heat but that the microcanonical ensemble lends stronger support to a bounded specific heat. Our conclusion is that either much larger system sizes are needed for Monte Carlo studies of this model in four dimensions or the field-theory prediction of a logarithmic singularity is wrong.

• 481.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory. KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova.
EXACT AND APPROXIMATE COMPRESSION OF TRANSFER MATRICES FOR GRAPH HOMOMORPHISMS2008In: LMS Journal of Computation and Mathematics, ISSN 1461-1570, E-ISSN 1461-1570, Vol. 11, p. 1-14Article in journal (Refereed)

The aim of this paper is to extend the previous work on transfer matrix compression in the case of graph homomorphisms. For H-homomorphisms of lattice-like graphs we demonstrate how the automorphisms of H, as well as those of the underlying lattice, can be used to reduce the size of the relevant transfer matrices. As applications of this method we give currently best known bounds for the number of 4- and 5-colourings of the square grid, and the number of 3- and 4-colourings of the three-dimensional cubic lattice. Finally, we also discuss approximate compression of transfer matrices.

• 482.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
Reconstruction of the finite size canonical ensemble from incomplete micro-canonical data2009In: Central European Journal of Physics, ISSN 1895-1082, E-ISSN 1644-3608, Vol. 7, no 3, p. 490-502Article in journal (Refereed)

In this paper we discuss how partial knowledge of the density of states for a model can be used to give good approximations of the energy distributions in a given temperature range. From these distributions one can then obtain the statistical moments corresponding to e. g. the internal energy and the specific heat. These questions have gained interest apropos of several recent methods for estimating the density of states of spin models. As a worked example we finally apply these methods to the 3-state Potts model for cubic lattices of linear order up to 128. We give estimates of e. g. latent heat and critical temperature, as well as the micro-canonical properties of interest.

• 483.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
Non-vanishing boundary effects and quasi-first-order phase transitions in high dimensional Ising models2011In: Nuclear Physics B, ISSN 0550-3213, E-ISSN 1873-1562, Vol. 845, no 1, p. 120-139Article in journal (Refereed)

In order to gain a better understanding of the Ising model in higher dimensions we have made a comparative study of how the boundary, open versus cyclic, of a d-dimensional simple lattice, for d = 1,...,5, affects the behaviour of the specific heat C and its microcanonical relative, the entropy derivative -partial derivative S-2/partial derivative U-2. In dimensions 4 and 5 the boundary has a strong effect on the critical region of the model and for cyclic boundaries in dimension 5 we find that the model displays a quasi-first-order phase transition with a bimodal energy distribution. The latent heat decreases with increasing systems size but for all system sizes used in earlier papers the effect is clearly visible once a wide enough range of values for K is considered. Relations to recent rigorous results for high dimensional percolation and previous debates on simulation of Ising models and gauge fields are discussed.

• 484.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
The Ising model for the bcc, fcc and diamond lattices: A comparison2009In: Philosophical Magazine, ISSN 1478-6435, E-ISSN 1478-6443, Vol. 89, no 22-24, p. 2009-2042Article in journal (Refereed)

A large-scale Monte Carlo simulation study of the Ising model for the simple cubic lattice was recently performed by us. In this paper, we complement that study with the bcc, fcc and diamond lattices. Both the canonical and microcanonical ensembles are employed. We give estimates of the critical temperature and also other quantities in the critical region. An analysis of the critical behaviour points to distinct high-and low-temperature exponents, especially for the specific heat, as was also obtained for the simple cubic lattice, although the agreement is good between the different lattices. The source of this discrepancy is briefly discussed.

• 485.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
On the p, q-binomial distribution and the Ising model2010In: Philosophical Magazine, ISSN 1478-6435, E-ISSN 1478-6443, Vol. 90, no 24, p. 3313-3353Article in journal (Refereed)

We employ p, q-binomial coefficients, a generalisation of the binomial coefficients, to describe the magnetisation distributions of the Ising model. For the complete graph this distribution corresponds exactly to the limit case p = q. We apply our investigation to the simple d-dimensional lattices for d = 1, 2, 3, 4, 5 and fit p, q-binomial distributions to our data, some of which are exact but most are sampled. For d = 1 and d = 5, the magnetisation distributions are remarkably well-fitted by p,q-binomial distributions. For d = 4 we are only slightly less successful, while for d = 2, 3 we see some deviations (with exceptions!) between the p, q-binomial and the Ising distribution. However, at certain temperatures near Tc the statistical moments of the fitted distribution agree with the moments of the sampled data within the precision of sampling. We begin the paper by giving results of the behaviour of the p, q-distribution and its moment growth exponents given a certain parameterisation of p, q. Since the moment exponents are known for the Ising model (or at least approximately for d = 3) we can predict how p, q should behave and compare this to our measured p, q. The results speak in favour of the p, q-binomial distribution's correctness regarding its general behaviour in comparison to the Ising model. The full extent to which they correctly model the Ising distribution, however, is not settled.

