Molecular dynamics and principal components analysis of human telomeric quadruplex multimers.

Guanine-rich DNA repeat sequences located at the terminal ends of chromosomal DNA can fold in a sequence-dependent manner into G-quadruplex structures, notably the terminal 150–200 nucleotides at the 3' end, which occur as a single-stranded DNA overhang. The crystal structures of quadruplexes with two and four human telomeric repeats show an all-parallel-stranded topology that is readily capable of forming extended stacks of such quadruplex structures, with external TTA loops positioned to potentially interact with other macromolecules. This study reports on possible arrangements for these quadruplex dimers and tetramers, which can be formed from 8 or 16 telomeric DNA repeats, and on a methodology for modeling their interactions with small molecules. A series of computational methods including molecular dynamics, free energy calculations, and principal components analysis have been used to characterize the properties of these higher-order G-quadruplex dimers and tetramers with parallel-stranded topology. The results confirm the stability of the central G-tetrads, the individual quadruplexes, and the resulting multimers. Principal components analysis has been carried out to highlight the dominant motions in these G-quadruplex dimer and multimer structures. The TTA loop is the most flexible part of the model and the overall multimer quadruplex becoming more stable with the addition of further G-tetrads. The addition of a ligand to the model confirms the hypothesis that flat planar chromophores stabilize G-quadruplex structures by making them less flexible.

The triazatruxene derivative azatrux binds to the parallel form of the human telomeric G-quadruplex under molecular crowding conditions: Biophysical and molecular modeling studies

The present study has employed a combination of spectroscopic, calorimetric and computational methods to explore the binding of the three side-chained triazatruxene derivative, termed azatrux, to a human telomeric G-quadruplex sequence, under conditions of molecular crowding. The binding of azatrux to the tetramolecular parallel [d(TGGGGT)](4) quadruplex in the presence and absence of crowding conditions, was also characterized. The data indicate that azatrux binds in an end-stacking mode to the parallel G-quadruplex scaffold and highlights the key structural elements involved in the binding. The selectivity of azatrux for the human telomeric G-quadruplex relative to another biologically relevant G-quadruplex (c-Kit87up) and to duplex DNA was also investigated under molecular crowding conditions, showing that azatrux has good selectivity for the human telomeric G-quadruplex over the other investigated DNA structures. (C) 2011 Elsevier Masson SAS. All rights reserved.

Effect of alkali on methylene blue (CI Basic Blue 9) and other thiazine dyes

A detailed study of the action of alkali on methylene blue (Cl. Basic Blue 9) and other thiazine dyes was carried out through a combination of UV/visible spectroscopy, thin layer chromatography, mass and NMR spectrometry and computational methods. In 0.1 M aq alkali solution, methylene blue forms a highly coloured, lipophilic species that is mainly Bernthsen's methylene violet i.e. a hydrolysis decomposition product, this being contrary to the report of a red N-hydroxy methylene blue adduct. The nature of the heterocyclic nitrogen atom in C.I. Basic Blue 9 is discussed and it is concluded there is no basis for the proposal of nucleophile addition at this site of the dye. In contrast, other thiazine dyes are deprotonated by alkali to form their neutral, highly coloured, lipophilic conjugate base forms. (C) 2010 Elsevier Ltd. All rights reserved.

Molecular Dynamics of HIV1-Integrase in Complex with 93del - A Structural Perspective on the Mechanism of Inhibition

HIV1 integrase is an important target for the antiviral therapy. Guanine-rich quadruplex, such as 93del, have been shown to be potent inhibitors of this enzyme and thus representing a new class of antiviral agents. Although X-ray and NMR structures of HIV1 integrase and 93del have been reported, there is no structural information of the complex and the mechanism of inhibition still remains unexplored. A number of computational methods including automated protein-DNA docking and molecular dynamics simulation in explicit solvent were used to model the binding of 93del to HIV1 integrase. Analysis of the dynamic behaviour of the complex using principal components analysis and elastic network modelling techniques allow us to understand how the binding of 93del aptamer and its interactions with key residues affect the intrinsic motions of the catalytic loops by stabilising them in catalytically inactive conformations. Such insights into the structural mechanism of inhibition can aid in improving the design of anti-HIV aptamers.

