On the importance of backbone loop and peptide flip in the Walker sequence in F-1-ATPase action

The Walker sequence, GXXXXGKT, present in all the six subunits of F-1-ATPase exists in a folded form, known as phosphate-binding loop (P-loop). Analysis of the Ramachandran angles showed only small RMS deviation between the nucleotide-bound and nucleotide-free forms. This indicated a good overlap of the backbone loops. The catalytic beta-subunits (chains D, E and F) showed significant changes in the Ramachandran angles and the side chain torsion angles, but not the structural alpha-subunits (chains A, B and C). Most striking among these are the changes associated with Val160 and Gly161 corresponding to a flip in the peptide unit between them when a nucleotide is bound (chains D or F compared to nucleotide-free chain E). The conformational analysis further revealed a hitherto unnoticed hydrogen bond between amide-N of the flipped Gly161 and terminal phosphate-O of the nucleotide. This assigns a role for this conserved amino acid, otherwise ignored, of making an unusual direct interaction between the peptide backbone of the enzyme protein and the incoming nucleotide substrate. Significance of this interaction is enhanced, as it is limited only to the catalytic subunits, and also likely to involve a mechanical rotation of bonds of the peptide unit. Hopefully this is part of the overall events that link the chemical hydrolysis of ATP with the mechanical rotation of this molecule, now famous as tiny molecular motor.

Unimolecular HCl elimination from 1,2-dichloroethane: A single pulse shock tube and ab initio study

Thermal decomposition of 1,2-dichloroethane (1,2-DCE) has been studied in the temperature range of 10501175 K behind reflected shock waves in a single pulse shock tube. The unimolecular elimination of HCl is found to be the major channel through which 1,2-DCE decomposes under these conditions. The rate constant for the unimolecular elimination of HCl from 1,2-dichloroethane is found to be 10(13.98+/-0.80) exp(-57.8+/-2.0/RT) s(-1), where the activation energy is given in kcal mol(-1) and is very close to that value for CH3CH2Cl (EC). Ab initio (HF and MP2) and DFT calculations have been carried out to find the activation barrier and the structure of the transition state for this reaction channel from both EC and 1,2-DCE. The preexponential factors calculated at various levels of theory (BF/6-311++G**, MP2/6-311++G**, and B3LYP/6-311++G**) are (approximate to10(15) s(-1)) significantly larger than the experimental results. If the torsional mode in the ground state is treated as free internal rotation the preexponential factors reduce significantly, giving excellent agreement with experimental values. The DFT results are in excellent (fortuitous?) agreement with the experimental value for activation energy for 1,2-DCE while the MP2 and HF results seem to overestimate the barrier. However, DFT results for EC is 4.5 kcal mol(-1) less than the previously reported experimental values. At all levels, theory predicts an increase in HCI elimination barrier on beta-Cl substitution on EC.

Mutagenicity associated with O6-methylguanine-DNA damage and mechanism of nucleotide flipping by AGT during repair

Methylated guanine damage at O6 position (i.e. O6MG) is dangerous due to its mutagenic and carcinogenic character that often gives rise to G:C-A:T mutation. However, the reason for this mutagenicity is not known precisely and has been a matter of controversy. Further, although it is known that O6-alkylguanine-DNA alkyltransferase (AGT) repairs O6MG paired with cytosine in DNA, the complete mechanism of target recognition and repair is not known completely. All these aspects of DNA damage and repair have been addressed here by employing high level density functional theory in gas phase and aqueous medium. It is found that the actual cause of O6MG mediated mutation may arise due to the fact that DNA polymerases incorporate thymine opposite to O6MG, misreading the resulting O6MG:T complex as an A:T base pair due to their analogous binding energies and structural alignments. It is further revealed that AGT mediated nucleotide flipping occurs in two successive steps. The intercalation of the finger residue Arg 128 into the DNA double helix and its interaction with the O6MG: C base pair followed by rotation of the O6MG nucleotide are found to be crucial for the damage recognition and nucleotide flipping.

