Chain folding and A:T pairing in human telomeric DNA: a model-building and molecular dynamics study

The various types of chain folding and possible intraloop as well as interloop base pairing in human telomeric DNA containing d(TTAG(3)) repeats have been investigated by model-building, molecular mechanics, and molecular dynamics techniques. Model-building and molecular mechanics studies indicate that it is possible to build a variety of energetically favorable folded-back structures with the two TTA loops on same side and the 5' end thymines in the two loops forming TATA tetrads involving a number of different intraloop as well as interloop A:T pairing schemes. In these folded-back structures, although both intraloop and interloop Watson-Crick pairing is feasible, no structure is possible with interloop Hoogsteen pairing. MD studies of representative structures indicate that the guanine-tetraplex stem is very rigid and, while the loop regions are relatively much more flexible, most of the hydrogen bonds remain intact throughout the 350-ps in vacuo simulation. The various possible TTA loop structures, although they are energetically similar, have characteristic inter proton distances, which could give rise to unique cross-peaks in two-dimensional nuclear Overhauser effect spectroscopy (NOESY) experiments. These folded-back structures with A:T pairings in the loop region help in rationalizing the data from chemical probing and other biochemical studies on human telomeric DNA.

Revised density of magnetized nuclear matter at the neutron drip line

We study the onset of the neutron drip in high-density matter in the presence of a magnetic field. It has been found that, for systems having only protons and electrons, in the presence of a magnetic field greater than or similar to 10(15) G, neutronization occurs at a density that is at least an order of magnitude higher compared to that in a nonmagnetic system. In a system with heavier ions, the effect of the magnetic field, however, starts arising at a much higher field, greater than or similar to 10(17) G. These results may have important implications for high-magnetic-field neutron stars and white dwarfs and, in general, in nuclear astrophysics when the system is embedded within a strong magnetic field.

The effect of radiation on the electron pairing in a multiband system

The possible occurrence of a generalized (1-wave) nonequilibrium superconducting state in a multiband system under certain conditions is studied. In the model the radiation field causes interband mixing, and phonons of an appropriate mode (branch) are involved in the interband scattering of electrons of two conduction bands of the system. The strength of the generalized 1-wave pairing interaction between quasiparticles belonging to new radiation admixed states depends on the density (n o/V) of quanta in the system. The coupling constant has the form Xl= AiB(n o/V)/[C + B(no/V)], where A1, B, and C are parameters. For C > B(n0/V), the transition temperature T1* increases with (no/V) in the initial stages. It levels off with higher power. With further increase of power, the transition temperature is expected to drop sharply due to heating effects which cause pair breaking. Estimates show that p-wave (triplet state) pairing may be possible under radiation-induced nonequilibrium situations in appropriate systems. Estimates for lifetimes of various processes quasiparticle, phonon, pair relaxation, and photon-induced mixing) show that the coherence required for the mixing and pairing effects will be maintained for the temperature range and photon density considered.

Hole Pairing In Antiferromagnetically Correlated Layered Oxides

We have considered a two-band Hubbard model having interlaced Cu-3d(x2−y2) and O-2p(x, y) orbitals representing the CuO2 square planes. Simple CuO2 -cluster calculation suggests that the additional holes created by doping stay mainly on oxygen. Motion of an oxygen hole interlacing with the antiferromagnetically correlated background of copper spins, creates a string of high energy spin configuration of finite length giving mass renormalization. Another hole of opposite spin can now anneal this string tension providing a triangular pairing potential for large pair momentum. The latter implies unusual Bose condensation of the wake-bound compact Bose-like pairs on a non-zero momentum shell. Effect of disorder favouring condensation at the mobility edge is pointed out.

Intra-band electron pairing in the presence of a radiation field

A semiconductor with almost overlapping conduction bands b and c is considered. It is found that an attractive interaction leading to superconductivity can be induced between electrons in the conduction band b by a strong radiation field of monochromatic photons whose energy differs slightly from the band gap Ebc. The mechanism is the exchange of a photon and a phonon between the interacting electrons and the interaction is found to be proportional to the photon density.