Validated ligand binding sites in CCK receptors. Next step: Computer aided design of novel CCK ligands

Computer-aided drug design becomes an important part of G-protein coupled receptors (GPCR) drug discovery process that is applied for improving the efficiency of derivation and optimization of novel ligands. It represents the combination of methods that-use-structural information of a receptor binding site of known ligands to design new ligands. In this report, we give a brief description of ligand binding sites in cholecystokinin and gastrin receptors (CK1R and CCK2R) which were delineated using experimental and computational methods, and then, we show how the validated ligand binding sites can be used to design and improve novel ligands. The translation of the knowledge of ligand-binding sites of different GPCRs to computer-aided design of novel ligands is summarized.

Implementation and testing of Lanczos-based algorithms for Random-Phase Approximation eigenproblems

The treatment of the Random-Phase Approximation Hamiltonians, encountered in different frameworks, like time-dependent density functional theory or Bethe-Salpeter equation, is complicated by their non-Hermicity. Compared to their Hermitian Hamiltonian counterparts, computational methods for the treatment of non-Hermitian Hamiltonians are often less efficient and less stable, sometimes leading to the breakdown of the method. Recently [Gruning et al. Nano Lett. 8 (2009) 28201, we have identified that such Hamiltonians are usually pseudo-Hermitian. Exploiting this property, we have implemented an algorithm of the Lanczos type for Random-Phase Approximation Hamiltonians that benefits from the same stability and computational load as its Hermitian counterpart, and applied it to the study of the optical response of carbon nanotubes. We present here the related theoretical grounds and technical details, and study the performance of the algorithm for the calculation of the optical absorption of a molecule within the Bethe-Salpeter equation framework. (C) 2011 Elsevier B.V. All rights reserved.

Tip leakage flow and heat transfer on turbine blade tip and casing, Part 1: Effect of tip clearance height and rotation speed

Steady simulations were performed to investigate tip leakage flow and heat transfer characteristics on the rotor blade tip and casing in a single-stage gas turbine engine. A typical high-pressure gas turbine stage was modeled with a pressure ratio of 3.2. The predicted isentropic Mach number and adiabatic wall temperature on the casing showed good agreement with available experimental data under similar operating condition. The present numerical study focuses extensively on the effects of tip clearance heights and rotor rotational speeds on the blade tip and casing heat transfer characteristics. It was observed that the tip leakage flow structure is highly dependent on the height of the tip gap and the speed of the rotor. In all cases, the tip leakage flow was seen to separate and recirculate just around the corner of the pressure side of the blade tip. This region of re-circulating flow enlarges with increasing clearance heights. The separated leakage flow reattaches afterwards on the tip surface. Leakage flow reattachment was shown to enhance surface heat transfer at the tip. The interaction between tip leakage flow and secondary flows that is induced by the relative casing motion is found to significantly influence the blade tip and casing heat transfer distribution. A region of critical heat transfer exists on the casing near the blade tip leading edge and along the pressure-side edge for all the clearance heights that were investigated. At high rotation speed, the region of critical heat transfer tends to move towards the trailing edge due to the change in inflow angle.

Tip Leakage Flow and Heat Transfer on Turbine Stage Tip and Casing: Effect of Unsteady Stator-Rotor Interactions

Unsteady simulations were performed to investigate time dependent behaviors of the leakage flow structures and heat transfer on the rotor blade tip and casing in a single stage gas turbine engine. This paper mainly illustrates the unsteady nature of the leakage flow and heat transfer, particularly, that caused by the stator–rotor interactions. In order to obtain time-accurate results, the effects of varying the number of time steps, sub iterations, and the number of vane passing periods was firstly examined. The effect of tip clearance height and rotor speeds was also examined. The results showed periodic patterns of the tip leakage flow and heat transfer rate distribution for each vane passing. The relative position of the vane and vane trailing edge shock with respect to time alters the flow conditions in the rotor domain, and results in significant variations in the tip leakage flow structures and heat transfer rate distributions. It is observed that the trailing edge shock phenomenon results in a critical heat transfer region on the blade tip and casing. Consequently, the turbine blade tip and casing are subjected to large fluctuations of Nusselt number (about Nu = 2000 to 6000 and about Nu = 1000 to 10000, respectively) at a high frequency (coinciding with the rotor speed).

