Downloads & Free Reading Options - Results

Project for High School Chemistry: groups were assigned a molecule to research and find its molecular shape and bond angles. I made sure each group got a different molecular shape. Then they spent a class period using TinkerCad doing tutorials. Then they built their model. Then I taught them VSEPR Theory and the molecular shapes. Then they presented their model to the class and explained how it was an example of one of the molecular shapes. So they basically built their own manipulatives.

Ab initio modeling of molecular electronics is nowadays routinely performed by combining the Density Functional Theory (DFT) and Nonequilibrium Green function (NEGF) techniques. This method has its roots in the current formula given by Meir and Wingreen, and we discuss some applications and accompanying pitfalls and restrictions of this approach. Quite recently papers have begun to appear where inelastic effects are considered, and we illustrate these new developments by describing our own work on transport in atomic gold wires.

x,165p. ; 24 cm

We present a first-principles method for calculating the charging energy of a molecular single-electron transistor operating in the Coulomb blockade regime. The properties of the molecule are modeled using density-functional theory, the environment is described by a continuum model, and the interaction between the molecule and the environment are included through the Poisson equation. The model is used to calculate the charge stability diagrams of a benzene and C$_{60}$ molecular single-electron transistor.

The main aim of this work is to improve the understanding of the mechanisms of adhesion of organosilanes on metal surfaces for the design of improved adhesion promoters/primers. Our approach is to conduct molecular simulations to determine binding energies of the various molecular structures and the influence of surface contaminants, on the interaction of organosilanes with metal oxides. The initial problems have been overcome and good progress has been made in the last few months. p1

This article is from International Journal of Molecular Sciences , volume 15 . Abstract Neuronal nitric oxide synthase (nNOS) plays an important role in neurotransmission and smooth muscle relaxation. Selective inhibition of nNOS over its other isozymes is highly desirable for the treatment of neurodegenerative diseases to avoid undesirable effects. In this study, we present a workflow for the identification and prioritization of compounds as potentially selective human nNOS inhibitors. Three-dimensional pharmacophore models were constructed based on a set of known nNOS inhibitors. The pharmacophore models were evaluated by Pareto surface and CoMFA (Comparative Molecular Field Analysis) analyses. The best pharmacophore model, which included 7 pharmacophore features, was used as a search query in the SPECS database (SPECS®, Delft, The Netherlands). The hit compounds were further filtered by scoring and docking. Ten hits were identified as potential selective nNOS inhibitors.

A concise presentation of molecular modelling and dynamics with examples of DNA structural models

A concise presentation of molecular modelling and dynamics with examples of DNA structural models

This is a review of molecular modelling techniques which may be applied to studies of energetic materials. It focuses on ab initio (first-principles') molecular orbital calculations, since these methods offer the greatest accuracy. Since ab initio calculations are very computer-intensive, approximate MO methods are also discussed, which offer reasonably accurate predictions with reduced calculation times. These approximate methods include density functional theory and layered' techniques which combine different levels of theoretical sophistication into one calculation.

The main aim of this work is to improve the understanding of the Molecular-level mechanism of adhesion of organosilanes on metal surfaces for the design of improved adhesion promoters/primers. Our approach will be to carry out molecular simulations to determine binding energies of the various molecular structures and the influence of surface contaminants, on the interaction of organosilanes with metal oxides. We will be using a variety of computer simulation methods incorporated in the Cerius(2) software. jg p1

The main aim of this work is to improve the understanding of the Molecular-level mechanism of adhesion of organosilanes on metal surfaces for the design of improved adhesion promoters/primers. Our approach will be to carry out molecular simulations to determine binding energies of the various molecular structures and the influence of surface contaminants, on the interaction of organosilanes with metal oxides. We will be using a variety of computer simulation methods incorporated in the Cerius(2) software. jg p1

The main aim of this work is to improve the understanding of the Molecular-level mechanism of adhesion of organosilanes on metal surfaces for the design of improved adhesion promoters/primers. Our approach will be to carry out molecular simulations to determine binding energies of the various molecular structures and the influence of surface contaminants, on the interaction of organosilanes with metal oxides. We will be using a variety of computer simulation methods incorporated in the Cerius(2) software. jg p1