Analysis of shear bands in slow granular flows using a frictional Cosserat model

The slow flow of granular materials is often marked by the existence of narrow shear layers, adjacent to large regions that suffer little or no deformation. This behaviour, in the regime where shear stress is generated primarily by the frictional interactions between grains, has so far eluded theoretical description. In this paper, we present a rigid-plastic frictional Cosserat model that captures thin shear layers by incorporating a microscopic length scale. We treat the granular medium as a Cosserat continuum, which allows the existence of localised couple stresses and, therefore, the possibility of an asymmetric stress tensor. In addition, the local rotation is an independent field variable and is not necessarily equal to the vorticity. The angular momentum balance, which is implicitly satisfied for a classical continuum, must now be solved in conjunction with the linear momentum balances. We extend the critical state model, used in soil plasticity, for a Cosserat continuum and obtain predictions for flow in plane and cylindrical Couette devices. The velocity profile predicted by our model is in qualitative agreement with available experimental data. In addition, our model can predict scaling laws for the shear layer thickness as a function of the Couette gap, which must be verified in future experiments. Most significantly, our model can determine the velocity field in viscometric flows, which classical plasticity-based model cannot.

Full Sphere Axisymmetric Simulations of the Solar Dynamo

We explore a full sphere (2D axisymmetric) kinematic solar dynamo model based on the Babcock-Leighton idea that the poloidal field is generated in the surface layers from the decay of tilted bipolar solar active regions. This model incorporates the helioseismically deduced solar rotation profile and an algorithm for buoyancy motivated from simulations of flux tube dynamics. A prescribed deep meridional circulation plays an important role in the advection of magnetic flux. We specifically address the parity issue and show that – contrary to some recent claims – the Babcock-Leighton dynamo can reproduce solar-like dipolar parity if certain reasonable conditions are satisfied in the solar interior, the most important requirement being that the poloidal field of the two hemispheres be efficiently coupled across the equator.

Cloning, expression, purification and preliminary X-ray diffraction studies of a putative Mycobacterium smegmatis thiolase

Thiolases are important in fatty-acid degradation and biosynthetic pathways. Analysis of the genomic sequence of Mycobacterium smegmatis suggests the presence of several putative thiolase genes. One of these genes appears to code for an SCP-x protein. Human SCP-x consists of an N-terminal domain (referred to as SCP2 thiolase) and a C-terminal domain (referred as sterol carrier protein 2). Here, the cloning, expression, purification and crystallization of this putative SCP-x protein from M. smegmatis are reported. The crystals diffracted X-rays to 2.5 angstrom resolution and belonged to the triclinic space group P1. Calculation of rotation functions using X-ray diffraction data suggests that the protein is likely to possess a hexameric oligomerization with 32 symmetry which has not been observed in the other six known classes of this enzyme.

Dynamics of bound dyes in a nonpolymeric aqueous gel derived from a tripodal bile salt

Rotational dynamics of polarity sensitive fluorescent dyes (ANS and DPH) in a nonpolymertic aqueous gel derived from tripodal cholamide I was studied using ultrafast time-resolved fluorescence technique. Results were compared with that of naturally occurring di- and trihydroxy bile salts. ANS in the gel showed two rotational correlation time (phi) components, 13.2 ns (bound to the hydrophobic region of the gel) and 1.0 ns (free aqueous ANS), whereas DPH showed only one component (4.8 ns). In the sol state, faster rotational motion was observed, both for ANS and DPH. Our data revealed that dyes get encapsulated more tightly in the gel network when compared to the micellar aggregates. ANS has more restrained rotation compared to DPH. This was attributed to the interaction of the sulfonate group of ANS with water molecules and hydrophilic parts of the gelator molecule. No restricted rotation was observed for DPH in the gel state unlike when it is in the gel phase of lipid bilayer.

