On the forbidden gap of finite graphene nanoribbons

The electronic structure of isolated finite graphene nanoribbons is investigated by solving, at the Hartree-Fock (HF) level, the Pariser, Parr and Pople (PPP) many-body Hamiltonian. The study is mainly focused on 7-AGNR and 13-AGNR (Armchair Graphene Nano-Ribbons), whose electronic structures have been recently experimentally investigated. Only paramagnetic solutions are considered. The characteristics of the forbidden gap are studied as a function of the ribbon length. For a 7-AGNR, the gap monotonically decreases from a maximum value of ~6.5 eV for short nanoribbons to a very small value of ~0.12 eV for the longer calculated systems. Gap edges are defined by molecular orbitals that are spatially localized near the nanoribbon extremes, that is, near both zig-zag edges. On the other hand, two delocalized orbitals define a much larger gap of about 5 eV. Conductance measurements report a somewhat smaller gap of ~3 eV. The small real gap lies in the middle of the one given by extended states and has been observed by STM and reproduced by DFT calculations. On the other hand, the length dependence of the gap is not monotonous for a 13-AGNR. It decreases initially but sharply increases for lengths beyond 30 Å remaining almost constant thereafter at a value of ~2.1 eV. Two additional states localized at the nanoribbon extremes show up at energies 0.31 eV below the HOMO (Highest Occupied Molecular Orbital) and above the LUMO (Lowest Unoccupied Molecular Orbital). These numbers compare favorably with those recently obtained by means of STS for a 13-AGNR sustained by a gold surface, namely 1.4 eV for the energy gap and 0.4 eV for the position of localized band edges. We show that the important differences between 7- and 13-AGNR should be ascribed to the charge rearrangement near the zig-zag edges obtained in our calculations for ribbons longer than 30 Å, a feature that does not show up for a 7-AGNR no matter its length.

A multi-scaled approach for simulating chemical reaction systems

In this paper we give an overview of some very recent work, as well as presenting a new approach, on the stochastic simulation of multi-scaled systems involving chemical reactions. In many biological systems (such as genetic regulation and cellular dynamics) there is a mix between small numbers of key regulatory proteins, and medium and large numbers of molecules. In addition, it is important to be able to follow the trajectories of individual molecules by taking proper account of the randomness inherent in such a system. We describe different types of simulation techniques (including the stochastic simulation algorithm, Poisson Runge–Kutta methods and the balanced Euler method) for treating simulations in the three different reaction regimes: slow, medium and fast. We then review some recent techniques on the treatment of coupled slow and fast reactions for stochastic chemical kinetics and present a new approach which couples the three regimes mentioned above. We then apply this approach to a biologically inspired problem involving the expression and activity of LacZ and LacY proteins in E. coli, and conclude with a discussion on the significance of this work.

Phase-space analysis of bosonic spontaneous emission

We present phase-space techniques for the modelling of spontaneous emission in two-level bosonic atoms. The positive-P representation is shown to give a full and complete description within the limits of our model. The Wigner representation, even when truncated at second order, is shown to need a doubling of the phase-space to allow for a positive-definite diffusion matrix in the appropriate Fokker-Planck equation and still fails to agree with the full quantum results of the positive-P representation. We show that quantum statistics and correlations between the ground and excited states affect the dynamics of the emission process, so that it is in general non-exponential. (c) 2005 Elsevier B.V. All rights reserved.

Towards a theoretical framework for human performance modelling within manufacturing systems design

The performance of direct workers has a significant impact on the competitiveness of many manufacturing systems. Unfortunately, system designers are ill equipped to assess this impact during the design process. An opportunity exists to assist designers by expanding the capabilities of popular simulation modelling tools, and using them as a vehicle to better consider human factors during the process of system design manufacture. To support this requirement, this paper reports on an extensive review of literature that develops a theoretical framework, which summarizes the principal factors and relationships that such a modelling tool should incorporate.

Transition of legacy systems to semantically enabled applications:TAO method and tools

Despite expectations being high, the industrial take-up of Semantic Web technologies in developing services and applications has been slower than expected. One of the main reasons is that many legacy systems have been developed without considering the potential of theWeb in integrating services and sharing resources.Without a systematic methodology and proper tool support, the migration from legacy systems to SemanticWeb Service-based systems can be a tedious and expensive process, which carries a significant risk of failure. There is an urgent need to provide strategies, allowing the migration of legacy systems to Semantic Web Services platforms, and also tools to support such strategies. In this paper we propose a methodology and its tool support for transitioning these applications to Semantic Web Services, which allow users to migrate their applications to Semantic Web Services platforms automatically or semi-automatically. The transition of the GATE system is used as a case study. © 2009 - IOS Press and the authors. All rights reserved.

