Exploring CP violation in the MSSM

We explore the prospects for observing CP violation in the minimal supersymmetric extension of the Standard Model (MSSM) with six CP-violating parameters, three gaugino mass phases and three phases in trilinear soft supersymmetry-breaking parameters, using the CPsuperH code combined with a geometric approach to maximise CP-violating observables subject to the experimental upper bounds on electric dipole moments. We also implement CP-conserving constraints from Higgs physics, flavour physics and the upper limits on the cosmological dark matter density and spin-independent scattering. We study possible values of observables within the constrained MSSM (CMSSM), the non-universal Higgs model (NUHM), the CPX scenario and a variant of the phenomenological MSSM (pMSSM). We find values of the CP-violating asymmetry A(CP) in b -> s gamma decay that may be as large as 3 %, so future measurements of ACP may provide independent information about CP violation in the MSSM. We find that CP-violating MSSM contributions to the B-s meson mass mixing term Delta M-Bs are in general below the present upper limit, which is dominated by theoretical uncertainties. If these could be reduced, Delta M-Bs could also provide an interesting and complementary constraint on the six CP-violating MSSM phases, enabling them all to be determined experimentally, in principle. We also find that CP violation in the h(2,3)tau(+)tau(-) and h(2,3) (t) over bart couplings can be quite large, and so may offer interesting prospects for future pp, e(+) e(-), mu(+) mu(-) and gamma gamma colliders.

Intramolecular hydrogen bonds involving organic fluorine in the derivatives of hydrazides: an NMR investigation substantiated by DFT based theoretical calculations

The rare examples of intramolecular hydrogen bonds (HB) of the type the N-H center dot center dot center dot F-C, detected in a low polarity solvent in the derivatives of hydrazides, by utilizing one and two-dimensional solution state multinuclear NMR techniques, are reported. The observation of through-space couplings, such as, (1h)J(FH), and (1h)J(FN), provides direct evidence for the existence of intra-molecular HB. Solvent induced perturbations and the variable temperature NMR experiments unambiguously establish the presence of intramolecular HB. The existence of multiple conformers in some of the investigated molecules is also revealed by two dimensional HOESY and N-15-H-1 HSQC experiments. The H-1 DOSY experimental results discard any possibility of self or cross dimerization of the molecules. The derived NMR experimental results are further substantiated by Density Function Theory (DFT) based Non Covalent Interaction (NCI), and Quantum Theory of Atom in Molecule (QTAIM) calculations. The NCI calculations served as a very sensitive tool for detection of non-covalent interactions and also confirm the presence of bifurcated HBs.

A Disulfide Stabilized beta-Sandwich Defines the Structure of a New Cysteine Framework M-Superfamily Conotoxin

The structure of a new cysteine framework (-C-CC-C-C-C) ``M''-superfamily conotoxin, Mo3964, shows it to have a beta-sandwich structure that is stabilized by inter-sheet cross disulfide bonds. Mo3964 decreases outward K+ currents in rat dorsal root ganglion neurons and increases the reversal potential of the Na(V)1.2 channels. The structure of Mo3964 (PDB ID: 2MW7) is constructed from the disulfide connectivity pattern, i.e., 1-3, 2-5, and 4-6, that is hitherto undescribed for the ``M''-superfamily conotoxins. The tertiary structural fold has not been described for any of the known conus peptides. NOE (549), dihedral angle (84), and hydrogen bond (28) restraints, obtained by measurement of (h3)J(NC') scalar couplings, were used as input for structure calculation. The ensemble of structures showed a backbone root mean square deviation of 0.68 +/- 0.18 angstrom, with 87% and 13% of the backbone dihedral (phi, psi) angles lying in the most favored and additional allowed regions of the Ramachandran map. The conotoxin Mo3964 represents a new bioactive peptide fold that is stabilized by disulfide bonds and adds to the existing repertoire of scaffolds that can be used to design stable bioactive peptide molecules.

Longitudinal top polarisation measurement and anomalous Wtb coupling

Kinematical distributions of decay products of the top quark carry information on the polarisation of the top as well as on any possible new physics in the decay of the top quark. We construct observables in the form of asymmetries in the kinematical distributions to probe their effects. Charged-lepton angular distributions in the decay are insensitive to anomalous couplings to leading order. Hence these can be a robust probe of top polarisation. However, these are difficult to measure in the case of highly boosted top quarks as compared to energy distributions of decay products. These are then sensitive, in general, to both top polarisation and top anomalous couplings. We compare various asymmetries for their sensitivities to the longitudinal polarisation of the top quark as well as to possible new physics in the Wtb vertex, paying special attention to the case of highly boosted top quarks. We perform a chi(2) analysis to determine the regions in the plane of longitudinal polarisation of the top quark and the couplings of the Wtb vertex constrained by different combinations of the asymmetries. Moreover, we find that the use of observables sensitive to the longitudinal top polarisation can add to the sensitivity to which the Wtb vertex can be probed.

