Molecular Dynamics Study of the Opening Mechanism for DNA Polymerase I

During DNA replication, DNA polymerases follow an induced fit mechanism in order to rapidly distinguish between correct and incorrect dNTP substrates. The dynamics of this process are crucial to the overall effectiveness of catalysis. Although Xray crystal structures of DNA polymerase I with substrate dNTPs have revealed key structural states along the catalytic pathway, solution fluorescence studies indicate that those key states are populated in the absence of substrate. Herein, we report the first atomistic simulations showing the conformational changes between the closed, open, and ajar conformations of DNA polymerase I in the binary (enzyme:DNA) state to better understand its dynamics. We have applied long time-scale, unbiased molecular dynamics to investigate the opening process of the fingers domain in the absence of substrate for B. stearothermophilis DNA polymerase in silico. These simulations are biologically and/or physiologically relevant as they shed light on the transitions between states in this important enzyme. All closed and ajar simulations successfully transitioned into the fully open conformation, which is known to be the dominant binary enzyme-DNA conformation from solution and crystallographic studies. Furthermore, we have detailed the key stages in the opening process starting from the open and ajar crystal structures, including the observation of a previously unknown key intermediate structure. Four backbone dihedrals were identified as important during the opening process, and their movements provide insight into the recognition of dNTP substrate molecules by the polymerase binary state. In addition to revealing the opening mechanism, this study also demonstrates our ability to study biological events of DNA polymerase using current computational methods without biasing the dynamics

An ansatz for the exclusion statistics parameters in macroscopic physical systems described by fractional exclusion statistics

I introduce an ansatz for the exclusion statistics parameters of fractional exclusion statistics (FES) systems and I apply it to calculate the statistical distribution of particles from both, bosonic and fermionic perspectives. Then, to check the applicability of the ansatz, I calculate the FES parameters in three well-known models: in a Fermi liquid type of system, a one-dimensional quantum systems described in the thermodynamic Bethe ansatz and quasiparticle excitations in the fractional quantum Hall (FQH) systems. The FES parameters of the first two models satisfy the ansatz, whereas those of the third model, although close to the form given by the ansatz, represent an exception. With this ocasion I also show that the general properties of the FES parameters, deduced elsewhere (EPL 87, 60009, 2009), are satisfied also by the parameters of the FQH liquid.Comment: 6 pages, EPL styl

Electronic Collective Modes and Superconductivity in Layered Conductors

A distinctive feature of layered conductors is the presence of low-energy electronic collective modes of the conduction electrons. This affects the dynamic screening properties of the Coulomb interaction in a layered material. We study the consequences of the existence of these collective modes for superconductivity. General equations for the superconducting order parameter are derived within the strong-coupling phonon-plasmon scheme that account for the screened Coulomb interaction. Specifically, we calculate the superconducting critical temperature Tc taking into account the full temperature, frequency and wave-vector dependence of the dielectric function. We show that low-energy plasmons may contribute constructively to superconductivity. Three classes of layered superconductors are discussed within our model: metal-intercalated halide nitrides, layered organic materials and high-Tc oxides. In particular, we demonstrate that the plasmon contribution (electronic mechanism) is dominant in the first class of layered materials. The theory shows that the description of so-called ``quasi-two-dimensional superconductors'' cannot be reduced to a purely 2D model, as commonly assumed. While the transport properties are strongly anisotropic, it remains essential to take into account the screened interlayer Coulomb interaction to describe the superconducting state of layered materials.Comment: Final version (minor changes) 14 pages, 6 figure

Electronic structure of superconducting graphite intercalate compounds: The role of the interlayer state

Although not an intrinsic superconductor, it has been long--known that, when intercalated with certain dopants, graphite is capable of exhibiting superconductivity. Of the family of graphite--based materials which are known to superconduct, perhaps the most well--studied are the alkali metal--graphite intercalation compounds (GIC) and, of these, the most easily fabricated is the C${}_8$K system which exhibits a transition temperature $\bm{T_c\simeq 0.14}$K. By increasing the alkali metal concentration (through high pressure fabrication techniques), the transition temperature has been shown to increase to as much as $\bm 5$K in C${}_2$Na. Lately, in an important recent development, Weller \emph{et al.} have shown that, at ambient conditions, the intercalated compounds \cyb and \cca exhibit superconductivity with transition temperatures $\bm{T_c\simeq 6.5}$K and $\bm{11.5}$K respectively, in excess of that presently reported for other graphite--based compounds. We explore the architecture of the states near the Fermi level and identify characteristics of the electronic band structure generic to GICs. As expected, we find that charge transfer from the intercalant atoms to the graphene sheets results in the occupation of the $\bm\pi$--bands. Yet, remarkably, in all those -- and only those -- compounds that superconduct, we find that an interlayer state, which is well separated from the carbon sheets, also becomes occupied. We show that the energy of the interlayer band is controlled by a combination of its occupancy and the separation between the carbon layers.Comment: 4 Figures. Please see accompanying experimental manuscript "Superconductivity in the Intercalated Graphite Compounds C6Yb and C6Ca" by Weller et a