• 486.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
The p,q-binomial distribution applied to the 5d Ising model2013In: Philosophical Magazine, ISSN 1478-6435, E-ISSN 1478-6443, Vol. 93, no 14, p. 1755-1770Article in journal (Refereed)

The leading order form of the magnetization distribution is well-known for the 5d Ising model close to . Its corrections-to-scaling are not known though. Since we have earlier established that this distribution is extremely well-fitted by a -binomial distribution, we report considerably longer series expansions for its moments in terms of three parameters, providing new details on the scaling behaviour of the Ising distribution and its moments near . As applications, we give for example the scaling formulas for the ratios , and the full distribution at .

• 487.
Univ Calif San Diego, Ludwig Inst Canc Res, San Diego Branch, 9500 Gilman Dr, La Jolla, CA 92093 USA. i, Jie; Cavenee, Webster K.; Kolodner, Richard D.; Chen, Clark C.; Furnari, Frank B..
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
Inhibition of Nuclear PTEN Tyrosine Phosphorylation Enhances Glioma diation Sensitivity through Attenuated DNA Repair2019In: Cancer Cell, ISSN 1535-6108, E-ISSN 1878-3686, Vol. 35, no 3, p. 504-518.e7Article in journal (Refereed)

Ionizing radiation (IR) and chemotherapy are standard-of-care treatments for glioblastoma (GBM) patients and both result in DNA damage, however, the clinical efficacy is limited due to therapeutic resistance. We identified a mechanism of such resistance mediated by phosphorylation of PTEN on tyrosine 240 (pY240-PTEN) by FGFR2. pY240-PTEN is rapidly elevated and bound to chromatin through interaction with Ki-67 in response to IR treatment and facilitates the recruitment of RAD51 to promote DNA repair. Blocking Y240 phosphorylation confers radiation sensitivity to tumors and extends survival in GBM preclinical models. Y240F-Pten knockin mice showed radiation sensitivity. These results suggest that FGFR-mediated pY240-PTEN is a key mechanism of radiation resistance and is an actionable target for improving radiotherapy efficacy.

• 488.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Particle Physics.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Particle Physics. KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Particle Physics.
Non-unitary neutrino mixing and CP violation in the minimal inverse seesaw model2009In: Physics Letters B, ISSN 0370-2693, E-ISSN 1873-2445, Vol. 679, no 3, p. 242-248Article in journal (Refereed)

We propose a simplified version of the inverse seesaw model, in which only two pairs of the gauge-singlet neutrinos are introduced, to interpret the observed neutrino mass hierarchy and lepton flavor mixing at or below the TeV scale. This "minimal" inverse seesaw scenario (MISS) is technically natural and experimentally testable. In particular, we show that the effective parameters describing the non-unitary neutrino mixing matrix are strongly correlated in the MISS, and thus, their upper bounds can be constrained by current experimental data in a more restrictive way. The Jarlskog invariants of non-unitary CP violation are calculated, and the discovery potential of such new CP-violating effects in the near detector of a neutrino factory is discussed.

• 489.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Particle Physics.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Particle Physics. KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Particle Physics.
Nonstandard neutrino interactions from a triplet seesaw model2009In: Physical Review D, ISSN 1550-7998, Vol. 79, no 1, p. 011301(R)-Article in journal (Refereed)

We investigate nonstandard neutrino interactions (NSIs) in the triplet seesaw model featuring nontrivial correlations between NSI parameters and neutrino masses and mixing parameters. We show that sizable NSIs can be generated as a consequence of a nearly degenerate neutrino mass spectrum. Thus, these NSIs could lead to quite significant signals of lepton flavor violating decays such as mu(-) --> e(-) nu(e)(nu) over bar (mu) and mu(+) --> e(+)(nu) over bar (e)nu(mu) at a future neutrino factory, effects adding to the uncertainty in determination of the Earth matter density profile, as well as characteristic patterns of the doubly charged Higgs decays observable at the Large Hadron Collider.

