Sequence specificity in spermine-induced structural changes in CG-oligomers

The role of spermine in inducing A-DNA conformation in deoxyoligonucleotides has been studied using CCGG and GGCC as model sequences. It has been found that while CCGG adopts an alternating B-DNA conformation in low salt solution at low temperature, addition of spermine to this medium induces a B --greater than A transition. In contrast, the A-DNA-like structure of GGCC in low salt solution at low temperature does not change under the influence of spermine. This suggests a sequence-dependent behaviour of spermine. Further these results suggest that the A-DNA conformation observed in the crystals of d(iCCGG) and d(GGCC)2 might have been due to the presence of spermine in the crystallization cocktail.

New a posteriori error estimator and adaptive mesh refinement strategy for 2-D crack problems

A posteriori error estimation and adaptive refinement technique for fracture analysis of 2-D/3-D crack problems is the state-of-the-art. The objective of the present paper is to propose a new a posteriori error estimator based on strain energy release rate (SERR) or stress intensity factor (SIF) at the crack tip region and to use this along with the stress based error estimator available in the literature for the region away from the crack tip. The proposed a posteriori error estimator is called the K-S error estimator. Further, an adaptive mesh refinement (h-) strategy which can be used with K-S error estimator has been proposed for fracture analysis of 2-D crack problems. The performance of the proposed a posteriori error estimator and the h-adaptive refinement strategy have been demonstrated by employing the 4-noded, 8-noded and 9-noded plane stress finite elements. The proposed error estimator together with the h-adaptive refinement strategy will facilitate automation of fracture analysis process to provide reliable solutions.

An Application of 3-D Kinematical Conservation Laws: Propagation of a 3-D Wavefront

Three-dimensional (3-D) kinematical conservation laws (KCL) are equations of evolution of a propagating surface Omega(t) in three space dimensions. We start with a brief review of the 3-D KCL system and mention some of its properties relevant to this paper. The 3-D KCL, a system of six conservation laws, is an underdetermined system to which we add an energy transport equation for a small amplitude 3-D nonlinear wavefront propagating in a polytropic gas in a uniform state and at rest. We call the enlarged system of 3-D KCL with the energy transport equation equations of weakly nonlinear ray theory (WNLRT). We highlight some interesting properties of the eigenstructure of the equations of WNLRT, but the main aim of this paper is to test the numerical efficacy of this system of seven conservation laws. We take several initial shapes for a nonlinear wavefront with a suitable amplitude distribution on it and let it evolve according to the 3-D WNLRT. The 3-D WNLRT is a weakly hyperbolic 7 x 7 system that is highly nonlinear. Here we use the staggered Lax-Friedrichs and Nessyahu-Tadmor central schemes and have obtained some very interesting shapes of the wavefronts. We find the 3-D KCL to be suitable for solving many complex problems for which there presently seems to be no other method capable of giving such physically realistic features.

Sequence specificity of Z-DNA formation in oligonucleotides

The sequence specific requirement for B----Z transition in solution was examined in d(CGTGCGCACG), d(CGTACGTACG), d(ACGTACGT) in presence of various Z-inducing factors. Conformational studies show that inspite of the alternating nature of purines and pyrimidines, the aforementioned sequences do not undergo B----Z transition under the influence of NaCl, hexamine cobalt chloride and ethanol. A comparison with the crystal structures of an assorted array of purine and pyrimidine sequences show that the sequence requirement for B----Z transition is much more stringent in solution as compared to the solid state. The disruptive influence of AT base pairs in B to Z transition is discussed.

Fin de millénaire eli maailmanlopun satiiri : Frédéric Beigbederin Au secours pardon, Marie Darrieussecqin Truismes ja Michel Houellebecqin La Possibilité d'une île

