Partition function for hindered, one-and multi-dimensional rotors

Writing the hindered rotor (hr) partition function as the trace of (rho) over cap = e(-beta(H) over cap hr), we approximate it by the sum of contributions from a set of points in position space. The contribution of the density matrix from each point is approximated by performing a local harmonic expansion around it. The highlight of this method is that it can be easily extended to multidimensional systems. Local harmonic expansion leads to a breakdown of the method a low temperatures. In order to calculate the partition function at low temperatures, we suggest a matrix multiplication procedure. The results obtained using these methods closely agree with the exact partition function at all temperature ranges. Our method bypasses the evaluation of eigenvalues and eigenfunctions and evaluates the density matrix for internal rotation directly. We also suggest a procedure to account for the antisymmetry of the total wavefunction in the same. (C) 2012 Elsevier B.V. All rights reserved.

Excitation energy transfer from dye molecules to doped graphene

Recently, we have reported theoretical studies on the rate of energy transfer from an electronically excited molecule to graphene. It was found that graphene is a very efficient quencher of the electronically excited states and that the rate infinity z(-4). The process was found to be effective up to 30 nm which is well beyond the traditional FRET limit. In this report, we study the transfer of an amount of energy (h) over bar Omega from a dye molecule to doped graphene. We find a crossover of the distance dependence of the rate from z(-4) to exponential as the Fermi level is increasingly shifted into the conduction band, with the crossover occurring at a shift of the Fermi level by an amount (h) over bar Omega/2.

Study of molecular structure and vibrational spectra of poly (beta,-1-malic acid) PMLA] using DFT approach

Poly (beta-L-malic acid) (PMLA) is a biodegradable polymer and it has various important applications in the biomedical field. In the present work the structural and spectral characteristics of PMLA have been studied by methods of infrared. Raman spectroscopy and quantum chemistry. Electrostatic potential surface, optimized geometry, harmonic vibrational frequencies, infrared intensities and activities of Raman scattering were calculated by density functional theory (DFT) using oligomeric approach employing B3LYP with complete relaxation in the potential energy surface using 6-311++G (d, p) basis set. Based on results, we have discussed the correlation between the vibrational modes and the structure of the PMLA. A complete analysis of the experimental infrared and Raman spectra has been reported on the basis of wavenumber of the vibrational bands and potential energy distribution. The calculated HOMO and LUMO energies shows that charge transfer occur within the molecule. The calculated infrared and the Raman spectra of the polymer based on DFT calculations show reasonable agreement with the experimental results. (c) 2012 Elsevier Ltd. All rights reserved.

Path-integral formulation for Levy flights: Evaluation of the propagator for free, linear, and harmonic potentials in the over- and underdamped limits

Levy flights can be described using a Fokker-Planck equation, which involves a fractional derivative operator in the position coordinate. Such an operator has its natural expression in the Fourier domain. Starting with this, we show that the solution of the equation can be written as a Hamiltonian path integral. Though this has been realized in the literature, the method has not found applications as the path integral appears difficult to evaluate. We show that a method in which one integrates over the position coordinates first, after which integration is performed over the momentum coordinates, can be used to evaluate several path integrals that are of interest. Using this, we evaluate the propagators for (a) free particle, (b) particle subjected to a linear potential, and (c) harmonic potential. In all the three cases, we have obtained results for both overdamped and underdamped cases. DOI: 10.1103/PhysRevE.86.061105

Effect of Metal Ions (Ag, Co, Ni, and Pd) on the Visible Light Degradation of Rhodamine B by Carbon-Covered Alumina-Supported TiO2 in Aqueous Solutions

Metal-ion (Ag, Co, Ni, and Pd) doped TiO2 nanocatalysts were successfully embedded on carbon-covered alumina supports. The CCA-embedded catalysts were crystalline and had a high surface area compared to the free metal-ion doped titania nanocatalysts while they still retained the anatase phase of the core TiO2. These catalysts were photocatalytically active under solar light irradiation. Rhodamine B was used as a model pollutant and the reactivity followed a pseudo-first-order reaction kinetics. The reaction rate of the CCA-supported catalysts was Pd > Ag > Co > Ni. Among the ratios of the CCA:catalyst used, it was found that the 1:1 ratio had the fastest reaction rate, followed by the 1:2 ratio, while the 2:1 ratio exhibited the lowest reaction rate. The CCA/metal-ion doped titania were found to have photocatalytic activities comparable with those of CCA-supported titania.

