Temperature dependent free energy surface of polymer folding from equilibrium and quench studies

Langevin dynamics simulation studies have been employed to calculate the temperature dependent free energy surface and folding characteristics of a 500 monomer long linear alkane (polyethylene) chain with a realistic interaction potential. Both equilibrium and temperature quench simulation studies have been carried out. Using the shape anisotropy parameter (S) of the folded molecule as the order parameter, we find a weakly first order phase transition between the high-temperature molten globule and low-temperature rodlike crystalline states separated by a small barrier of the order of k(B)T. Near the melting temperature (580 K), we observe an intriguing intermittent fluctuation with pronounced ``1/f noise characteristics'' between these two states with large difference in shape and structure. We have also studied the possibilities of different pathways of folding to states much below the melting point. At 300 K starting from the all-trans linear configuration, the chain folds stepwise into a very regular fourfold crystallite with very high shape anisotropy. Whereas, when quenched from a high temperature (900 K) random coil regime, we identify a two step transition from the random coiled state to a molten globulelike state and, further, to a anisotropic rodlike state. The trajectory reveals an interesting coupling between the two order parameters, namely, radius of gyration (R-g) and the shape anisotropy parameter (S). The rodlike final state of the quench trajectory is characterized by lower shape anisotropy parameter and significantly larger number of gauche defects as compared to the final state obtained through equilibrium simulation starting from all-trans linear chain. The quench study shows indication of a nucleationlike pathway from the molten globule to the rodlike state involving an underlying rugged energy landscape. (C) 2010 American Institute of Physics. doi:10.1063/1.3509398]

Metal-insulator transitions in metal clusters: a high-energy spectroscopy study of palladium and silver clusters

Bremsstrahlung isochromat spectroscopy (BIS) along with ultraviolet and X-ray photoelectron spectroscopy (UPS and XPS) has been employed to investigate the electron states of Pd and Ag deposited on amorphous graphite at different coverages. The metal core level binding energies increase with decreasing cluster size while the UPS valence bands show a decrease in the 4d states at E(F) accompanied by a shift in the intensity maximum to higher binding energies. BIS measurements show the emergence of new states closer to E(F) with increase in the cluster size. It is pointed out that the observed spectral shifts cannot be accounted for by final-state effects alone and that initial-state effects have a significant role. It therefore appears that a decrease in cluster size is accompanied by a metal-insulator transition.

R-parity violation in neutralino decays at an e gamma collider

At an e gamma collider, a selectron (e) over tilde(L,R) may be produced in association with a (lightest) neutralino <(chi)over tilde>(0)(1). Decay of the selectron may be expected to yield a final state with an electron and another <(chi)over tilde>(0)(1). If R-parity is violated, these two neutralinos will decay, giving rise to distinctive signatures, which are identified and studied. (C) 1998 Published by Elsevier Science B.V.

Study of the CP property of the Higgs boson at a photon collider using gamma gamma -> t(t)over-bar -> lX

We study the possible effects of CP violation in the Higgs sector on t (t) over bar production at a gammagamma collider. These studies are performed in a model-independent way in terms of six form factors {R(S-gamma), J(S-gamma), R(P-gamma), J(P-gamma), S-t, P-t} which parametrize the CP mixing in the Higgs sector, and a strategy for their determination is developed. We observe that the angular distribution of the decay lepton from t/(t) over bar produced in this process is independent of any CP violation in the tbW vertex and hence best suited for studying CP mixing in the Higgs sector. Analytical expressions are obtained for the angular distribution of leptons in the c.m. frame of the two colliding photons for a general polarization state of the incoming photons. We construct combined asymmetries in the initial state lepton (photon) polarization and the final state lepton charge. They involve CP even (x's) and odd (y's) combinations of the mixing parameters. We study limits up to which the values of x and y, with only two of them allowed to vary at a time, can be probed by measurements of these asymmetries, using circularly polarized photons. We use the numerical values of the asymmetries predicted by various models to discriminate among them. We show that this method can be sensitive to the loop-induced CP violation in the Higgs sector in the minimal supersymmetric standard model.

Isolating CP-violating gamma ZZ coupling in e(+)e(-) -> gamma Z with transverse beam polarizations

We revisit the process e(+)e(-) -> gamma Z at the ILC with transverse beam polarization in the presence of anomalous CP- violating gamma ZZ coupling lambda(1) and gamma gamma Z coupling lambda(2). We point out that if the final- state spins are resolved, then it becomes possible to fingerprint the anomalous coupling Re lambda(1). 90% confidence level limit on Re lambda(1) achievable at ILC with center- of- mass energy of 500 GeVor 800 GeV with realistic initial beam polarization and integrated luminosity is of the order of few times of 10(-2) when the helicity of Z is used and 10(-3) when the helicity of gamma is used. The resulting corrections at quadratic order to the cross section and its influence on these limits are also evaluated and are shown to be small. The benefits of such polarization programmes at the ILC are compared and contrasted for the process at hand. We also discuss possible methods by which one can isolate events with a definite helicity for one of the final- state particles.