Symbolic Dynamics in the Free-Fall Equal-Mass Three-Body Problem

The paper has been presented at the 12th International Conference on Applications of Computer Algebra, Varna, Bulgaria, June, 2006

Understanding Ten-Eleven Translocation-2 in Hematological and Nervous Systems

I proposed the study of two distinct aspects of Ten-Eleven Translocation 2 (TET2) protein for understanding specific functions in different body systems. In Part I, I characterized the molecular mechanisms of Tet2 in the hematological system. As the second member of Ten-Eleven Translocation protein family, TET2 is frequently mutated in leukemic patients. Previous studies have shown that the TET2 mutations frequently occur in 20% myelodysplastic syndrome/myeloproliferative neoplasm (MDS/MPN), 10% T-cell lymphoma leukemia and 2% B-cell lymphoma leukemia. Genetic mouse models also display distinct phenotypes of various types of hematological malignancies. I performed 5-hydroxymethylcytosine (5hmC) chromatin immunoprecipitation sequencing (ChIP-Seq) and RNA sequencing (RNA-Seq) of hematopoietic stem/progenitor cells to determine whether the deletion of Tet2 can affect the abundance of 5hmC at myeloid, T-cell and B-cell specific gene transcription start sites, which ultimately result in various hematological malignancies. Subsequent Exome sequencing (Exome-Seq) showed that disease-specific genes are mutated in different types of tumors, which suggests that TET2 may protect the genome from being mutated. The direct interaction between TET2 and Mutator S Homolog 6 (MSH6) protein suggests TET2 is involved in DNA mismatch repair. Finally, in vivo mismatch repair studies show that the loss of Tet2 causes a mutator phenotype. Taken together, my data indicate that TET2 binds to MSH6 to protect genome integrity. In Part II, I intended to better understand the role of Tet2 in the nervous system. 5-hydroxymethylcytosine regulates epigenetic modification during neurodevelopment and aging. Thus, Tet2 may play a critical role in regulating adult neurogenesis. To examine the physiological significance of Tet2 in the nervous system, I first showed that the deletion of Tet2 reduces the 5hmC levels in neural stem cells. Mice lacking Tet2 show abnormal hippocampal neurogenesis along with 5hmC alternations at different gene promoters and corresponding gene expression downregulation. Through the luciferase reporter assay, two neural factors Neurogenic differentiation 1 (NeuroD1) and Glial fibrillary acidic protein (Gfap) were down-regulated in Tet2 knockout cells. My results suggest that Tet2 regulates neural stem/progenitor cell proliferation and differentiation in adult brain.

Optical and Spin Properties of Defect-Bound Excitons in Semiconductors

Thesis (Ph.D.)--University of Washington, 2016-08

Resonant five-body recombination in an ultracold gas of bosonic atoms

We combine theory and experiment to investigate five-body recombination in an ultracold gas of atomic cesium at negative scattering length. A refined theoretical model, in combination with extensive laboratory tunability of the interatomic interactions, enables the five-body resonant recombination rate to be calculated and measured. The position of the new observed recombination feature agrees with a recent theoretical prediction and supports the prediction of a family of universal cluster states at negative a that are tied to an Efimov trimer.

Degenerate Gases of Strontium for Studies of Quantum Magnetism

We describe the construction and characterization of a new apparatus that can produce degenerate quantum gases of strontium. The realization of degenerate gases is an important first step toward future studies of quantum magnetism. Three of the four stable isotopes of strontium have been cooled into the degenerate regime. The experiment can make nearly pure Bose-Einstein condensates containing approximately 1x10^4 atoms, for strontium-86, and approximately 4x10^5 atoms, for strontium-84. We have also created degenerate Fermi gases of strontium-87 with a reduced temperature, T/T_F of approximately 0.2. The apparatus will be able to produce Bose-Einstein condensates of strontium-88 with straightforward modifications. We also report the first experimental and theoretical results from the strontium project. We have developed a technique to accelerate the continuous loading of strontium atoms into a magnetic trap. By applying a laser addressing the 3P1 to 3S1 transition in our magneto-optical trap, the rate at which atoms populate the magnetically-trapped 3P2 state can be increased by up to 65%. Quantum degenerate gases of atoms in the metastable 3P0 and 3P2 states are a promising platform for quantum simulation of systems with long-range interactions. We have performed an initial numerical study of a method to transfer the ground state degenerate gases that we can currently produce into one of the metastable states via a three-photon transition. Numerical simulations of the Optical Bloch equations governing the three-photon transition indicate that >90% of a ground state degenerate gas can be transferred into a metastable state.

Stochastic and infinite dimensional analysis

This volume presents a collection of papers covering applications from a wide range of systems with infinitely many degrees of freedom studied using techniques from stochastic and infinite dimensional analysis, e.g. Feynman path integrals, the statistical mechanics of polymer chains, complex networks, and quantum field theory. Systems of infinitely many degrees of freedom create their particular mathematical challenges which have been addressed by different mathematical theories, namely in the theories of stochastic processes, Malliavin calculus, and especially white noise analysis. These proceedings are inspired by a conference held on the occasion of Prof. Ludwig Streit’s 75th birthday and celebrate his pioneering and ongoing work in these fields.