• 490.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Particle Physics.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Particle Physics. KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Particle Physics.
Nonunitarity effects in a realistic low-scale seesaw model2009In: Physical Review D, ISSN 1550-7998, Vol. 79, no 7, p. 073009-Article in journal (Refereed)

We analyze the structure of the nonunitary leptonic mixing matrix in the inverse seesaw model with heavy singlets accessible at the LHC. In this model, unlike in the usual TeV seesaw scenarios, the low-scale right-handed neutrinos do not suffer from naturalness issues. Underlying correlations among various parameters governing the nonunitarity effects are established, which leads to a considerable improvement of the generic nonunitarity bounds. In view of this, we study the discovery potential of the nonunitarity effects at future experiments, focusing on the sensitivity limits at a neutrino factory.

• 491.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Particle Physics.
Intermediate scales in non-supersymmetric SO(10) grand unified theories2009In: Proceedings of Science: European Physical Society Europhysics Conference on High Energy Physics, Scuola Internazionale Superiore di Studi Avanzati (S I S S A) , 2009, p. PoS(EPS-HEP 2009)288-Conference paper (Refereed)

It is often argued that in the class of non-supersymmetric SO(10) grand unified theories there is barely any room for reconciling the lower bound on the position of the GUT scale emerging from the proton decay searches and the lower limit on the absolute neutrino mass scale derived from the neutrino oscillation experiments with the gauge coupling unification constraints. The recent two-loop reassessment of the gauge running provides the first complete picture of the situation, complementing the existing studies in several aspects. The improved analysis reveals a new room in the parametric space that could support a class of non-supersymmetric SO(10) models potentially compatible with all current physical data, including constraints on the relevant Yukawa sector emerging from the quark and lepton masses and mixings. This, in turn, brings back the question of viability of some of the simplest non-supersymmetric GUT scenarios.

• 492.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Particle Physics.
Non-unitarity effects in the minimal inverse seesaw model2009In: Proceedings of Science: European Physical Society Europhysics Conference on High Energy Physics, Scuola Internazionale Superiore di Studi Avanzati (S I S S A) , 2009, p. PoS(EPS-HEP 2009)288-Conference paper (Refereed)

A minimal version of the inverse seesaw model featuring only two pairs of TeV-scale singlet neutrinos is discussed from the perspective of non-standard neutrino interactions. A particular attention is paid to the non-standard patterns of flavour and CP violation emerging due to the possibly enhanced non-decoupling effects of the heavy sector and the associated non-unitarity of the effective lepton mixing matrix.

• 493.
KTH, School of Engineering Sciences (SCI), Theoretical Physics.
Measuring CP violation in neutrino oscillations originating at ESS2015Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis

In this report, I review previous efforts to probe CP vilations through the measurement of neutrino oscillations, and discuss simulated results in an effort to gauge the potential to glean new insights from a proposed neutrino experiment at the European Spallation Source in Lund, Sweden. We find that the precise measurement of $\theta$13 opens up new possibilities for neutrino oscillation experiments, making it likely that we will be able to rule out CP-conserving values for the oscillation parameter $\delta$CP within a near future.

• 494.
KTH, School of Engineering Sciences (SCI), Theoretical Physics. KTH, Centres, Nordic Institute for Theoretical Physics NORDITA.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Statistical Physics. KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
Angular momentum blockade in nanoscale high-T-c superconducting grains2013In: Superconductors Science and Technology, ISSN 0953-2048, E-ISSN 1361-6668, Vol. 26, no 12Article in journal (Refereed)

We discuss the angular momentum blockade in small d-wave superconducting grains in an external field. We find that abrupt changes in the angular momentum state of the condensate, angular momentum blockade, occur as a result of changes in the angular momentum of the condensate in an external magnetic field. The effect represents a direct analogy with the Coulomb blockade. We use the Ginzburg-Landau formalism to illustrate how a magnetic field induces a deviation from the d-wave symmetry which is described by a (d(x2-y2)+id(xy))-order parameter. We derive the behavior of the volume magnetic susceptibility as a function of the magnetic field, and corresponding magnetization jumps at critical values of the field that should be experimentally observable in superconducting grains.