Probing strongly interacting W's at the ILC with polarized beams

We study the possibility of finger printing a strongly interacting W boson sector which is consistent with present day LHC searches at the ILC with longitudinal as well as transversely polarized electron and positron beams. We account for the final state interaction using a suitable Omnes formalism in terms of a plausible resonance description, and carry out thorough analyses of cross sections, asymmetries and angular distributions of the W's. We carry out a comparison with other extensions of the Standard Model, where heavy additional Z' bosons arise naturally. We also consider the effect of the strong final state interaction on a correlation that depends on (phi(-) -phi(+)),where the phi-(+) are the azimuthal angles of decay leptons, and find that it is a useful discriminant.

Looking for an invisible Higgs signal at the LHC

While the recent discovery of a Higgs-like boson at the LHC is an extremely important and encouraging step towards the discovery of the complete Standard Model (SM), the current information on this state does not rule out possibility of beyond standard model (BSM) physics. In fact the current data can still accommodate reasonably large values of the branching fractions of the Higgs into a channel with `invisible' decay products, such a channel being also well motivated theoretically. In this study we revisit the possibility of detecting the Higgs in this invisible channel for both choices of the LHC energies, 8 and 14 TeV, for two production modes; vector boson fusion (VBF) and associated production (ZH). We perform a comprehensive collider analysis for all the above channels and project the reach of LHC to constrain the invisible decay branching fraction for both 8 and 14 TeV energies. For the ZH case we consider decays of the Z boson into a pair of leptons as well as a b (b) over bar pair. For the VBF channel the sensitivity is found to be more than 5 sigma for both the energies up to an invisible branching ratio (Br-inv) similar to 0.80, with luminosities similar to 20/30 fb(-1). The sensitivity is further extended to values of Br-inv similar to 0.25 for 300 fb(-1) at 14 TeV. However the reach is found to be more modest for the ZH mode with leptonic final state; with about 3.5 sigma for the planned luminosity at 8 TeV, reaching 8 sigma only for 14 TeV for 50 fb(-1). In spite of the much larger branching ratio (BR) of the Z into a b (b) over bar channel compared to the dilepton case, the former channel, can provide useful reach up to Br-inv greater than or similar to 0.75, only for the higher luminosity (300 fb(-1)) option using both jet-substructure and jet clustering methods. (C) 2013 Elsevier B.V. All rights reserved.

Free turbulent shear layer in a point vortex gas as a problem in nonequilibrium statistical mechanics

This paper attempts to unravel any relations that may exist between turbulent shear flows and statistical mechanics through a detailed numerical investigation in the simplest case where both can be well defined. The flow considered for the purpose is the two-dimensional (2D) temporal free shear layer with a velocity difference Delta U across it, statistically homogeneous in the streamwise direction (x) and evolving from a plane vortex sheet in the direction normal to it (y) in a periodic-in-x domain L x +/-infinity. Extensive computer simulations of the flow are carried out through appropriate initial-value problems for a ``vortex gas'' comprising N point vortices of the same strength (gamma = L Delta U/N) and sign. Such a vortex gas is known to provide weak solutions of the Euler equation. More than ten different initial-condition classes are investigated using simulations involving up to 32 000 vortices, with ensemble averages evaluated over up to 10(3) realizations and integration over 10(4)L/Delta U. The temporal evolution of such a system is found to exhibit three distinct regimes. In Regime I the evolution is strongly influenced by the initial condition, sometimes lasting a significant fraction of L/Delta U. Regime III is a long-time domain-dependent evolution towards a statistically stationary state, via ``violent'' and ``slow'' relaxations P.-H. Chavanis, Physica A 391, 3657 (2012)], over flow time scales of order 10(2) and 10(4)L/Delta U, respectively (for N = 400). The final state involves a single structure that stochastically samples the domain, possibly constituting a ``relative equilibrium.'' The vortex distribution within the structure follows a nonisotropic truncated form of the Lundgren-Pointin (L-P) equilibrium distribution (with negatively high temperatures; L-P parameter lambda close to -1). The central finding is that, in the intermediate Regime II, the spreading rate of the layer is universal over the wide range of cases considered here. The value (in terms of momentum thickness) is 0.0166 +/- 0.0002 times Delta U. Regime II, extensively studied in the turbulent shear flow literature as a self-similar ``equilibrium'' state, is, however, a part of the rapid nonequilibrium evolution of the vortex-gas system, which we term ``explosive'' as it lasts less than one L/Delta U. Regime II also exhibits significant values of N-independent two-vortex correlations, indicating that current kinetic theories that neglect correlations or consider them as O(1/N) cannot describe this regime. The evolution of the layer thickness in present simulations in Regimes I and II agree with the experimental observations of spatially evolving (3D Navier-Stokes) shear layers. Further, the vorticity-stream-function relations in Regime III are close to those computed in 2D Navier-Stokes temporal shear layers J. Sommeria, C. Staquet, and R. Robert, J. Fluid Mech. 233, 661 (1991)]. These findings suggest the dominance of what may be called the Kelvin-Biot-Savart mechanism in determining the growth of the free shear layer through large-scale momentum and vorticity dispersal.

