An extension of the coupled-cluster method: A variational formalism

A general quantum many-body theory in configuration space is developed by extending the traditional coupled cluter method (CCM) to a variational formalism. Two independent sets of distribution functions are introduced to evaluate the Hamiltonian expectation. An algebraic technique for calculating these distribution functions via two self-consistent sets of equations is given. By comparing with the traditional CCM and with Arponen's extension, it is shown that the former is equivalent to a linear approximation to one set of distribution functions and the later is equivalent to a random-phase approximation to it. In additional to these two approximations, other higher-order approximation schemes within the new formalism are also discussed. As a demonstration, we apply this technique to a quantum antiferromagnetic spin model.Comment: 15 pages. Submitted to Phys. Rev.

Mouse gut microbiomics of short chain fatty acid metabolism and mucosal responses

Summary The microbiota of the gastrointestinal (GI) tract plays a key role in the digestion of our food. The human gut microbiota can be studied using in vitro and animal models. In this thesis the mouse model is used to study the microbiota interaction with the diet and the host in different regions along the GI tract. These interacting microbes in the GI tract of humans and other mammals yield a wide range of metabolites, among which the short chain fatty acids (SCFA), in particular butyrate, acetate, and propionate, are the most abundant products of carbohydrate fermentation. Fermentable carbohydrates can modify the composition of the gut microbiota and change the SCFA concentrations in the gut. Opportunities for increasing specific SCFA by targeting their producers with carbohydrates are discussed. Five different fibres – resistant starch, inulin, fructooligosaccharides, arabinoxylan and guar gum – are tested for their modification of the mucosal tissue transcriptome, luminal microbiota composition and SCFA concentrations in the murine colon. The fibres inulin, fructooligosaccharides, arabinoxylan and guar gum led to increased SCFA concentrations and induced similar changes in relative abundance of microbial groups as determined by the MITChip, a phylogenetic microarray targeting the 16S ribosomal RNA of mouse intestinal microorganisms. Furthermore, these four fibres induced regulation of overlapping sets of genes in the mouse intestinal mucosa, where the transcription factor PPARγ was predicted to be a prominent upstream regulator of these processes. Multivariate data integration revealed strong correlations between the expression of genes involved in energy metabolism and the relative abundance of bacteria belonging to Clostridium cluster XIVa. Similar analyses were done for the caeca of the same mice, and were complemented with metatransciptome analyses. To comprehensively analyse RNAseq data of complex natural microbial communities, a de novo metatranscriptome assembly pipeline was developed and applied to unravel the activity profiles of the microbiota residing in the mouse cecum. This revealed distinct contributions of bacterial families to the fermentation of fibres into SCFA, involving the Bifidobacteriaceae, Lachnospiraceae, Clostridiaceae, Bacteroidaceae, Erysipelotrichaceae and Ruminococcaceae in some or all stages of the overall fibre fermentation activity. All families expressed genes encoding enzymes involved in the production of SCFA in different ratios. Specifically, butyrate producing bacteria correlated with a set of host genes involved in processes such as energy metabolism, transcriptional regulation and the mucosal immune system. In addition to complex carbohydrates, amino acids derived from dietary proteins can also serve as substrates for SCFA formation, leading to expansion of the fermentation end-product palet by including branched-SCFA. The long-term effects of high protein-diets on microbial community composition and activity were analysed. The caecal microbiota composition was changed by the high dietary protein. Most of the gene functions detected by metatranscriptomics in these caecal samples were assigned to the Lachnospiraceae, Erysipelotrichaceae and Clostridiaceae. High protein diets induced a decrease of Lachnospiraceae activity, but stimulated the activity of the Erysipelotrichaceae, while the Clostridiaceae appeared to express the broadest range of amino acid metabolism associated pathways. In conclusion, this thesis describes dietary interventions to modulate the mouse intestinal microbiota and mucosa. The data provides expansion of the knowledge on interactions between the diet, microbiota and host. This information can be used to optimize the design and validation on dietary intervention studies in humans. </p