Real space imaging of the metal - insulator phase separation in the band width controlled organic Mott system κ\kappa-(BEDT-TTF)2_{2}Cu[N(CN)2_{2}]Br

Systematic investigation of the electronic phase separation on macroscopic scale is reported in the organic Mott system $\kappa$-(BEDT-TTF)$_{2}$Cu[N(CN)$_{2}$]Br. Real space imaging of the phase separation is obtained by means of scanning micro-region infrared spectroscopy using the synchrotron radiation. The phase separation appears near the Mott boundary and changes its metal-insulator fraction with the substitution ratio $x$ in $\kappa$-[($h$-BEDT-TTF)$_{1-x}$($d$-BEDT-TTF)$_{x}$]$_{2}$Cu[N(CN)$_{2}$]Br, of which band width is controlled by the substitution ratio $x$ between the hydrogenated BEDT-TTF molecule ($h$-BEDT-TTF) and the deuterated one ($d$-BEDT-TTF). The phase separation phenomenon observed in this class of organics is considered on the basis of the strongly correlated electronic phase diagram with the first order Mott transition.Comment: 10 pages, 8 figure

Neutron Scattering and the B_{1g} Phonon in the Cuprates

The momentum dependent lineshape of the out-of-phase oxygen vibration as measured in recent neutron scattering measurements is investigated. Starting from a microscopic coupling of the phonon vibration to a local crystal field, the phonon lineshift and broadening is calculated as a function of transfered momentum in the superconducting state of YBa$_{2}$Cu$_{3}$O$_{7}$. It is shown that the anisotropy of the density of states, superconducting energy gap, and the electron-phonon coupling are all crucial in order to explain these experiments.Comment: new figures and discussio

Progress in treatment by percutaneous coronary intervention: The stent of the future

First generation drug-eluting stents have considerably reduced in-stent restenosis and broadened the applications of percutaneous coronary interventions for the treatment of coronary artery disease. The polymer is an integral part of drug-eluting stents in that, it controls the release of an antiproliferative drug. The main safety concern of first generation drug-eluting stents with permanent polymers - stent thrombosis - has been caused by local hypersensitivity, delayed vessel healing, and endothelial dysfunction. This has prompted the development of newer generation drug-eluting stents with biodegradable polymers or even polymer-free drug-eluting stents. Recent clinical trials have shown the safety and efficacy of drug-eluting stents with biodegradable polymer, with proven reductions in very late stent thrombosis as compared to first generation drug-eluting stents. However, the concept of using a permanent metallic prosthesis implies major drawbacks, such as the presence of a foreign material within the native coronary artery that causes vascular inflammation and neoatherosclerosis, and also impedes the restoration of the vasomotor function of the stented segment. Bioresorbable scaffolds have been introduced to overcome these limitations, since they provide temporary scaffolding and then disappear, liberating the treated vessel from its cage. This update article presents the current status of these new technologies and highlights their future perspectives in interventional cardiology

Tree-Level Formalism

We review two novel techniques used to calculate tree-level scattering amplitudes efficiently: MHV diagrams, and on-shell recursion relations. For the MHV diagrams, we consider applications to tree-level amplitudes and focus in particular on the N=4 supersymmetric formulation. We also briefly describe the derivation of loop amplitudes using MHV diagrams. For the recursion relations, after presenting their general proof, we discuss several applications to massless theories with and without supersymmetry, to theories with massive particles, and to graviton amplitudes in General Relativity. This article is an invited review for a special issue of Journal of Physics A devoted to "Scattering Amplitudes in Gauge Theories".Comment: 40 pages, 8 figures, invited review for a special issue of Journal of Physics A devoted to "Scattering Amplitudes in Gauge Theories", R. Roiban(ed), M. Spradlin(ed), A. Volovich(ed); v2: minor corrections, references adde

Physical origin of the buckling in CuO2_2: Electron-phonon coupling and Raman spectra

It is shown theoretically that the buckling of the CuO$_{2}$ planes in certain cuprate systems can be explained in terms of an electric field across the planes which originates from different valences of atoms above and below the plane. This field results also in a strong coupling of the Raman-active out-of-phase vibration of the oxygen atoms ($B_{1g}$ mode) to the electronic charge transfer between the two oxygens in the CuO$_{2}$ plane. Consequently, the electric field can be deduced from the Fano-type line shape of the $B_{1g}$ phonon. Using the electric field estimated from the electron-phonon coupling the amplitude of the buckling is calculated and found to be in good agreement with the structural data. Direct experimental support for the idea proposed is obtained in studies of YBa$_{2}$Cu$_{3}$O$_{6+x}$ and Bi$_{2}$Sr$_{2}$(Ca$_{1-x}$Y$_{x}$)Cu$_{2}$O$_{8}$ with different oxygen and yttrium doping, respectively, including antiferromagnetic samples. In the latter compound, symmetry breaking by replacing Ca partially by Y leads to an enhancement of the electron-phonon coupling by an order of magnitude.Comment: 12 pages, 4 figures, and 1 tabl