The main aim of this work is to improve the understanding of the Molecular-level mechanism of adhesion of organosilanes on metal surfaces for the design of improved adhesion promoters/primers. Our approach will be to carry out molecular simulations to determine binding energies of the various molecular structures and the influence of surface contaminants, on the interaction of organosilanes with metal oxides. We will be using a variety of computer simulation methods incorporated in the Cerius(2) software. jg p1

The main aim of this work is to improve the understanding of the Molecular-level mechanism of adhesion of organosilanes on metal surfaces for the design of improved adhesion promoters/primers. Our approach will be to carry out molecular simulations to determine binding energies of the various molecular structures and the influence of surface contaminants, on the interaction of organosilanes with metal oxides. We will be using a variety of computer simulation methods incorporated in the Cerius(2) software. jg p1

In this paper, we combine the stellar spectral synthesis code STARBURST 99, the nebular modelling code MAPPINGS IIIq, a 1-D dynamical evolution model of \HII regions around massive clusters of young stars and a simplified model of synchrotron emissivity to produce purely theoretical self-consistent synthetic spectral energy distributions (SEDs) for (solar metallicity) starbursts lasting some $10^8$ years. These SEDs extend from the Lyman Limit to beyond 21 cm. We find that two ISM parameters control the form of the SED; the pressure in the diffuse phase of the ISM (or, equivalently, its density), and the molecular cloud dissipation timescale. We present detailed SED fits to Arp 220 and NGC 6240, and we give the predicted colors for starburst galaxies derived from our models for the IRAS and the Spitzer Space Observatory MIPS and IRAC instruments. Our models reproduce the spread in observed colors of starburst galaxies. Finally, we present absolute calibrations to convert observed fluxes into star formation rates in the UV (GALEX), at optical wavelengths (H$\alpha$), and in the IR (IRAS or the Spitzer Space Observatory). (Abstract Truncated)

The improved techniques of molecular graphics have triggered very fast advances in molecular modelling, be it concerned with structures or behaviour. Jean-Louis Rivail's proposal to devote our international meeting to molecular modelling was therefore approved practically without discussion. The way our conference went it had been a good choice. Crystal structures compelled very lengthy work, whereas nowadays one must select, because of its interest, a structure which will be determined very quickly. Conversely the field of chemical computation is still shared between some research on molecular reactivity that involve laborious number crunching , while the field of molecular modelling offers many subtle examples of software which can visualize simply enough the structures and behaviours of complex molecules.

The improved techniques of molecular graphics have triggered very fast advances in molecular modelling, be it concerned with structures or behaviour. Jean-Louis Rivail's proposal to devote our international meeting to molecular modelling was therefore approved practically without discussion. The way our conference went it had been a good choice. Crystal structures compelled very lengthy work, whereas nowadays one must select, because of its interest, a structure which will be determined very quickly. Conversely the field of chemical computation is still shared between some research on molecular reactivity that involve laborious number crunching , while the field of molecular modelling offers many subtle examples of software which can visualize simply enough the structures and behaviours of complex molecules.

This article is from International Journal of Molecular Sciences , volume 15 . Abstract The comprehensive understanding of the precise mode of action and/or adverse outcome pathway (MoA/AOP) of chemicals has become a key step toward the development of a new generation of predictive toxicology tools. One of the challenges of this process is to test the feasibility of the molecular modelling approaches to explore key molecular initiating events (MIE) within the integrated strategy of MoA/AOP characterisation. The description of MoAs leading to toxicity and liver damage has been the focus of much interest. Growing evidence underlines liver PPARγ ligand-dependent activation as a key MIE in the elicitation of liver steatosis. Synthetic PPARγ full agonists are of special concern, since they may trigger a number of adverse effects not observed with partial agonists. In this study, molecular modelling was performed based on the PPARγ complexes with full agonists extracted from the Protein Data Bank. The receptor binding pocket was analysed, and the specific ligand-receptor interactions were identified for the most active ligands. A pharmacophore model was derived, and the most important pharmacophore features were outlined and characterised in relation to their specific role for PPARγ activation. The results are useful for the characterisation of the chemical space of PPARγ full agonists and could facilitate the development of preliminary filtering rules for the effective virtual ligand screening of compounds with PPARγ full agonistic activity.