Conservation of connectivity of model-space effective interactions under a class of similarity transformation

Effective interaction operators usually act on a restricted model space and give the same energies (for Hamiltonian) and matrix elements (for transition operators etc.) as those of the original operators between the corresponding true eigenstates. Various types of effective operators are possible. Those well defined effective operators have been shown being related to each other by similarity transformation. Some of the effective operators have been shown to have connected-diagram expansions. It is shown in this paper that under a class of very general similarity transformations, the connectivity is conserved. The similarity transformation between hermitian and non-hermitian Rayleigh-Schr\"{o}dinger perturbative effective operators is one of such transformation and hence the connectivity can be deducted from each other.Comment: 12 preprint page

Procoagulant changes in fibrin clot structure in patients with cirrhosis are associated with oxidative modifications of fibrinogen

Patients with cirrhosis have hemostatic changes, which may contribute to a risk of thrombosis. This in vitro study compares clot formation and structure between patients and healthy subjects. Clot formation is delayed in patients; ultimately, however, clot permeability is decreased. The thrombogenic structure of fibrin clots may contribute to the thrombotic risk in cirrhosis. Background and Objectives: Patients with cirrhosis can be at risk of thrombotic complications due to an imbalance between hemostatic components. However, little is known on how the disease affects clot generation or how alterations in the structure of fibrin clots may affect the hemostatic function of these patients. Methods: We investigated the formation and structure of clots generated with plasma and purified fibrinogen of 42 patients with cirrhosis. Clots generated with plasma and fibrinogen of 29 healthy volunteers were studied for comparison. Clot formation and structure were assessed by turbidity, permeation studies, confocal laser and scanning electron microscopy (SEM). The extent of fibrinogen oxidation was assessed by measuring the carbonyl content of purified fibrinogen samples. Results: Tissue factor and thrombin-induced clotting of plasma was delayed in patients. The clotting rate was also decreased, but change in turbidity, fibrin density and fiber thickness were largely comparable to healthy volunteers. Conversely, clot permeability was significantly decreased in patients. When clots were generated with purified fibrinogen, differences in clot formation and structure similar to those in plasma were found. The carbonyl content was increased in patient fibrinogen and correlated with disease severity and clot permeability. Conclusions: Delayed clot formation in cirrhosis ultimately results in decreased clot permeability. Similar alterations in clots generated with purified fibrinogen suggest that modifications of the molecule are (partly) responsible. Taken together, these findings are indicative of hypercoagulable features of clots of patients with cirrhosis, which may explain the increased risk of thrombosis associated with this condition

Saturation properties and incompressibility of nuclear matter: A consistent determination from nuclear masses

Starting with a two-body effective nucleon-nucleon interaction, it is shown that the infinite nuclear matter model of atomic nuclei is more appropriate than the conventional Bethe-Weizsacker like mass formulae to extract saturation properties of nuclear matter from nuclear masses. In particular, the saturation density thus obtained agrees with that of electron scattering data and the Hartree-Fock calculations. For the first time using nuclear mass formula, the radius constant $r_0$=1.138 fm and binding energy per nucleon $a_v$ = -16.11 MeV, corresponding to the infinite nuclear matter, are consistently obtained from the same source. An important offshoot of this study is the determination of nuclear matter incompressibility $K_{\infty}$ to be 288$\pm$ 28 MeV using the same source of nuclear masses as input.Comment: 14 latex pages, five figures available on request ( to appear in Phy. Rev. C

Towards a fully self-consistent spectral function of the nucleon in nuclear matter