NMR relaxation study of disorder in condensed matter: solid solutions of betaine phosphate and phosphite

Proton NMR relaxation measurements have been carried out in anti-ferroelectric Betaine phosphate (BP), ferroelectric Betaine phosphite (BPI) and the mixed system BPI(1-x)BPx, at 11.4MHz and 23.3MHz from 300K to 80K for x=0.0, 0.25, 0.45, 0.85, and 1.0. The temperature dependence of spin lattice relaxation time T, exhibits two minima as expected from the BPP model in BP and BPI. The Larmor frequency dependence of T, in the mixed system is rather unusual and exhibits different slopes for the low temperature wings at the two frequencies, which is a clear experimental evidence of the presence of different methyl groups with different activation energies (E-a) indicating disorder.

Disulfide Bond Assignments by Mass Spectrometry of Native Natural Peptides: Cysteine Pairing in Disulfide Bonded Conotoxins

The critical, and often most difficult, step in structure elucidation of diverse classes of natural peptides is the determination of correct disulfide pairing between multiple cysteine residues. Here, we present a direct mass spectrometric analytical methodology for the determination of disulfide pairing. Protonated peptides, having multiple disulfide bonds, fragmented under collision induced dissociation (CID) conditions and preferentially cleave along the peptide backbone, with occasional disulfide fragmentation either by C-beta-S bond cleavage through H-alpha abstraction to yield dehydroalanine and cysteinepersulfide, or by S-S bond cleavage through H-beta abstraction to yield the thioaldehyde and cysteine. Further fragmentation of the initial set of product ions (MSn) yields third and fourth generation fragment ions, permitting a distinction between the various possible disulfide bonded structures. This approach is illustrated by establishing cysteine pairing patterns in five conotoxins containing two disulfide bonds. The methodology is extended to the Conus araneosus peptides An 446 and Ar1430, two 14 residue sequences containing 3 disulfide bonds. A distinction between 15 possible disulfide pairing schemes becomes possible using direct mass spectral fragmentation of the native peptides together with fragmentation of enzymatically nicked peptides.

Conformational Polymorphism in Telomeric Structures: Loop Orientation and Interloop Pairing in d(G4TnG4),

Sequence repeats constituting the telomeric regions of chromosomes are known to adopt a variety of unusual structures, consisting of a G tetraplex stem and short stretches of thymines or thymines and adenines forming loops over the stem. Detailed model building and molecular mechanics studies have been carried out for these telomeric sequences to elucidate different types of loop orientations and possible conformations of thymines in the loop. The model building studies indicate that a minimum of two thymines have to be interspersed between guanine stretches to form folded-back structures with loops across adjacent strands in a G tetraplex (both over the small as well as large groove), while the minimum number of thymines required to build a loop across the diagonal strands in a G tetraplex is three. For two repeat sequences, these hairpins, resulting from different types of folding, can dimerize in three distinct ways-i.e., with loops across adjacent strands and on same side, with loops across adjacent strands and on opposite sides, and with loops across diagonal strands and on opposite sides-to form hairpin dimer structures. Energy minimization studies indicate that all possible hairpin dimers have very similar total energy values, though different structures are stabilized by different types of interactions. When the two loops are on the same side, in the hairpin dimer structures of d(G(4)T(n)G(4)), the thymines form favorably stacked tetrads in the loop region and there is interloop hydrogen bonding involving two hydrogen bonds for each thymine-thymine pair. Our molecular mechanics calculations on various folded-back as well as parallel tetraplex structures of these telomeric sequences provide a theoretical rationale for the experimentally observed feature that the presence of intervening thymine stretches stabilizes folded-back structures, while isolated stretches of guanines adopt a parallel tetraplex structure

