Molecular dynamics simulations on parallel and antiparallel C.G*G triplexes

Molecular dynamics (MD) studies have been carried out on the Hoogsteen hydrogen bonded parallel and the reverse Hoogsteen hydrogen banded antiparallel C.G*G triplexes. Earlier, the molecular mechanics studies had shown that the parallel structure was energetically more favourable than the antiparallel structure. To characterize the structural stability of the two triplexes and to investigate whether the antiparallel structure can transit to an energetically more favourable structure, due to the local fluctuations in the structure during the MD simulation, the two structures were subjected to 200ps of constant temperature vacuum MD simulations at 300K. Initially no constraints were applied to the structures and it was observed that for the antiparallel tripler, the structure showed a large root mean square deviation from the starting structure within the first 12ps and the N4-H41-O6 hydrogen bond in the WC duplex got distorted due to a high propeller twist and a moderate increase in the opening angle in the basepairs. Starting from an initial value of 30 degrees, helical twist of the average structure from this simulation had a value of 36 degrees, while the parallel structure stabilized at a twist of 33 degrees. In spite of the hydrogen bond distortions in the antiparallel tripler, it was energetically comparable to the parallel tripler. To examine the structural characteristics of an undistorted structure, another MD simulation was performed on the antiparallel tripler by constraining all the hydrogen bonds. This structure stabilized at an average twist of 33 degrees. In the course of the dynamics though the energy of the molecule - compared to the initial structure - improved, it did not become comparable to the parallel structure. Energy minimization studies performed in the presence of explicit water and counterions also showed the two structures to be equally favourable energetically Together these results indicate that the parallel C.G*G tripler with Hoogsteen hydrogen bonds also represents a stereochemically and energetically favourable structure for this class of triplexes.

E. C. G. Sudarshan and Symmetry in Classical Dynamics, Optics and Quantum Mechanics

We review work initiated and inspired by Sudarshan in relativistic dynamics, beam optics, partial coherence theory, Wigner distribution methods, multimode quantum optical squeezing, and geometric phases. The 1963 No Interaction Theorem using Dirac's instant form and particle World Line Conditions is recalled. Later attempts to overcome this result exploiting constrained Hamiltonian theory, reformulation of the World Line Conditions and extending Dirac's formalism, are reviewed. Dirac's front form leads to a formulation of Fourier Optics for the Maxwell field, determining the actions of First Order Systems (corresponding to matrices of Sp(2,R) and Sp(4,R)) on polarization in a consistent manner. These groups also help characterize properties and propagation of partially coherent Gaussian Schell Model beams, leading to invariant quality parameters and the new Twist phase. The higher dimensional groups Sp(2n,R) appear in the theory of Wigner distributions and in quantum optics. Elegant criteria for a Gaussian phase space function to be a Wigner distribution, expressions for multimode uncertainty principles and squeezing are described. In geometric phase theory we highlight the use of invariance properties that lead to a kinematical formulation and the important role of Bargmann invariants. Special features of these phases arising from unitary Lie group representations, and a new formulation based on the idea of Null Phase Curves, are presented.

Reversal of handedness in DNA: A stable link between RU and LZ helices

Two types of left-handed zig-zag (LZ) helices were obtained following stereochemical guideline. They are referred to as LZ1 and LZ2 helices. LZ1 helices have conformations similar to those found in the single crystals of d(C-G)3 and d(C-G)25,6. Z-character is more prominent in LZ2 than in LZ1 helix. The conformations of a stable link between RU and LZ helical fragments are given. The link involves inverted stacking arrangement of the bases: a characteristic feature of all RL models proposed by us

Strong gravity and the Yukawa field

A study of strong gravity field coupled to the Yukawa field is carried out for a conformally flat space-time. A quantitative relation between the strong interaction coupling constantg 2/hstrokc and the strong gravity constants (Lambda f~1028 cm–2,G f ~6.6×1030 C.G.S. units) is obtained givingg 2/hstroksim17, which is of the right order of magnitude. This justifies the contention that strong gravity is relevant for elementary particles (e.g., hadrons).