Kinetics of levoglucosan and formaldehyde formation during cellulose pyrolysis process

The mechanisms and kinetics studies of the formation of levoglucosan and formaldehyde from anhydroglucose radical have been carried out theoretically in this paper. The geometries and frequencies of all the stationary points are calculated at the B3LYP/6-31+G(D,P) level based on quantum mechanics, Six elementary reactions are found, and three global reactions are involved. The variational transition-state rate constants for the elementary reactions are calculated within 450-1500 K. The global rate constants for every pathway are evaluated from the sum of the individual elementary reaction rate constants. The first-order Arrhenius expressions for these six elementary reactions and the three pathways are suggested. By comparing with the experimental data, computational methods without tunneling correction give good description for Path1 (the formation of levoglucosan); while methods with tunneling correction (zero-curvature tunneling and small-curvature tunneling correction) give good results for Path2 (the first possibility for the formation of formaldehyde), all the test methods give similar results for Path3 (the second possibility for the formation of formaldehyde), all the modeling results for Path3 are in good agreement with the experimental data, verifying that it is the most possible way for the formation of formaldehyde during cellulose pyrolysis. © 2012 Elsevier Ltd. All rights reserved.

A Review of Wave Makers for 3D Numerical Simulations

Numerical methods have enabled the simulation of complex problems in off-shore and marine engineering. A significant challenge in these simulations is the creation of a realistic wave field. A good numerical tank requires wave creation and absorption of waves at various locations. Several numerical wavemakers with these capabilities have been presented in the past. This paper reviews four different wave-maker methods and discusses limitations, computational efficiency, requirements on the mesh and preprocessing and complexity of implementation.

Using Process Algebra to Model Radiation Induced Bystander Effects

Radiation induced bystander effects are secondary effects caused by the production of chemical signals by cells in response to radiation. We present a Bio-PEPA model which builds on previous modelling work in this field to predict: the surviving fraction of cells in response to radiation, the relative proportion of cell death caused by bystander signalling, the risk of non-lethal damage and the probability of observing bystander signalling for a given dose. This work provides the foundation for modelling bystander effects caused by biologically realistic dose distributions, with implications for cancer therapies.

A Molecular Mechanism for Sequential Activation of a G Protein-Coupled Receptor

Ligands targeting G protein-coupled receptors (GPCRs) are currently classified as either orthosteric, allosteric, or dualsteric/bitopic. Here, we introduce a new pharmacological concept for GPCR functional modulation: sequential receptor activation. A hallmark feature of this is a stepwise ligand binding mode with transient activation of a first receptor site followed by sustained activation of a second topographically distinct site. We identify 4-CMTB (2-(4-chlorophenyl)-3-methyl-N-(thiazol-2-yl)butanamide), previously classified as a pure allosteric agonist of the free fatty acid receptor 2, as the first sequential activator and corroborate its two-step activation in living cells by tracking integrated responses with innovative label-free biosensors that visualize multiple signaling inputs in real time. We validate this unique pharmacology with traditional cellular readouts, including mutational and pharmacological perturbations along with computational methods, and propose a kinetic model applicable to the analysis of sequential receptor activation. We envision this form of dynamic agonism as a common principle of nature to spatiotemporally encode cellular information.

Electron-impact excitation of open d-shell ions

Astrophysics is driven by observations, and in the present era there are a wealth of state-of-the-art ground-based and satellite facilities. The astrophysical spectra emerging from these are of exceptional quality and quantity and cover a broad wavelength range. To meaningfully interpret these spectra, astronomers employ highly complex modelling codes to simulate the astrophysical observations. Important input to these codes include atomic data such as excitation rates, photoionization cross sections, oscillator strengths, transition probabilities and energy levels/line wavelengths. Due to the relatively low temperatures associated with many astrophysical plasmas, the accurate determination of electron-impact excitation rates in the low energy region is essential in generating a reliable spectral synthesis. Hence it is these atomic data, and the main computational methods used to evaluate them, which we focus on in this publication. We consider in particular the complicated open d- shell structures of the Fe-peak ions in low ionization stages. While some of these data can be obtained experimentally, they are usually of insufficient accuracy or limited to a small number of transitions.