Violation of entropic Leggett-Garg inequality in nuclear spins

We report an experimental study of recently formulated entropic Leggett-Garg inequality (ELGI) by Usha Devi et al. Phys. Rev. A 87, 052103 (2013)]. This inequality places a bound on the statistical measurement outcomes of dynamical observables describing a macrorealistic system. Such a bound is not necessarily obeyed by quantum systems, and therefore provides an important way to distinguish quantumness from classical behavior. Here we study ELGI using a two-qubit nuclear magnetic resonance system. To perform the noninvasive measurements required for the ELGI study, we prepare the system qubit in a maximally mixed state as well as use the ``ideal negative result measurement'' procedure with the help of an ancilla qubit. The experimental results show a clear violation of ELGI by over four standard deviations. These results agree with the predictions of quantum theory. The violation of ELGI is attributed to the fact that certain joint probabilities are not legitimate in the quantum scenario, in the sense they do not reproduce all the marginal probabilities. Using a three-qubit system, we also demonstrate that three-time joint probabilities do not reproduce certain two-time marginal probabilities.

One Subject, Two Lands: My Journey in Condensed Matter Physics

This is an account of a professional life in the field that was generally known as solid-state physics when I started working in it; India and the United States of America are the countries in which this life was largely played out. My attempts to understand various things in condensed matter physics, and efforts to put together people and activities in India in this field, are mainly the story.

Hypernuclear matter in strong magnetic field

Compact stars with strong magnetic fields (magnetars) have been observationally determined to have surface magnetic fields of order of 10(14)-10(15) G, the implied internal field strength being several orders larger. We study the equation of state and composition of dense hypernuclear matter in strong magnetic fields in a range expected in the interiors of magnetars. Within the non-linear Boguta-Bodmer-Walecka model we find that the magnetic field has sizable influence on the properties of matter for central magnetic field B >= 10(17) G, in particular the matter properties become anisotropic. Moreover, for the central fields B >= 10(18) G, the magnetized hypernuclear matter shows instability, which is signalled by the negative sign of the derivative of the pressure parallel to the field with respect to the density, and leads to vanishing parallel pressure at the critical value B-cr congruent to 10(19) G. This limits the range of admissible homogeneously distributed fields in magnetars to fields below the critical value B-cr. (c) 2012 Elsevier B.V. All rights reserved.

Photon-Induced Electron Pairing

The earlier work on the possibility of interband electron pairing in the presence of a strong radiation field has been further extended. Some additional terms, neglected earlier, have been taken into account and generalized to a situation where the electron-phonon coupling coefficients for the two conduction bands (valleys) are different. It is found that the pairing interaction is attractive and the strength depends on the photon density.

Possibility of a condensed phase of excitons because of phonon induced exciton-exciton pairing

In this paper we study the phonon-induced exciton-exciton interaction. It is found that the interaction can be attractive under certain conditions. Taking into account this attractive interaction, the pairing of excitons with opposite momenta is studied and the excitation spectrum determined. The results are similar to a system of bosons. There appears to be some possibility of superfluid behaviour.

DNA-induced conformational changes in RecA protein. Evidence for structural heterogeneity among nucleoprotein filaments and implications for homologous pairing

We have used circular dichroism as a probe to characterize the solution conformational changes in RecA protein upon binding to DNA. This approach revealed that RecA protein acquires significant amounts of alpha-helix upon interaction with DNA. These observations, consistent with the data from crystal structure (Story, R. M., Weber, I., and Steitz, T. (1992) Nature 355, 318-325), support the notion that some basic domains including the DNA binding motifs of RecA protein are unstructured and might contribute to the formation of alpha-helix. A comparison of nucleoprotein filaments comprised of RecA protein and a variety of DNA substrates revealed important structural heterogeneity. The most significant difference was observed with poly(dG). poly(dC) and related polymers, rich in GC sequences, which induced minimal amounts of alpha-helix in RecA protein. The magnitude of induction of alpha-helix in RecA protein, which occurred concomitant with the production of ternary complexes, was 2-fold higher with homologous than heterologous duplex DNA. Most importantly, the stimulation of ATP hydrolysis by high salt coincided with that of the induction of alpha-helix in RecA protein. These conformational differences provide a basis for thinking about the biochemical and structural transitions that RecA protein experiences during the formal steps of presynapsis, recognition, and alignment of homologous sequences.