CsrA interacting small RNAs in Haemophilus spp genomes: a theoretical analysis

The csrA is a carbon storage regulator gene that encodes a protein with multiple RNA interaction sites. Bacterial non-coding small RNAs like csrB, csrC and their counterparts in diverse bacterial genus are identified to control the regulatory activities of CsrA and its orthologs. An attempt has been made in this study to identify 'novel' non-coding small RNAs that are involved in the regulatory activities of csrA gene. All CsrA-interacting small RNAs are computationally fingerprinted to have multiple occurrence of 7-nucleotide CsrA interacting repeats [CAGGA(U/A/C)G] along with a 18-nucleotide upstream binding site. However, in several of the genomes like Haemophilus spp, the upstream binding site is not identified. The current methodology overcomes this difficulty by identifying small RNA-specific orphan transcriptional units within the intergenic regions of the genome. The results could identify all known CsrA-interacting small RNAs in E. coli, Vibrio cholerae and Pseudomonas aeruginosa genomes and additionally has picked six new possible CsrA-interacting small RNA regions in E. coli. Our computational analysis indicates that known rygD and rprA sRNAs in E. coli could possibly interact with CsrA proteins. The study is extended to three of the Haemophilus genomes that could identify seven new possible CsrA interacting small RNAs.

Neural network approach for fault location in unbalanced distribution networks with limited measurements

This paper presents an Artificial Neural Network (ANN) approach for locating faults in distribution systems. Different from the traditional Fault Section Estimation methods, the proposed approach uses only limited measurements. Faults are located according to the impedances of their path using a Feed Forward Neural Networks (FFNN). Various practical situations in distribution systems, such as protective devices placed only at the substation, limited measurements available, various types of faults viz., three-phase, line (a, b, c) to ground, line to line (a-b, b-c, c-a) and line to line to ground (a-b-g, b-c-g, c-a-g) faults and a wide range of varying short circuit levels at substation, are considered for studies. A typical IEEE 34 bus practical distribution system with unbalanced loads and with three- and single- phase laterals and a 69 node test feeder with different configurations are considered for studies. The results presented show that the proposed approach of fault location gives close to accurate results in terms of the estimated fault location.

Sequence Independent Recombination Triple Helices: A Molecular Dynamics Study

Recent experimental studies have shown that the Rec-A mediated homologous recombination reaction involves a triple helical intermediate, in which the third strand base forms hydrogen bonds with both the bases in the major groove of the Watson-Crick duplex. Such 'mixed' hydrogen bonds allow formation of sequence independent triplexes. DNA triple helices involving 'mixed' hydrogen bonds have been studied, using model building, molecular mechanics (MM) and molecular dynamics (MD). Models were built for a tripler comprising all four possible triplets viz., G.C*C, C.G*G, A.T*T and T.A*A. To check the stability of all the 'mixed' hydrogen bonds in such triplexes and the conformational preferences of such tripler structures, MD studies were carried out starting from two structures with 30 degrees and 36 degrees twist between the basepairs. It was observed that though the two triplexes converged towards a similar structure, the various hydrogen bonds between the WC duplex and the third strand showed differential stabilities. An MD simulation with restrained hydrogen bonds showed that the resulting structure was stable and remained close to the starting structure. These studies help us in defining stable hydrogen bond geometries involving the third strand and the WC duplex. It was observed that in the C.G*G triplets the N7 atom of the second strand is always involved in hydrogen bonding. In the G.C*C triplets, either N3 or O2 in the third strand cytosine can interchangeably act as a hydrogen bond acceptor.

Molecular Mechanics Studies of Homopolymeric and Mixed Sequence Py.Pu*Pu Triple Helices,

DNA triple helices containing two purine strands and one pyrimidine strand (C.G*G and T.A*A) have been studied, using model building followed by energy minimisation, for different orientations of the third strand resulting from variation in the hydrogen bonding between the Watson-Crick duplex and the third strand and the glycosidic torsion angle in the third strand. Our results show that in the C.G*G case the structure with a parallel orientation of the third strand, resulting from Hoogsteen hydrogen bonds between the third strand and the Watson-Crick duplex, is energetically the most favourable while in the T.A*A case the antiparallel orientation of the third strand, resulting from reverse Hoogsteen hydrogen bonds, is energetically the most favourable. These studies when extended to the mixed sequence triplexes, in which the second strand is a mixture of G and A, correspondingly the third strand is a mixture of G and APT, show that though the parallel orientation is still energetically more favourable, the antiparallel orientation becomes energetically comparable with an increasing number of thymines in the third strand. Structurally, for the mixed triplexes containing G and T in the third strand, it is seen that the basepair non-isomorphism between the C.G*G and the T.A*T triplets can be overcome with some changes in the base pair parameters without much distortion of either the backbone or the hydrogen bonds.