Optical properties of an inhomogeneously broadened Lambda V-system with multiple excited states

We present a theoretical model using a density matrix approach to show the influence of multiple excited states on the optical properties of an inhomogeneously broadened Lambda V-system of the Rb-87 D2 line. These closely spaced multiple excited states cause asymmetry in absorption and dispersion profiles. We observe the reduced absorption profiles, due to dressed state interactions of the applied electromagnetic fields, which results the Mollow sideband-like transparency windows. In a room temperature vapor, we obtain a narrow enhanced absorption and steep positive dispersion at the line center when the strengths of control and pump fields are equal. Here, we show how the probe transmittance varies when it passes through the atomic medium. We also discuss the transient behavior of our system which agrees well with the corresponding absorption and dispersion profiles. This study has potential applications in controllability of group velocity, and for optical and quantum information processing.

Multidimensional free energy surface of unfolding of HP-36: Microscopic origin of ruggedness

The protein folding funnel paradigm suggests that folding and unfolding proceed as directed diffusion in a multidimensional free energy surface where a multitude of pathways can be traversed during the protein's sojourn from initial to final state. However, finding even a single pathway, with the detail chronicling of intermediates, is an arduous task. In this work we explore the free energy surface of unfolding pathway through umbrella sampling, for a small globular a-helical protein chicken-villin headpiece (HP-36) when the melting of secondary structures is induced by adding DMSO in aqueous solution. We find that the unfolding proceeds through the initial separation or melting of aggregated hydrophobic core that comprises of three phenylalanine residues (Phe7, Phe11, and Phe18). This separation is accompanied by simultaneous melting of the second helix. Unfolding is found to be a multistage process involving crossing of three consecutive minima and two barriers at the initial stage. At a molecular level, Phe18 is observed to reorient itself towards other hydrophobic grooves to stabilize the intermediate states. We identify the configuration of the intermediates and correlate the intermediates with those obtained in our previous works. We also give an estimate of the barriers for different transition states and observe the softening of the barriers with increasing DMSO concentration. We show that higher concentration of DMSO tunes the unfolding pathway by destabilizing the third minimum and stabilizing the second one, indicating the development of a solvent modified, less rugged pathway. The prime outcome of this work is the demonstration that mixed solvents can profoundly transform the nature of the energy landscape and induce unfolding via a modified route. A successful application of Kramer's rate equation correlating the free energy simulation results shows faster rate of unfolding with increasing DMSO concentration. This work perhaps presents the first systematic theoretical study of the effect of a chemical denaturant on the microscopic free energy surface and rates of unfolding of HP-36. (C) 2014 AIP Publishing LLC.

Experimental studies on the influence of intermediate principal stress and inclination on the mechanical behaviour of angular sands

A comprehensive experimental study has been made on angular sand to investigate various aspects of mechanical behavior. A hollow cylinder torsion testing apparatus is used in this program to apply a range of stress conditions on this angular quartzitic fine sand under monotonic drained shear. The effect of the magnitude and inclination of the principal stresses on an element of sand is studied through these experiments. This magnitude and inclination of the principal stresses are presented as an ``ensemble measure of fabric in sands''. This ensemble measure of fabric in the sands evolves through the shearing process, and reaches the final state, which indeed has a unique fabric. The sand shows significant variation in strength with changing inclination of the principal stresses. The locus of the final stress state in principal stress space is also mapped from these series of experiments. Additional aspects of non-coaxiality, a benchmarking exercise with a few constitutive models is presented here. This experimental approach albeit indirect shows that a unique state which is dependent on the fabric, density and confining stress exists. This suite of experiments provides a well-controlled data set for a clear understanding on the mechanical behavior of sands.