Theoretical determination of HI vertical scale heights in the dwarf galaxies DDO 154, Ho II, IC 2574 and NGC 2366

In this paper, we model dwarf galaxies as a two-component system of gravitationally coupled stars and atomic hydrogen gas in the external force field of a pseudo-isothermal dark matter halo, and numerically obtain the radial distribution of HI vertical scale heights. This is done for a group of four dwarf galaxies (DDO 154, Ho II, IC 2574 and NGC 2366) for which most necessary input parameters are available from observations. The formulation of the equations takes into account the rising rotation curves generally observed in dwarf galaxies. The inclusion of self-gravity of the gas into the model at par with that of the stars results in scale heights that are smaller than what was obtained by previous authors. This is important as the gas scale height is often used for deriving other physical quantities. The inclusion of gas self-gravity is particularly relevant in the case of dwarf galaxies where the gas cannot be considered a minor perturbation to the mass distribution of the stars. We find that three out of four galaxies studied show a flaring of their HI discs with increasing radius, by a factor of a few within several disc scale lengths. The fourth galaxy has a thick HI disc throughout. This flaring arises as a result of the gas velocity dispersion remaining constant or decreasing only slightly while the disc mass distribution declines exponentially as a function of radius.

Finite Signal-set Capacity of Two-user Gaussian Multiple Access Channel

The capacity region of a two-user Gaussian Multiple Access Channel (GMAC) with complex finite input alphabets and continuous output alphabet is studied. When both the users are equipped with the same code alphabet, it is shown that, rotation of one of the user’s alphabets by an appropriate angle can make the new pair of alphabets not only uniquely decodable, but will result in enlargement of the capacity region. For this set-up, we identify the primary problem to be finding appropriate angle(s) of rotation between the alphabets such that the capacity region is maximally enlarged. It is shown that the angle of rotation which provides maximum enlargement of the capacity region also minimizes the union bound on the probability of error of the sumalphabet and vice-verse. The optimum angle(s) of rotation varies with the SNR. Through simulations, optimal angle(s) of rotation that gives maximum enlargement of the capacity region of GMAC with some well known alphabets such as M-QAM and M-PSK for some M are presented for several values of SNR. It is shown that for large number of points in the alphabets, capacity gains due to rotations progressively reduce. As the number of points N tends to infinity, our results match the results in the literature wherein the capacity region of the Gaussian code alphabet doesn’t change with rotation for any SNR.

Micro stepping of Shape Memory Alloy based Poly Phase motor

In literature we find broadly two types of shape memory alloy based motors namely limited rotation motor and unlimited rotation motor. The unlimited rotation type SMA based motor reported in literature uses SMA springs for actuation. An attempt has been made in this paper to develop an unlimited rotation type balanced poly phase motor based on SMA wire in series with a spring in each phase. By isolating SMA actuation and spring action we are able achieve a constant force by the SMA wire through out its range of operation. The Poly phase motor can be used in stepping mode for generating incremental motion and servo mode for generating continuous motion. A method of achieving servo motion by micro stepping is presented. Micro stepping consists of controlling single-phase temperature with a position feedback. The motor has been modeled with a new approach to the SMA wire Hysterysis model. Motor is simulated for different responses and the results are compared with the experimental data.

Dark Matter Halo Properties as Deduced from the Observed H I Scale Height Data, in The Low-Frequency Radio Universe

We use the HΙ scale height data along with the HΙ rotation curve as constraints to probe the shape and density profile of the dark matter halos of M31 (Andromeda) and the superthin, low surface brightness (LSB) galaxy UGC 07321. We model the galaxy as a two component system of gravitationally-coupled stars and gas subjected to the force field of a dark matter halo. For M31, we get a flattened halo which is required to match the outer galactic HΙ scale height data, with our best-fit axis ratio (0.4) lying at the most oblate end of the distributions obtained from cosmological simulations. For UGC 07321, our best-fit halo core radius is only slightly larger than the stellar disc scale length, indicating that the halo is important even at small radii in this LSB galaxy. The high value of the gas velocity dispersion required to match the scale height data can explain the low star-formation rate of this galaxy.