Pro gradu -työni käsittelee ranskalaisen nykykirjallisuuden yhteiskunnallista suuntausta, jota kirjallisuudentutkija Ruth Cruickshank kutsuu fin de millénaire -kirjallisuudeksi. Tutkimani teokset ovat Frédéric Beigbederin Au secours pardon (2007), Marie Darrieussecqin Truismes (1996) ja Michel Houellebecqin La Possibilité d'une île (2005). Pohdin, millaisena ja millaisin keinoin teokset kuvaavat seksuaalisuutta ja sen tulevaisuudennäkymiä kulutusyhteiskunnassa, ja millaisiin yhteiskunnallisiin olosuhteisiin niiden havainnot perustuvat. Hahmottelen reittejä, joita pitkin globaalin mittakaavan yhteiskunnalliset muutokset vaikuttavat ihmisten intiimeihin tunteisiin ja ihmissuhteisiin. Seksuaalisuuden tarkastelun avulla osoitan, että ranskalaisessa nykykirjallisuudessa ilmenee varsin yhteneviä näkemyksiä ja uhkakuvia aikamme sosiaalisesta todellisuudesta. Tällä tavoin tarkennan ja vankennan vielä hajanaista fin de millénaire -käsitettä. Fin de millénaire -kirjallisuuden oma lajityyppi on massakulttuurin, esimerkiksi viihteen ja mainosten, kielestä vaikutteita ammentava dystopian ja satiirin liitto. Kuten Cruickshank kirjoittaa, fin de millénaire -kirjallisuus heijastaa Ranskassa vuosituhannen vaihteessa korostunutta tunnetta käännekohtaan saapumisesta. Dystopian ohella voidaankin puhua myös apokalyptisesta tekstistä, etenkin siksi, että teokset tarjoavat niukasti ratkaisuja kuvaamiinsa ongelmiin. Eritoten Houellebecqin ja Beigbederin teokset käsittelevät tarpeiden luomista kuluttajille seksuaalivietin ja seksuaalisen kilpailun avulla. Kutsun tätä järjestelmää halutaloudeksi, ja käytän sen toiminnan analysoimisessa apuna Michel Foucault'n käsityksiä vallasta ja Jean Baudrillardin käsityksiä kulutusyhteiskunnasta. Halutalouden sosiaalisia seurauksia ovat vieraantuminen, seksuaalisten hierarkioiden jyrkentyminen ja valinnanvapauden kaventuminen. Teosten kuvaamassa yhteiskunnassa erilaiset esimerkiksi sukupuolen, iän ja ulkonäön perusteella rakentuvat seksuaaliset hierarkiat käyvät yhä merkittävämmiksi. Au secours pardon ja La Possibilité d'une île kuvaavat tapahtumaketjua, jossa etenkin heteromiehistä yhä useampi luisuu seksuaaliseen kurjuuteen muun muassa naisten emansipaation sekä yleisen nuoruuden ja kauneuden palvonnan myötä. Truismesissa taas kuvitellaan yhteiskunta, johon feminismi ei ole päässyt vaikuttamaan mutta pornoistuminen on; naisten ruumiista on tullut miesten yhteistä omaisuutta ja seksuaalinen väkivalta on arkipäivää. Sen maailmassa viehättävä ulkonäkö on naisille miltei elinehto. Yleistäen Houellebecqin ja Beigbederin teokset edustavat miesnäkökulmaa ja Darrieussecqin teos naisnäkökulmaa. Teosten näkemyksiä naisten ja miesten välisistä valtasuhteista pohdin naisten seksuaalisesta vallasta kirjoittaneen Henry Laasasen käyttökelpoisten käsitteiden avulla. Kolmea teosta yhdistävät kuvaukset kulttuurista, jossa ihmissuhteet ovat kaupankäyntiä ja seksuaalinen viehätysvoima määrittelee ihmisen arvon. Darrieussecqin teos on lähitulevaisuuteen sijoittuva dystopia, jossa Beigbederin ja Houellebecqin kuvaama arvoliberalismia ja taloudellista liberalismia yhdistävä kulttuuri on vaihtunut uuskonservatiiviseen ja kaksinaismoralistiseen, naisia räikeästi sortavaan yhteiskuntaan. Teoksen kertoja vähättelee itseensä kohdistuvia koskemattomuuden loukkauksia ja pahoittelee kertomuksensa käänteiden säädyttömyyttä varsinkin kuvatessaan omaa haluaan ja seksuaalista subjektiuttaan. Katson teoksen kritisoivan kirjallisuudentutkija Shirley Ann Jordanin termein poliittisen korrektiuden tyranniaa ja peräänkuuluttavan suoraa puhetta pornografiasta ja naisen halusta. Seksuaalisuus toimii tutkimuksessani lähtökohtana, jonka avulla teoksista nousee esiin julma ja rakkaudeton, säälimättömän kilpailun ja väkivallan täyttämä yhteiskunta. Viime kädessä teosten kuvaama maailmanloppu on se, että rakkaus katoaa ihmisten välisistä suhteista, koska rakkaudessa ei ole voiton tavoittelun kannalta mitään järkeä. Satiirin keinojen, kuten päättymättömän ja monikerroksisen ironian, yhdistyminen dystopiaan pelastaa teokset osoittelevalta moralisoinnilta ja tekee niistä toimivaa yhteiskunnallista kirjallisuutta.

Mechanism of interaction of O-amino-D-serine with sheep liver serine hydroxymethyltransferase

The mechanism of interaction of 0-amino-D-serine (OADS) with sheep liver serine hydroxymethyltransferase (EC 2.1.2.1) (SHMT) was established by measuring changes in the enzyme activity,absorption spectra, circular dichroism (CD) spectra, and stopped-flow spectrophotometry. OADS was a reversible noncompetitive inhibitor (Ki = 1.8 pM) when serine was the varied substrate. The first step in the interaction of OADS with the enzyme was the disruption of enzyme-Schiff base, characterized by the rapid disappearance of absorbance at 425 nm (6.5 X lo3 M-' s-') and CD intensity at 430 nm. Concomitantly,there was a rapid increase in absorbance and CD intensity at 390 nm. The spectral properties of this intermediate enabled its identification as pyridoxal 5'-phosphate (PLP). These changes were followed by a slow unimolecular step (2 X s-') leading to the formation of PLP-OADS oxime, which was confirmed by its absorbance and fluorescence spectra and retention time on high-performance liquid chromatography. The PLP-OADS oxime was displaced from the enzyme by the addition of PLP as evidenced by the restoration of complete enzyme activity as well as by the spectral properties. The unique feature of the mechanism proposed for the interaction of OADS with sheep liver SHMT was the formation of PLP as an intermediate.