Role of supersymmetric heavy Higgs boson production in the self-coupling measurement of 125 GeV Higgs boson at the LHC

Measurement of the self-coupling of the 125 GeV Higgs boson is one of the most crucial tasks for a high luminosity run of the LHC, and it can only be measured in the di-Higgs final state. In the minimal supersymmetric standard model, heavy CP even Higgs (H) can decay into a lighter 125 GeV Higgs boson (h) and, therefore, can influence the rate of di-Higgs production. We investigate the role of single H production in the context of measuring the self-coupling of h. We have found that the H -> hh decay can change the value of Higgs (h) self-coupling substantially, in a low tan beta regime where the mass of the heavy Higgs boson lies between 250 and 600 GeV and, depending on the parameter space, it may be seen as an enhancement of the self-coupling of the 125 GeV Higgs boson.

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.

Searches for new symmetries in pp collisions with the razor kinematic variables at √s = 7 TeV

The construction and LHC phenomenology of the razor variables M_R, an event-by-event indicator of the heavy particle mass scale, and R, a dimensionless variable related to the transverse momentum imbalance of events and missing transverse energy, are presented.  The variables are used  in the analysis of the first proton-proton collisions dataset at CMS  (35 pb^-1) in a search for superpartners of the quarks and gluons, targeting indirect hints of dark matter candidates in the context of supersymmetric theoretical frameworks. The analysis produced the highest sensitivity results for SUSY to date and extended the LHC reach far beyond the previous Tevatron results.  A generalized inclusive search is subsequently presented for new heavy particle pairs produced in √s = 7 TeV proton-proton collisions at the LHC using 4.7±0.1 fb^-1 of integrated luminosity from the second LHC run of 2011.  The selected events are analyzed in the 2D razor-space of M_R and R and the analysis is performed in 12 tiers of all-hadronic, single and double leptons final states in the presence and absence of b-quarks, probing the third generation sector using the event heavy-flavor content.   The search is sensitive to generic supersymmetry models with minimal assumptions about the superpartner decay chains. No excess is observed in the number or shape of event yields relative to Standard Model predictions. Exclusion limits are derived in the CMSSM framework with  gluino masses up to 800 GeV and squark masses up to 1.35 TeV excluded at 95% confidence level, depending on the model parameters. The results are also interpreted for a collection of simplified models, in which gluinos are excluded with masses as large as 1.1 TeV, for small neutralino masses, and the first-two generation squarks, stops and sbottoms are excluded for masses up to about 800, 425 and 400 GeV, respectively.

With the discovery of a new boson by the CMS and ATLAS experiments in the γ-γ and 4 lepton final states, the identity of the putative Higgs candidate must be established through the measurements of its properties. The spin and quantum numbers are of particular importance, and we describe a method for measuring the J^PC of this particle using the observed signal events in the H to ZZ^* to 4 lepton channel developed before the discovery. Adaptations of the razor kinematic variables are introduced for the H to WW^* to 2 lepton/2 neutrino channel, improving the resonance mass resolution and increasing the discovery significance. The prospects for incorporating this channel in an examination of the new boson J^PC is discussed, with indications that this it could provide complementary information to the H to ZZ^* to 4 lepton final state, particularly for measuring CP-violation in these decays.

Experimental and theoretical developments in extended x-ray absorption fine structure (EXAFS) spectroscopy

To obtain accurate information from a structural tool it is necessary to have an understanding of the physical principles which govern the interaction between the probe and the sample under investigation. In this thesis a detailed study of the physical basis for Extended X-ray Absorption Fine Structure (EXAFS) spectroscopy is presented. A single scattering formalism of EXAFS is introduced which allows a rigorous treatment of the central atom potential. A final state interaction formalism of EXAFS is also discussed. Multiple scattering processes are shown to be significant for systems of certain geometries. The standard single scattering EXAFS analysis produces erroneous results if the data contain a large multiple scattering contribution. The effect of thermal vibrations on such multiple scattering paths is also discussed. From symmetry considerations it is shown that only certain normal modes contribute to the Debye-Waller factor for a particular scattering path. Furthermore, changes in the scattering angles induced by thermal vibrations produces additional EXAFS components called modification factors. These factors are shown to be small for most systems.

A study of the physical basis for the determination of structural information from EXAFS data is also presented. An objective method of determining the background absorption and the threshold energy is discussed and involves Gaussian functions. In addition, a scheme to determine the nature of the scattering atom in EXAFS experiments is introduced. This scheme is based on the fact that the phase intercept is a measure of the type of scattering atom. A method to determine bond distances is also discussed and does not require the use of model compounds or calculated phase shifts. The physical basis for this method is the absence of a linear term in the scattering phases. Therefore, it is possible to separate these phases from the linear term containing the distance information in the total phase.