Mapping joint ROM on a cube using electromagnetic trackers

This paper presents a unified framework using the unit cube for measurement, representation and usage of the range of motion (ROM) of body joints with multiple degrees of freedom (d.o.f) to be used for digital human models (DHM). Traditional goniometry needs skill and kn owledge; it is intrusive and has limited applicability for multi-d.o.f. joints. Measurements using motion capture systems often involve complicated mathematics which itself need validation. In this paper we use change of orientation as the measure of rotation; this definition does not require the identification of any fixed axis of rotation. A two-d.o.f. joint ROM can be represented as a Gaussian map. Spherical polygon representation of ROM, though popular, remains inaccurate, vulnerable due to singularities on parametric sphere and difficult to use for point classification. The unit cube representation overcomes these difficulties. In the work presented here, electromagnetic trackers have been effectively used for measuring the relative orientation of a body segment of interest with respect to another body segment. The orientation is then mapped on a surface gridded cube. As the body segment is moved, the grid cells visited are identified and visualized. Using the visual display as a feedback, the subject is instructed to cover as many grid cells as he can. In this way we get a connected patch of contiguous grid cells. The boundary of this patch represents the active ROM of the concerned joint. The tracker data is converted into the motion of a direction aligned with the axis of the segment and a rotation about this axis later on. The direction identifies the grid cells on the cube and rotation about the axis is represented as a range and visualized using color codes. Thus the present methodology provides a simple, intuitive and accura te determination and representation of up to 3 d.o.f. joints. Basic results are presented for the shoulder. The measurement scheme to be used for wrist and neck, and approach for estimation of the statistical distribution of ROM for a given population are also discussed.

Superparamagnetic behaviour and T-1, T-2 relaxivity of ZnFe2O4 nanoparticles for magnetic resonance imaging

In the present study, ZnFe2O4 nanoparticles were synthesized by the chemical co-precipitation followed by calcinations at 473 and 673K for 4h. Particle sizes obtained were 4 and 6nm for the calcination temperatures of 473 and 673K, respectively. To study the origin of system's low temperature spin dynamic behaviour, temperature dependence of susceptibility was investigated as a function of particle size and frequency. Slight increase in the grain size from 4nm at 473K to 6nm at 673K has led to a peak shift of temperature dependence of susceptibility measured at a constant frequency of 400Hz. Temperature dependence of at different frequencies also resulted in peak shift. Relaxation time dependence of peak temperature obeys a power law, which provides the fitting parameters within the range of superparamagnetic nature of the particles. Further, dependence of relaxation time and peak temperature obeys VogelFulcher law rather than NeelBrown equation demonstrating that the particles follow the behaviour of superparamagnetism of slightly interacting system. Spinlattice, T-1 and spinspin, T-2 relaxivity of proton of the water molecule in the presence of chitosan-coated superparamagnetic ZnFe2O4 nanoparticle yields the values of 0.002 and 0.360s(1)perppm.

Adiabatic eigenfunction-based approach for coherent excitation transfer: An almost analytical treatment of the Fenna-Matthews-Olson complex

We suggest a method of studying coherence in finite-level systems coupled to the environment and use it for the Hamiltonian that has been used to describe the light-harvesting pigment-protein complex. The method works with the adiabatic states and transforms the Hamiltonian to a form in which the terms responsible for decoherence and population relaxation are separated out. Decoherence is then accounted for nonperturbatively and population relaxation using a Markovian master equation. Almost analytical results can be obtained for the seven-level system, and the calculations are very simple for systems with more levels. We apply the treatment to the seven-level system, and the results are in excellent agreement with the exact numerical results of Nalbach et al. Nalbach, Braun, and Thorwart, Phys. Rev. E 84, 041926 (2011)]. Our approach is able to account for decoherence and population relaxation separately. It is found that decoherence causes only damping of oscillations and does not lead to transfer to the reaction center. Population relaxation is necessary for efficient transfer to the reaction center, in agreement with earlier findings. Our results show that the transformation to the adiabatic basis followed by a Redfield type of approach leads to results in good agreement with exact simulation.