• 495.
KTH, School of Engineering Sciences (SCI), Theoretical Physics. KTH, Centres, Nordic Institute for Theoretical Physics NORDITA.
KTH, Centres, Nordic Institute for Theoretical Physics NORDITA. Institute for Materials Science, Los Alamos, NM, United States.
Josephson coupling between superconducting islands on single- and bi-layer graphene2016In: Superconductors Science and Technology, ISSN 0953-2048, E-ISSN 1361-6668, Vol. 29, no 5, article id 054004Article in journal (Refereed)

We study the Josephson coupling of superconducting (SC) islands through the surface of single-layer graphene (SLG) and bilayer graphene (BLG) in the long-junction regime, as a function of the distance between the grains, temperature, chemical potential and external (transverse) gate-voltage. For SLG, we provide a comparison with existing literature. The proximity effect is analyzed through a Matsubara Green's function approach. This represents the first step in a discussion of the conditions for the onset of a granular superconductivity within the film, made possible by Josephson currents flowing between superconductors. To ensure phase coherence over the 2D sample, a random spatial distribution can be assumed for the SC islands on the SLG sheet (or intercalating the BLG sheets). The tunable gate-voltage-induced band gap of BLG affects the asymptotic decay of the Josephson coupling-distance characteristic for each pair of SC islands in the sample, which results in a qualitatively strong field dependence of the relation between Berezinskii-Kosterlitz-Thouless transition critical temperature and gate voltage.

• 496.
KTH, School of Engineering Sciences (SCI), Theoretical Physics. KTH, Centres, Nordic Institute for Theoretical Physics NORDITA.
Energy-pressure relation for low-dimensional gases2014In: Nuclear Physics B, ISSN 0550-3213, E-ISSN 1873-1562, Vol. 887, p. 216-245Article in journal (Refereed)

A particularly simple relation of proportionality between internal energy and pressure holds for scale-invariant thermodynamic systems (with Hamiltonians homogeneous functions of the coordinates), including classical and quantum - Bose and Fermi - ideal gases. One can quantify the deviation from such a relation by introducing the internal energy shift as the difference between the internal energy of the system and the corresponding value for scale-invariant (including ideal) gases. After discussing some general thermodynamic properties associated with the scale-invariance, we provide criteria for which the internal energy shift density of an imperfect (classical or quantum) gas is a bounded function of temperature. We then study the internal energy shift and deviations from the energy pressure proportionality in low-dimensional models of gases interpolating between the ideal Bose and the ideal Fermi gases, focusing on the Lieb-Liniger model in id and on the anyonic gas in 2d. In Id the internal energy shift is determined from the thermodynamic Bethe ansatz integral equations and an explicit relation for it is given at high temperature. Our results show that the internal energy shift is positive, it vanishes in the two limits of zero and infinite coupling (respectively the ideal Bose and the Tonks-Girardeau gas) and it has a maximum at a finite, temperature-depending, value of the coupling. Remarkably, at fixed coupling the energy shift density saturates to a finite value for infinite temperature. In 2d we consider systems of Abelian anyons and non-Abelian Chern-Simons particles: as it can be seen also directly from a study of the virial coefficients, in the usually considered hard-core limit the internal energy shift vanishes and the energy is just proportional to the pressure, with the proportionality constant being simply the area of the system. Soft-core boundary conditions at coincident points for the two-body wavefunction introduce a length scale, and induce a non-vanishing internal energy shift: the soft-core thermodynamics is considered in the dilute regime for both the families of anyonic models and in that limit we can show that the energy pressure ratio does not match the area of the system, opposed to what happens for hard-core (and in particular 2d Bose and Fermi) ideal anyonic gases.

• 497.
KTH, School of Engineering Sciences (SCI), Theoretical Physics. NORDITA.
Statistical interparticle potential of an ideal gas of non-Abelian anyons2013In: Journal of Physics A: Mathematical and Theoretical, ISSN 1751-8113, E-ISSN 1751-8121, Vol. 46, no 27, p. 275001-Article in journal (Refereed)

We determine and study the statistical interparticle potential of an ideal system of non-Abelian Chern-Simons (NACS) particles, comparing our results with the corresponding results of an ideal gas of Abelian anyons. In the Abelian case, the statistical potential depends on the statistical parameter alpha; it has 'quasi-bosonic' behavior for 0 < alpha < 1/2 (non-monotonic with a minimum) and 'quasi-fermionic' behavior for 1/2 <= alpha < 1 (monotonically decreasing without a minimum). In the non-Abelian case, the behavior of the statistical potential depends on the Chern-Simons coupling and the isospin quantum number: as a function of these two parameters, a phase diagram with quasi-bosonic, quasi-fermionic and bosonic-like regions is obtained and investigated. Finally, using the obtained expression for the statistical potential, we compute the second virial coefficient of the NACS gas, which correctly reproduces the results available in the literature.