Longitudinal top polarisation measurement and anomalous Wtb coupling

Kinematical distributions of decay products of the top quark carry information on the polarisation of the top as well as on any possible new physics in the decay of the top quark. We construct observables in the form of asymmetries in the kinematical distributions to probe their effects. Charged-lepton angular distributions in the decay are insensitive to anomalous couplings to leading order. Hence these can be a robust probe of top polarisation. However, these are difficult to measure in the case of highly boosted top quarks as compared to energy distributions of decay products. These are then sensitive, in general, to both top polarisation and top anomalous couplings. We compare various asymmetries for their sensitivities to the longitudinal polarisation of the top quark as well as to possible new physics in the Wtb vertex, paying special attention to the case of highly boosted top quarks. We perform a chi(2) analysis to determine the regions in the plane of longitudinal polarisation of the top quark and the couplings of the Wtb vertex constrained by different combinations of the asymmetries. Moreover, we find that the use of observables sensitive to the longitudinal top polarisation can add to the sensitivity to which the Wtb vertex can be probed.

Longitudinal top polarisation measurement and anomalous Wtb coupling

Kinematical distributions of decay products of the top quark carry information on the polarisation of the top as well as on any possible new physics in the decay of the top quark. We construct observables in the form of asymmetries in the kinematical distributions to probe their effects. Charged-lepton angular distributions in the decay are insensitive to anomalous couplings to leading order. Hence these can be a robust probe of top polarisation. However, these are difficult to measure in the case of highly boosted top quarks as compared to energy distributions of decay products. These are then sensitive, in general, to both top polarisation and top anomalous couplings. We compare various asymmetries for their sensitivities to the longitudinal polarisation of the top quark as well as to possible new physics in the Wtb vertex, paying special attention to the case of highly boosted top quarks. We perform a chi(2) analysis to determine the regions in the plane of longitudinal polarisation of the top quark and the couplings of the Wtb vertex constrained by different combinations of the asymmetries. Moreover, we find that the use of observables sensitive to the longitudinal top polarisation can add to the sensitivity to which the Wtb vertex can be probed.

Statistics of an adiabatic charge pump

We investigate the effect of time-dependent cyclic-adiabatic driving on the charge transport in a quantum junction. We propose a nonequilibrium Green's function formalism to study the statistics of the charge pumped (at zero bias) through the junction. The formulation is used to demonstrate charge pumping in a single electronic level coupled to two (electronic) reservoirs with time-dependent couplings. An analytical expression for the average pumped current for a general cyclic driving is derived. It is found that for zero bias, for a certain class of driving, the Berry phase contributes only to the odd cumulants. In contrast, a quantum master equation formulation does not show a Berry-phase effect at all.

Heterotic string on the CHL orbifold of K3

We study N = 2 compactifications of heterotic string theory on the CHL orbifold (K3 x T-2)/Z(N) with N = 2, 3, 5, 7. Z(N) acts as an automorphism on K3 together with a shift of 1/N along one of the circles of T-2. These compactifications generalize the example of the heterotic string on K3 x T-2 studied in the context of dualities in string theories. We evaluate the new supersymmetric index for these theories and show that their expansion can be written in terms of the McKay-Thompson series associated with the Z(N) automorphism embedded in the Mathieu group M-24. We then evaluate the difference in one-loop threshold corrections to the non-Abelian gauge couplings with Wilson lines and show that their moduli dependence is captured by Siegel modular forms related to dyon partition functions of N = 4 string theories.

Heterotic string on the CHL orbifold of K3

We study N = 2 compactifications of heterotic string theory on the CHL orbifold (K3 x T-2)/Z(N) with N = 2, 3, 5, 7. Z(N) acts as an automorphism on K3 together with a shift of 1/N along one of the circles of T-2. These compactifications generalize the example of the heterotic string on K3 x T-2 studied in the context of dualities in string theories. We evaluate the new supersymmetric index for these theories and show that their expansion can be written in terms of the McKay-Thompson series associated with the Z(N) automorphism embedded in the Mathieu group M-24. We then evaluate the difference in one-loop threshold corrections to the non-Abelian gauge couplings with Wilson lines and show that their moduli dependence is captured by Siegel modular forms related to dyon partition functions of N = 4 string theories.