TeV scale implications of non commutative space time in laboratory frame with polarized beams

We analyze e(+)e(-) -> gamma gamma, e(-)gamma -> e(-)gamma and gamma gamma -> e(+)e(-) processes within the Seiberg-Witten expanded noncommutative scenario using polarized beams. With unpolarized beams the leading order effects of non commutativity starts from second order in non commutative(NC) parameter i.e. O(Theta(2)), while with polarized beams these corrections appear at first order (O(Theta')) in cross section. The corrections in Compton case can probe the magnetic component(Theta(B)) while in Pair production and Pair annihilation probe the electric component((Theta) over right arrow (E)) of NC parameter. We include the effects of earth rotation in our analysis. This study is done by investigating the effects of non commutativity on different time averaged cross section observables. The results which also depends on the position of the collider, can provide clear and distinct signatures of the model testable at the International Linear Collider(ILC).

A family of Runge-Kutta based explicit methods for rotational dynamics

The present paper develops a family of explicit algorithms for rotational dynamics and presents their comparison with several existing methods. For rotational motion the configuration space is a non-linear manifold, not a Euclidean vector space. As a consequence the rotation vector and its time derivatives correspond to different tangent spaces of rotation manifold at different time instants. This renders the usual integration algorithms for Euclidean space inapplicable for rotation. In the present algorithms this problem is circumvented by relating the equation of motion to a particular tangent space. It has been accomplished with the help of already existing relation between rotation increments which belongs to two different tangent spaces. The suggested method could in principle make any integration algorithm on Euclidean space, applicable to rotation. However, the present paper is restricted only within explicit Runge-Kutta enabled to handle rotation. The algorithms developed here are explicit and hence computationally cheaper than implicit methods. Moreover, they appear to have much higher local accuracy and hence accurate in predicting any constants of motion for reasonably longer time. The numerical results for solutions as well as constants of motion, indicate superior performance by most of our algorithms, when compared to some of the currently known algorithms, namely ALGO-C1, STW, LIEMID[EA], MCG, SUBCYC-M.

Tip Motion Control and Scanning of a Reorientable Micromanipulator With Axially Located Tip

Two-axis micromanipulators, whose tip orientation and position can be controlled in real time in the scanning plane, enable versatile probing systems for 2.5-D nanometrology. The key to achieve high-precision probing systems is to accurately control the interaction point of the manipulator tip when its orientation is changed. This paper presents the development of a probing system wherein the deviation in the end point due to large orientation changes is controlled to within 10 nm. To achieve this, a novel micromanipulator design is first proposed, wherein the end point of the tip is located on the axis of rotation. Next, the residual tip motion caused by fabrication error and actuation crosstalk is modeled and a systematic method to compensate it is presented. The manipulator is fabricated and the performance of the developed scheme to control tip position during orientation change is experimentally validated. Subsequently, the two-axis probing system is demonstrated to scan the full top surface of a micropipette down to a diameter of 300 nm.

Performance analysis for geometrical attack on digital image watermarking

We present a technique for irreversible watermarking approach robust to affine transform attacks in camera, biomedical and satellite images stored in the form of monochrome bitmap images. The watermarking approach is based on image normalisation in which both watermark embedding and extraction are carried out with respect to an image normalised to meet a set of predefined moment criteria. The normalisation procedure is invariant to affine transform attacks. The result of watermarking scheme is suitable for public watermarking applications, where the original image is not available for watermark extraction. Here, direct-sequence code division multiple access approach is used to embed multibit text information in DCT and DWT transform domains. The proposed watermarking schemes are robust against various types of attacks such as Gaussian noise, shearing, scaling, rotation, flipping, affine transform, signal processing and JPEG compression. Performance analysis results are measured using image processing metrics.