Between photocatalysis and photosynthesis: Synchrotron spectroscopy methods on molecules and materials for solar hydrogen generation

Energy research is to a large extent materials research, encompassing the physics and chemistry of materials, including their synthesis, processing toward components and design toward architectures, allowing for their functionality as energy devices, extending toward their operation parameters and environment, including also their degradation, limited life, ultimate failure and potential recycling. In all these stages, X-ray and electron spectroscopy are helpful methods for analysis, characterization and diagnostics for the engineer and for the researcher working in basic science.This paper gives a short overview of experiments with X-ray and electron spectroscopy for solar energy and water splitting materials and addresses also the issue of solar fuel, a relatively new topic in energy research. The featured systems are iron oxide and tungsten oxide as photoanodes, and hydrogenases as molecular systems. We present surface and subsurface studies with ambient pressure XPS and hard X-ray XPS, resonant photoemission, light induced effects in resonant photoemission experiments and a photo-electrochemical in situ/operando NEXAFS experiment in a liquid cell, and nuclear resonant vibrational spectroscopy (NRVS). (C) 2012 Elsevier B.V. All rights reserved.

Adiabatic Eigenfunction Based Approach to Coherent Transfer: Application to the Fenna-Matthews-Olson (FMO) Complex and the Role of Correlations in the Efficiency of Energy Transfer

We have recently suggested a method (Pallavi Bhattacharyya and K. L. Sebastian, Physical Review E 2013, 87, 062712) for the analysis of coherence in finite-level systems that are coupled to the surroundings and used it to study the process of energy transfer in the Fenna-Matthews-Olson (FMO) complex. The method makes use of adiabatic eigenstates of the Hamiltonian, with a subsequent transformation of the Hamiltonian into a form where the terms responsible for decoherence and population relaxation could be separated out at the lowest order. Thus one can account for decoherence nonperturbatively, and a Markovian type of master equation could be used for evaluating the population relaxation. In this paper, we apply this method to a two-level system as well as to a seven-level system. Comparisons with exact numerical results show that the method works quite well and is in good agreement with numerical calculations. The technique can be applied with ease to systems with larger numbers of levels as well. We also investigate how the presence of correlations among the bath degrees of freedom of the different bacteriochlorophyll a molecules of the FMO Complex affect the rate of energy transfer. Surprisingly, in the cases that we studied, our calculations suggest that the presence of anticorrelations, in contrast to correlations, make the excitation transfer more facile.

Asymmetric cell division in Mycobacterium tuberculosis and its unique features

Recently, several reports showed that about 80 % of mid-log phase Mycobacterium smegmatis, Mycobacterium marinum, and Mycobacterium bovis BCG cells divide symmetrically with 5-10 % deviation in the septum position from the median. However, the mode of cell division of the pathogenic mycobacterial species, Mycobacterium tuberculosis, remained unclear. Therefore, in the present study, using electron microscopy, fluorescence microscopy of septum- and nucleoid-stained live and fixed cells, and live cell time-lapse imaging, we show the occurrence of asymmetric cell division with unusually deviated septum/constriction in 20 % of the 15 % septating M. tuberculosis cells in the mid-log phase population. The remaining 80 % of the 15 % septating cells divided symmetrically but with 2-5 % deviation in the septum/constriction position, as reported for M. smegmatis, M. marinum, and M. bovis BCG cells. Both the long and the short portions of the asymmetrically dividing M. tuberculosis cells with unusually deviated septum contained nucleoids, thereby generating viable short and long cells from each asymmetric division. M. tuberculosis short cells were acid fast positive and, like the long cells, further readily underwent growth and division to generate micro-colony, thereby showing that they were neither mini cells, spores nor dormant forms of mycobacteria. The freshly diagnosed pulmonary tuberculosis patients' sputum samples, which are known for the prevalence of oxidative stress conditions, also contained short cells at the same proportion as that in the mid-log phase population. The probable physiological significance of the generation of the short cells through unusually deviated asymmetric cell division is discussed.