Dynamical generation of flavour

We propose the generation of Standard Model fermion hierarchy by the extension of renormalizable SO(10) GUT with O(N (g) ) family gauge symmetry. In this scenario, Higgs representations of SO(10) also carry family indices and are called Yukawons. Vacuum expectation values of these Yukawon fields break GUT and family symmetry and generate MSSM Yukawa couplings dynamically. We have demonstrated this idea using Higgs irrep, ignoring the contribution of 1 2 0-plet which is, however, required for complete fitting of fermion mass-mixing data. The effective MSSM matter fermion couplings to the light Higgs pair are determined by the null eigenvectors of the MSSM-type Higgs doublet superfield mass matrix . A consistency condition on the doublet (1,2,+/- 1]) mass matrix ( 0) is required to keep one pair of Higgs doublets light in the effective MSSM. We show that the Yukawa structure generated by null eigenvectors of are of generic kind required by the MSSM. A hidden sector with a pair of (S (a b) ; I center dot (a b) ) fields breaks supersymmetry and facilitates 0. SUSY breaking is communicated via supergravity. In this scenario, matter fermion Yukawa couplings are reduced from 15 to just 3 parameters in MSGUT with three generations.

Alternative search strategies for a BSM resonance fitting the ATLAS diboson excess

We study an s-channel resonance R as a viable candidate to fit the diboson excess reported by ATLAS. We compute the contribution of the similar to 2 TeV resonance R to semileptonic and leptonic final states at the 13 TeV LHC. To explain the absence of an excess in the semileptonic channel, we explore the possibility where the particle R decays to additional light scalars X, X or X, Y. A modified analysis strategy has been proposed to study the three-particle final state of the resonance decay and to identify decay channels of X. Associated production of R with gauge bosons has been studied in detail to identify the production mechanism of R. We construct comprehensive categories for vector and scalar beyond-standard-model particles which may play the role of particles R, X, Y and find alternate channels to fix the new couplings and search for these particles.

Multiscale Coupling: Challenges and Opportunities

Multiscale coupling is ubiquitous in nature and attracts broad interests of scientists from mathematicians, physicists, machinists, chemists to biologists. However, much less attention has been paid to its intrinsic implication. In this paper, multiscale coupling is introduced by studying two typical examples in classic mechanics: fluid turbulence and solid failure. The nature of multiscale coupling in the two examples lies in their physical diversities and strong coupling over wide-range scales. The theories of dynamical system and statistical mechanics provide fundamental methods for the multiscale coupling problems. The diverse multiscale couplings call for unified approaches and might expedite new concepts, theories and disciplines.

Asymptotic scaling in the two-dimensional O(3) Nonlinear sigma model: a Monte Carlo study on parallel computers

We investigate the 2d O(3) model with the standard action by Monte Carlo simulation at couplings β up to 2.05. We measure the energy density, mass gap and susceptibility of the model, and gather high statistics on lattices of size L ≤ 1024 using the Floating Point Systems T-series vector hypercube and the Thinking Machines Corp.'s Connection Machine 2. Asymptotic scaling does not appear to set in for this action, even at β = 2.10, where the correlation length is 420. We observe a 20% difference between our estimate m/Λ^─_(Ms) = 3.52(6) at this β and the recent exact analytical result . We use the overrelaxation algorithm interleaved with Metropolis updates and show that decorrelation time scales with the correlation length and the number of overrelaxation steps per sweep. We determine its effective dynamical critical exponent to be z' = 1.079(10); thus critical slowing down is reduced significantly for this local algorithm that is vectorizable and parallelizable.

We also use the cluster Monte Carlo algorithms, which are non-local Monte Carlo update schemes which can greatly increase the efficiency of computer simulations of spin models. The major computational task in these algorithms is connected component labeling, to identify clusters of connected sites on a lattice. We have devised some new SIMD component labeling algorithms, and implemented them on the Connection Machine. We investigate their performance when applied to the cluster update of the two dimensional Ising spin model.

Finally we use a Monte Carlo Renormalization Group method to directly measure the couplings of block Hamiltonians at different blocking levels. For the usual averaging block transformation we confirm the renormalized trajectory (RT) observed by Okawa. For another improved probabilistic block transformation we find the RT, showing that it is much closer to the Standard Action. We then use this block transformation to obtain the discrete β-function of the model which we compare to the perturbative result. We do not see convergence, except when using a rescaled coupling β_E to effectively resum the series. For the latter case we see agreement for m/ Λ^─_(Ms) at , β = 2.14, 2.26, 2.38 and 2.50. To three loops m/Λ^─_(Ms) = 3.047(35) at β = 2.50, which is very close to the exact value m/ Λ^─_(Ms) = 2.943. Our last point at β = 2.62 disagrees with this estimate however.