Understanding ten-eleven translocation-2 in hematological and nervous systems

I proposed the study of two distinct aspects of Ten-Eleven Translocation 2 (TET2) protein for understanding specific functions in different body systems. ^ In Part I, I characterized the molecular mechanisms of Tet2 in the hematological system. As the second member of Ten-Eleven Translocation protein family, TET2 is frequently mutated in leukemic patients. Previous studies have shown that the TET2 mutations frequently occur in 20% myelodysplastic syndrome/myeloproliferative neoplasm (MDS/MPN), 10% T-cell lymphoma leukemia and 2% B-cell lymphoma leukemia. Genetic mouse models also display distinct phenotypes of various types of hematological malignancies. I performed 5-hydroxymethylcytosine (5hmC) chromatin immunoprecipitation sequencing (ChIP-Seq) and RNA sequencing (RNA-Seq) of hematopoietic stem/progenitor cells to determine whether the deletion of Tet2 can affect the abundance of 5hmC at myeloid, T-cell and B-cell specific gene transcription start sites, which ultimately result in various hematological malignancies. Subsequent Exome sequencing (Exome-Seq) showed that disease-specific genes are mutated in different types of tumors, which suggests that TET2 may protect the genome from being mutated. The direct interaction between TET2 and Mutator S Homolog 6 (MSH6) protein suggests TET2 is involved in DNA mismatch repair. Finally, in vivo mismatch repair studies show that the loss of Tet2 causes a mutator phenotype. Taken together, my data indicate that TET2 binds to MSH6 to protect genome integrity. ^ In Part II, I intended to better understand the role of Tet2 in the nervous system. 5-hydroxymethylcytosine regulates epigenetic modification during neurodevelopment and aging. Thus, Tet2 may play a critical role in regulating adult neurogenesis. To examine the physiological significance of Tet2 in the nervous system, I first showed that the deletion of Tet2 reduces the 5hmC levels in neural stem cells. Mice lacking Tet2 show abnormal hippocampal neurogenesis along with 5hmC alternations at different gene promoters and corresponding gene expression downregulation. Through the luciferase reporter assay, two neural factors Neurogenic differentiation 1 (NeuroD1) and Glial fibrillary acidic protein (Gfap) were down-regulated in Tet2 knockout cells. My results suggest that Tet2 regulates neural stem/progenitor cell proliferation and differentiation in adult brain.^

Regimes de precipitação na América do Sul: uma revisão bibliográfica

Como a América do Sul se estende por diferentes latitudes e possui formas de relevo variadas, proporciona a atuação e o desenvolvimento de diferentes sistemas atmosféricos, os quais contribuem para a não homogeneidade climática da região. Portanto o objetivo deste estudo é apresentar uma revisão dos sistemas atmosféricos que atuam nos diferentes setores do continente sul-americano e que contribuem para a precipitação.

Rat pinealectomy: a modified direct visual approach

PURPOSE: To report a new, direct visual approach for rat pinealectomy. METHODS: Eighty adult female rats (Rattus norvegicus albinus EPM-1 strain) were weighted and anesthetized intraperitoneally with 15 mg/kg xylazine and 30 mg/kg ketamine. The animal was fastened to a dissection table, an incision was made in the skin and the subcutaneous tissue, bringing the lambda into view. The skullcap was opened with a dental drill, bringing the cerebral hemispheres and the superior sagittal sinus into view. The pineal gland, located under the venous sinus, was removed in a single piece using tweezers. Next, the bone fragment was returned to its place and the surgical layers were sutured. RESULTS: This new technique is easy to be done, avoids bleedings and removes only the pineal gland without damage to the remaining encephalon. In addition it makes possible the achievement of a sham surgery, allowing the pineal gland to remain intact. CONCLUSION: The proposed technique intends to facilitate studies aiming to better understanding the complexity and importance of the pineal gland on reproductive and other body systems.

Use of correlated potential harmonic basis functions for the description of the (4)He trimer and small clusters

A correlated many-body basis function is used to describe the (4)He trimer and small helium clusters ((4)HeN) with N = 4-9. A realistic helium dimer potential is adopted. The ground state results of the (4)He dimer and trimer are in close agreement with earlier findings. But no evidence is found for the existence of Efimov state in the trimer for the actual (4)He-(4)He interaction. However, decreasing the potential strength we calculate several excited states of the trimer which exhibit Efimov character. We also solve for excited state energies of these clusters which are in good agreement with Monte Carlo hyperspherical description. (C) 2011 American Institute of Physics. [doi:10.1063/1.3583365]