Transmission of elastic waves through a frictional boundary

Incident energy gets transmitted, reflected and absorbed across an interface in jointed rock mass leading to energy dissipation and alteration of waves. Wave velocities get attenuated during their propagation across joints and this behavior is studied using bender/extender element tests. The velocity attenuation and modulus reduction observed in experimental tests are modeled with three dimensional distinct element code and results are validated. Normal propagation of an incident shear wave through a jointed rock mass cause slip of the rock blocks if shear stress of wave exceeds the shear strength of the joint. As the properties of joint determine the transmission of energy across an interface, a parametric study is then conducted with the validated numerical model by varying the parameters that may determine the energy transmission across a joint using modified Miller's method. Results of the parametric study are analyzed and presented in the paper. (C) 2014 Elsevier Ltd. All rights reserved.

Efficiency limitations in a low band-gap diketopyrrolopyrrole-based polymer solar cell

We report the performance and photophysics of a low band-gap diketopyrrolopyrrole-based copolymer used in bulk heterojunction devices in combination with PC71BM. We show that the short lifetime of photogenerated excitons in the polymer constitutes an obstacle towards device efficiency by limiting the diffusion range of the exciton to the donor-acceptor heterojunction. We employ ultrafast transient-probe and fluorescence spectroscopy techniques to examine the excited state loss channels inside the devices. We use the high boiling point solvent additive 1,8-diiodooctane (DIO) to study the photoexcited state losses in different blend morphologies. The solvent additive acts as a compatibiliser between the donor and the acceptor material and leads to smaller domain sizes, higher charge formation yields and increased device efficiency.

Diffusion in an elastic medium: A model for macromolecule transport across the nuclear pore complex

Nuclear pore complexes (NPCs) are very selective filters that sit on the membrane of the nucleus and monitor the transport between the cytoplasm and the nucleoplasm. For the central plug of NPC two models have been suggested in the literature. The first suggests that the plug is a reversible hydrogel while the other suggests that it is a polymer brush. Here we propose a model for the transport of a protein through the plug, which is general enough to cover both the models. The protein stretches the plug and creates a local deformation, which together with the protein, we refer to as the bubble. We start with the free energy for creation of the bubble and consider its motion within the plug. The relevant coordinate is the center of the bubble which executes random walk. We find that for faster relaxation of the gel, the diffusion of the bubble is greater. (C) 2014 Elsevier-B.V. All rights reserved.

Linewidths and line shapes in the vicinity of graphene

It is well known that graphene, by virtue of its pi-cloud delocalization, has a continuum of electronic energy states and thus behaves nearly like a metal. Instances involving quenching of electronic energy excitation in fluorophores placed in the proximity of graphene sheets are well documented. In this paper, we perform theoretical investigations on the broadening of vibrational and electronic transitions in the vicinity of graphene. We find that for CO vibrations in the vicinity of undoped graphene, the broadening at a distance of 5 angstrom is similar to 0.008 cm(-1)((kappa) over tilde = 2, (kappa) over tilde being the effective dielectric constant). In comparison, for electronic transitions, the linewidth is much larger, being of the order of several cm(-1). Also, if the transition dipole were parallel to the graphene sheet, the linewidth would be reduced to half the value for the case where it is perpendicular, an observation which should be easy to check experimentally for electronic transitions. This should be observable for the f - f transitions (which are rather narrow) of Lanthanide complexes placed within a distance of a few nanometers from a graphene sheet. Further the linewidth would have a (distance)(-4) dependence as one varies the distance from graphene. (C) 2014 AIP Publishing LLC.