Preparation, characterization and intramolecular electron-transfer studies of ruthenium-modified cytochromes c

Redox-active ruthenium complexes have been covalently attached to the surface of a series of natural, semisynthetic and recombinant cytochromes c. The protein derivatives were characterized by a variety of spectroscopic techniques. Distant Fe^(2+) - Ru^(3+) electronic couplings were extracted from intramolecular electron-transfer rates in Ru(bpy)_2(im)HisX (where X= 33, 39, 62, and 72) derivatives of cyt c. The couplings increase according to 62 (0.0060) < 72 (0.057) < 33 (0.097) < 39 (0.11 cm^(-1)); however, this order is incongruent with histidine to heme edge-edge distances [62 (14.8) > 39 (12.3) > 33 (11.1) > =72 (8.4 Å)]. These results suggest the chemical nature of the intervening medium needs to be considered for a more precise evaluation of couplings. The rates (and couplings) correlate with the lengths of a-tunneling pathways comprised of covalent bonds, hydrogen bonds and through-space jumps from the histidines to the heme group. Space jumps greatly decrease couplings: one from Pro71 to Met80 extends the σ-tunneling length of the His72 pathway by roughly 10 covalent bond units. Experimental couplings also correlate well with those calculated using extended Hiickel theory to evaluate the contribution of the intervening protein medium.

Two horse heart cyt c variants incorporating the unnatural amino acids (S)-2- amino-3-(2,2'-bipyrid-6-yl)-propanoic acid (6Bpa) and (S)-2-amino-3-(2,2'-bipyrid-4-yl)propanoic acid ( 4Bpa) at position 72 have been prepared using semisynthetic protocols. Negligible perturbation of the protein structure results from this introduction of unnatural amino acids. Redox-active Ru(2,2'-bipyridine)_2^(2+) binds to 4Bpa72 cyt c but not to the 6Bpa protein. Enhanced ET rates were observed in the Ru(bpy)_2^(2+)-modified 4Bpa72 cyt c relative to the analogous His72 derivative. The rapid (< 60 nanosecond) photogeneration of ferrous Ru-modified 4Bpa72 cyt c in the conformationally altered alkaline state demonstrates that laser-induced ET can be employed to study submicrosecond protein-folding events.

Functional evaluation of noncovalent interactions in neuroreceptors and progress toward the expansion of unnatural amino acid methodology

This dissertation primarily describes chemical-scale studies of G protein-coupled receptors and Cys-loop ligand-gated ion channels to better understand ligand binding interactions and the mechanism of channel activation using recently published crystal structures as a guide. These studies employ the use of unnatural amino acid mutagenesis and electrophysiology to measure subtle changes in receptor function.

In chapter 2, the role of a conserved aromatic microdomain predicted in the D3 dopamine receptor is probed in the closely related D2 and D4 dopamine receptors. This domain was found to act as a structural unit near the ligand binding site that is important for receptor function. The domain consists of several functionally important noncovalent interactions including hydrogen bond, aromatic-aromatic, and sulfur-π interactions that show strong couplings by mutant cycle analysis. We also assign an alternate interpretation for the linear fluorination plot observed at W6.48, a residue previously thought to participate in a cation-π interaction with dopamine.

Chapter 3 outlines attempts to incorporate chemically synthesized and in vitro acylated unnatural amino acids into mammalian cells. While our attempts were not successful, method optimizations and data for nonsense suppression with an in vivo acylated tRNA are included. This chapter is aimed to aid future researchers attempting unnatural amino acid mutagenesis in mammalian cells.

Chapter 4 identifies a cation-π interaction between glutamate and a tyrosine residue on loop C in the GluClβ receptor. Using the recently published crystal structure of the homologous GluClα receptor, other ligand-binding and protein-protein interactions are probed to determine the similarity between this invertebrate receptor and other more distantly related vertebrate Cys-loop receptors. We find that many of the interactions previously observed are conserved in the GluCl receptors, however care must be taken when extrapolating structural data.

Chapter 5 examines inherent properties of the GluClα receptor that are responsible for the observed glutamate insensitivity of the receptor. Chimera synthesis and mutagenesis reveal the C-terminal portion of the M4 helix and the C-terminus as contributing to formation of the decoupled state, where ligand binding is incapable of triggering channel gating. Receptor mutagenesis was unable to identify single residue mismatches or impaired protein-protein interactions within this domain. We conclude that M4 helix structure and/or membrane dynamics are likely the cause of ligand insensitivity in this receptor and that the M4 helix has an role important in the activation process.