Search on a hypercubic lattice using a quantum random walk. I. d > 2

Random walks describe diffusion processes, where movement at every time step is restricted to only the neighboring locations. We construct a quantum random walk algorithm, based on discretization of the Dirac evolution operator inspired by staggered lattice fermions. We use it to investigate the spatial search problem, that is, to find a marked vertex on a d-dimensional hypercubic lattice. The restriction on movement hardly matters for d > 2, and scaling behavior close to Grover's optimal algorithm (which has no restriction on movement) can be achieved. Using numerical simulations, we optimize the proportionality constants of the scaling behavior, and demonstrate the approach to that for Grover's algorithm (equivalent to the mean-field theory or the d -> infinity limit). In particular, the scaling behavior for d = 3 is only about 25% higher than the optimal d -> infinity value.

Search on a hypercubic lattice using a quantum random walk. II. d = 2

We investigate the spatial search problem on the two-dimensional square lattice, using the Dirac evolution operator discretized according to the staggered lattice fermion formalism. d = 2 is the critical dimension for the spatial search problem, where infrared divergence of the evolution operator leads to logarithmic factors in the scaling behavior. As a result, the construction used in our accompanying article A. Patel and M. A. Rahaman, Phys. Rev. A 82, 032330 (2010)] provides an O(root N ln N) algorithm, which is not optimal. The scaling behavior can be improved to O(root N ln N) by cleverly controlling the massless Dirac evolution operator by an ancilla qubit, as proposed by Tulsi Phys. Rev. A 78, 012310 (2008)]. We reinterpret the ancilla control as introduction of an effective mass at the marked vertex, and optimize the proportionality constants of the scaling behavior of the algorithm by numerically tuning the parameters.

An algorithm to find distant repeats in a pair of protein sequences

Distant repeats between a pair of protein sequences can be exploited to study the various aspects of proteins such as structure-function relationship, disorders due to protein malfunction, evolutionary analysis, etc. An in-depth analysis of the distant repeats would facilitate to establish a stable evolutionary relation of the repeats with respect to their three-dimensional structure. To this effect, an algorithm has been devised to identify the distant repeats in a pair of protein sequences by essentially using the scores of PAM (Percent Accepted Mutation) matrices. The proposed algorithm will be of much use to researchers involved in the comparative study of various organisms based on the amino-acid repeats in protein sequences. (C) 2010 Elsevier B.V. All rights reserved.

Eigenvalues of kinematical conservation laws (KCL) based 3-D weakly nonlinear ray theory (WNLRT)

System of kinematical conservation laws (KCL) govern evolution of a curve in a plane or a surface in space, even if the curve or the surface has singularities on it. In our recent publication K. R. Arun, P. Prasad, 3-D kinematical conservation laws (KCL): evolution of a surface in R-3-in particular propagation of a nonlinear wavefront, Wave Motion 46 (2009) 293-311] we have developed a mathematical theory to study the successive positions and geometry of a 3-D weakly nonlinear wavefront by adding an energy transport equation to KCL. The 7 x 7 system of equations of this KCL based 3-D weakly nonlinear ray theory (WNLRT) is quite complex and explicit expressions for its two nonzero eigenvalues could not be obtained before. In this short note, we use two different methods: (i) the equivalence of KCL and ray equations and (ii) the transformation of surface coordinates, to derive the same exact expressions for these eigenvalues. The explicit expressions for nonzero eigenvalues are important also for checking stability of any numerical scheme to solve 3-D WNLRT. (C) 2010 Elsevier Inc. All rights reserved.

Performance comparison of dynamical decoupling sequences for a qubit in a rapidly fluctuating spin bath

Avoiding the loss of coherence of quantum mechanical states is an important prerequisite for quantum information processing. Dynamical decoupling (DD) is one of the most effective experimental methods for maintaining coherence, especially when one can access only the qubit system and not its environment (bath). It involves the application of pulses to the system whose net effect is a reversal of the system-environment interaction. In any real system, however, the environment is not static, and therefore the reversal of the system-environment interaction becomes imperfect if the spacing between refocusing pulses becomes comparable to or longer than the correlation time of the environment. The efficiency of the refocusing improves therefore if the spacing between the pulses is reduced. Here, we quantify the efficiency of different DD sequences in preserving different quantum states. We use C-13 nuclear spins as qubits and an environment of H-1 nuclear spins as the environment, which couples to the qubit via magnetic dipole-dipole couplings. Strong dipole-dipole couplings between the proton spins result in a rapidly fluctuating environment with a correlation time of the order of 100 mu s. Our experimental results show that short delays between the pulses yield better performance if they are compared with the bath correlation time. However, as the pulse spacing becomes shorter than the bath correlation time, an optimum is reached. For even shorter delays, the pulse imperfections dominate over the decoherence losses and cause the quantum state to decay.