V(2)O(5)-Anchored Carbon Nanotubes for Enhanced Electrochemical Energy Storage

Functionalized multiwalled carbon nanotubes (CNTs) are coated with a 4-5 nm thin layer of V(2)O(5) by controlled hydrolysis of vanadium alkoxide. The resulting V(2)O(5)/CNT composite has been investigated for electrochemical activity with lithium ion, and the capacity value shows both faradaic and capacitive (nonfaradaic) contributions. At high rate (1 C), the capacitive behavior dominates the intercalation as 2/3 of the overall capacity value out of 2700 C/g is capacitive, while the remaining is due to Li-ion intercalation. These numbers are in agreement with the Trasatti plots and are corroborated by X-ray photoelectron spectroscopy (XPS) studies on the V(2)O(5)/CNTs electrode, which show 85% of vanadium in the +4 oxidation state after the discharge at 1 C rate. The cumulative high-capacity value is attributed to the unique property of the nano V(2)O(5)/CNTs composite, which provides a short diffusion path for Lit-ions and an easy access to vanadium redox centers besides the high conductivity of CNTs. The composite architecture exhibits both high power density and high energy density, stressing the benefits of using carbon substrates to design high performance supercapacitor electrodes.

Wave propagation of phonon and phason displacement modes in quasicrystals: Determination of wave parameters

The paper presents the study of wave propagation in quasicrystals. Our interest is in the computation of the wavenumber (k(n)) and group speed (c(g)) of the phonon and phason displacement modes of one, two, and three dimensional quasicrystals. These wave parameter expressions are derived and computed using the elasto-hydrodynamic equations for quasicrystals. For the computation of the wavenumber and group speeds, we use Fourier transform approximation of the phonon and the phason displacement modes. The characteristic equations obtained are a polynomial equation of the wavenumber (k(n)), with frequency as a parameter. The corresponding group speeds (c(g)) for different frequencies are then computed from the wavenumber k(n). The variation of wavenumber and group speeds with frequency is plotted for the 1-D quasicrystal, 2-D decagonal Al-Ni-Co quasicrystals, and 3-D icosahedral Al-Pd-Mn and Zn-Mg-Sc quasicrystals. From the wavenumber and group speeds plots, we obtain the cut-off frequencies for different spatial wavenumber eta(m). The results show that for 1-D, 2-D, and 3-D quasicrystals, the phonon displacement modes are non-dispersive for low values of eta(m) and becomes dispersive for increasing values of eta(m). The cut-off frequencies are not observed for very low values of eta(m), whereas the cut-off frequency starts to appear with increasing eta(m). The group speeds of the phason displacement modes are orders of magnitude lower than that of the phonon displacement modes, showing that the phason modes do not propagate, and they are essentially the diffusive modes. The group speeds of the phason modes are also not influenced by eta(m). The group speeds for the 2-D quasicrystal at 35 kHz is also simulated numerically using Galerkin spectral finite element methods in frequency domain and is compared with the results obtained using wave propagation analysis. The effect of the phonon and phason elastic constants on the group speeds is studied using 3-D icosahedral Al-Pd-Mn and Zn-Mg-Sc quasicrystals. It is also shown that the phason elastic constants and the coupling coefficient do not affect the group speeds of the phonon displacement modes. (C) 2015 AIP Publishing LLC.

Biochemical Characterization of Nonamer Binding Domain of RAG1 Reveals its Thymine Preference with Respect to Length and Position

RAG complex consisting of RAG1 and RAG2 is a site-specific endonuclease responsible for the generation of antigen receptor diversity. It cleaves recombination signal sequence (RSS), comprising of conserved heptamer and nonamer. Nonamer binding domain (NBD) of RAG1 plays a central role in the recognition of RSS. To investigate the DNA binding properties of the domain, NBD of murine RAG1 was cloned, expressed and purified. Electrophoretic mobility shift assays showed that NBD binds with high affinity to nonamer in the context of 12/23 RSS or heteroduplex DNA. NBD binding was specific to thymines when single stranded DNA containing poly A, C, G or T were used. Biolayer interferometry studies showed that poly T binding to NBD was robust and comparable to that of 12RSS. More than 23 nt was essential for NBD binding at homothymidine stretches. On a double-stranded DNA, NBD could bind to A:T stretches, but not G:C or random sequences. Although NBD is indispensable for sequence specific activity of RAGs, external supplementation of purified nonamer binding domain to NBD deleted cRAG1/cRAG2 did not restore its activity, suggesting that the overall domain architecture of RAG1 is important. Therefore, we define the sequence requirements of NBD binding to DNA.