We present a calculation of nuclear matter which goes beyond the usual quasi-particle approximation in that it includes part of the off-shell dependence of the self-energy in the self-consistent solution of the single-particle spectrum. The spectral function is separated in contributions for energies above and below the chemical potential. For holes we approximate the spectral function for energies below the chemical potential by a $\delta$-function at the quasi-particle peak and retain the standard form for energies above the chemical potential. For particles a similar procedure is followed. The approximated spectral function is consistently used at all levels of the calculation. Results for a model calculation are presented, the main conclusion is that although several observables are affected by the inclusion of the continuum contributions the physical consistency of the model does not improve with the improved self-consistency of the solution method. This in contrast to expectations based on the crucial role of self-consistency in the proofs of conservation laws.Comment: 26 pages Revtex with 4 figures, submitted to Phys. Rev.

Infrared Behavior of Interacting Bosons at Zero Temperature

We exploit the symmetries associated with the stability of the superfluid phase to solve the long-standing problem of interacting bosons in the presence of a condensate at zero temperature. Implementation of these symmetries poses strong conditions on the renormalizations that heal the singularities of perturbation theory. The renormalized theory gives: For d>3 the Bogoliubov quasiparticles as an exact result; for 1<d<=3 a nontrivial solution with the exact exponent for the singular longitudinal correlation function, with phonons again as low-lying excitations.Comment: Minor Changes. 4 pages, RevTeX, no figures, uses multicol.sty e-mail: [email protected]

Stability and Related Properties of Vacua and Ground States

We consider the formal non relativistc limit (nrl) of the :\phi^4:_{s+1} relativistic quantum field theory (rqft), where s is the space dimension. Following work of R. Jackiw, we show that, for s=2 and a given value of the ultraviolet cutoff \kappa, there are two ways to perform the nrl: i.) fixing the renormalized mass m^2 equal to the bare mass m_0^2; ii.) keeping the renormalized mass fixed and different from the bare mass m_0^2. In the (infinite-volume) two-particle sector the scattering amplitude tends to zero as \kappa -> \infty in case i.) and, in case ii.), there is a bound state, indicating that the interaction potential is attractive. As a consequence, stability of matter fails for our boson system. We discuss why both alternatives do not reproduce the low-energy behaviour of the full rqft. The singular nature of the nrl is also nicely illustrated for s=1 by a rigorous stability/instability result of a different nature.Comment: Late

Thermodynamics of a weakly interacting Bose-Einstein gas

The one-loop effective potential for non-relativistic bosons with a delta function repulsive potential is calculated for a given chemical potential using functional methods. After renormalization and at zero temperature it reproduces the standard ground state energy and pressureas function of the particle density. At finite temperatures it is found necessary to include ring corrections to the one-loop result in order to satisfy the Goldstone theorem. It is natural to introduce an effective chemical potential directly related to the order parameter and which uniformly decreases with increasing temperatures. This is in contrast to the the ordinary chemical potential which peaks at the critical temperature. The resulting thermodynamics in the condensed phase at very low temperatures is found to be the same as in the Bogoliubov approximation where the degrees of freedom are given by the Goldstone bosons. At higher temperatures the ring corrections dominate and result in a critical temperature unaffected by the interaction.Comment: 39 pages, 9 figures, picTex, submitted to Annals of Physics. Discussions on renormalization and off-diagonal self energies are made clearer in this version. A short derivation of the non-relativistic limit is adde

Bose-Einstein Condensation in a Confined Geometry with and without a Vortex

Various widely-used mean-field type theories for a dilute Bose gas are critically examined in the light of the recent discovery of Bose-Einstein condensation of atomic gases in a confined geometry. By numerically solving the mean-field equations within the framework of the Bogoliubov approximation both stationary non-uniform case and the vortex case under rotation in a cylindrically symmetric vessel are investigated. We obtain spatial structures of condensate, non-condensate, anomalous correlation. The low lying excitation spectra, the local density of states and the circulating current density in a vortex corresponding to various levels of mean-field theories are predicted.Comment: 16 pages, LaTeX with jpsj.sty, 13 eps figures. Figures improve