• 498.
KTH, School of Engineering Sciences (SCI), Theoretical Physics.
KTH, School of Engineering Sciences (SCI), Theoretical Physics.
Distribution of Neutrino Mixing Parameters FromReal and Complex Random Neutrino Mass Matrices2013Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis

The theory of neutrino oscillations is covered. Also, the theory of Dirac, Majorana, and

Dirac-Majorana neutrinos is presented. From this theory, and the model presented in [7],

a program is constructed which creates a suitable number of neutrino mass matrices

M

using pseudo-random numbers generated in MATLAB. These matrices are diagonalised,

and from the general notion of the Pontecorvo-Maki-Nakagawa-Sakata matrix

UPMNS,

statistical distributions of six mixing parameters are presented, namely;

12; 13; 23, the

CP-violating Dirac phase delta (

), and two Majorana CP-violating phases alpha one

and two (

1; 2). Furthermore, from the diagonal matrix resulting from the diagonalisation

of

M, masses mi, of the mass states i; i = 1; 2; 3, are taken. All data is presented

in histograms using 90 bins. This numerical approach to determining how the neutrino

mixing parameters are distributed will be discussed in section 2.10, and possible conclusions

regarding the statistical distributions of the mixing angles

12; 13, and 23, and the

masses

mi will be presented in chapter 3.

• 499. Mattesini, Maurizio
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory. KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics.
Hemispherical anisotropic patterns of the Earth's inner core2010In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 107, no 21, p. 9507-9512Article in journal (Refereed)

It has been shown that the Earth's inner core has an axisymmetric anisotropic structure with seismic waves traveling similar to 3% faster along polar paths than along equatorial directions. Hemispherical anisotropic patterns of the solid Earth's core are rather complex, and the commonly used hexagonal-close-packed iron phase might be insufficient to account for seismological observations. We show that the data we collected are in good agreement with the presence of two anisotropically specular east and west core hemispheres. The detected travel-time anomalies can only be disclosed by a lattice-preferred orientation of a body-centered-cubic iron aggregate, having a fraction of their [111] crystal axes parallel to the Earth's rotation axis. This is compelling evidence for the presence of a body-centered-cubic Fe phase at the top of the Earth's inner core.

• 500.
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Statistical Physics.
Phase transitions in novel superfluids and systems with correlated disorder2015Doctoral thesis, comprehensive summary (Other academic)

Condensed matter systems undergoing phase transitions rarely allow exact solutions. The presence of disorder renders the situation  even worse but collective Monte Carlo methods and parallel algorithms allow numerical descriptions. This thesis considers classical phase transitions in disordered spin systems in general and in effective models of superfluids with disorder and novel interactions in particular. Quantum phase transitions are considered via a quantum to classical mapping. Central questions are if the presence of defects changes universal properties and what qualitative implications follow for experiments. Common to the cases considered is that the disorder maps out correlated structures. All results are obtained using large-scale Monte Carlo simulations of effective models capturing the relevant degrees of freedom at the transition.

Considering a model system for superflow aided by a defect network, we find that the onset properties are significantly altered compared to the $\lambda$-transition in $^{4}$He. This has qualitative implications on expected experimental signatures in a defect supersolid scenario.

For the Bose glass to superfluid quantum phase transition in 2D we determine the quantum correlation time by an anisotropic finite size scaling approach. Without a priori assumptions on critical parameters, we find the critical exponent $z=1.8 \pm 0.05$ contradicting the long standing result $z=d$.

Using a 3D effective model for multi-band type-1.5 superconductors we find that these systems possibly feature a strong first order vortex-driven phase transition. Despite its short-range nature details of the interaction are shown to play an important role.

Phase transitions in disordered spin models exposed to correlated defect structures obtained via rapid quenches of critical loop and spin models are investigated. On long length scales the correlations are shown to decay algebraically. The decay exponents are expressed through known critical exponents of the disorder generating models. For cases where the disorder correlations imply the existence of a new long-range-disorder fixed point we determine the critical exponents of the disordered systems via finite size scaling methods of Monte Carlo data and find good agreement with theoretical expectations.

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