This article is from International Journal of Molecular Sciences , volume 15 . Abstract The comprehensive understanding of the precise mode of action and/or adverse outcome pathway (MoA/AOP) of chemicals has become a key step toward the development of a new generation of predictive toxicology tools. One of the challenges of this process is to test the feasibility of the molecular modelling approaches to explore key molecular initiating events (MIE) within the integrated strategy of MoA/AOP characterisation. The description of MoAs leading to toxicity and liver damage has been the focus of much interest. Growing evidence underlines liver PPARγ ligand-dependent activation as a key MIE in the elicitation of liver steatosis. Synthetic PPARγ full agonists are of special concern, since they may trigger a number of adverse effects not observed with partial agonists. In this study, molecular modelling was performed based on the PPARγ complexes with full agonists extracted from the Protein Data Bank. The receptor binding pocket was analysed, and the specific ligand-receptor interactions were identified for the most active ligands. A pharmacophore model was derived, and the most important pharmacophore features were outlined and characterised in relation to their specific role for PPARγ activation. The results are useful for the characterisation of the chemical space of PPARγ full agonists and could facilitate the development of preliminary filtering rules for the effective virtual ligand screening of compounds with PPARγ full agonistic activity.

This article is from International Journal of Molecular Sciences , volume 15 . Abstract The comprehensive understanding of the precise mode of action and/or adverse outcome pathway (MoA/AOP) of chemicals has become a key step toward the development of a new generation of predictive toxicology tools. One of the challenges of this process is to test the feasibility of the molecular modelling approaches to explore key molecular initiating events (MIE) within the integrated strategy of MoA/AOP characterisation. The description of MoAs leading to toxicity and liver damage has been the focus of much interest. Growing evidence underlines liver PPARγ ligand-dependent activation as a key MIE in the elicitation of liver steatosis. Synthetic PPARγ full agonists are of special concern, since they may trigger a number of adverse effects not observed with partial agonists. In this study, molecular modelling was performed based on the PPARγ complexes with full agonists extracted from the Protein Data Bank. The receptor binding pocket was analysed, and the specific ligand-receptor interactions were identified for the most active ligands. A pharmacophore model was derived, and the most important pharmacophore features were outlined and characterised in relation to their specific role for PPARγ activation. The results are useful for the characterisation of the chemical space of PPARγ full agonists and could facilitate the development of preliminary filtering rules for the effective virtual ligand screening of compounds with PPARγ full agonistic activity.

The evolution of star-forming core analogues undergoing inside-out collapse is studied with a multi-point chemodynamical model which self-consistently computes the abundance distribution of chemical species in the core. For several collapse periods the output chemistry of infall tracer species such as HCO+, CS, and N2H+, is then coupled to an accelerated Lambda-iteration radiative transfer code, which predicts the emerging molecular line profiles using two different input gas/dust temperature distributions. We investigate the sensitivity of the predicted spectral line profiles and line asymmetry ratios to the core temperature distribution, the time-dependent model chemistry, as well as to ad hoc abundance distributions. The line asymmetry is found to be strongly dependent on the adopted chemical abundance distribution. In general, models with a warm central region show higher values of blue asymmetry in optically thick HCO+ and CS lines than models with a starless core temperature profile. We find that in the formal context of Shu-type inside-out infall, and in the absence of rotation or outflows, the relative blue asymmetry of certain HCO+ and CS transitions is a function of time and, subject to the foregoing caveats, can act as a collapse chronometer. The sensitivity of simulated HCO+ line profiles to linear radial variations, subsonic or supersonic, of the internal turbulence field is investigated in the separate case of static cores.

The evolution of star-forming core analogues undergoing inside-out collapse is studied with a multi-point chemodynamical model which self-consistently computes the abundance distribution of chemical species in the core. For several collapse periods the output chemistry of infall tracer species such as HCO+, CS, and N2H+, is then coupled to an accelerated Lambda-iteration radiative transfer code, which predicts the emerging molecular line profiles using two different input gas/dust temperature distributions. We investigate the sensitivity of the predicted spectral line profiles and line asymmetry ratios to the core temperature distribution, the time-dependent model chemistry, as well as to ad hoc abundance distributions. The line asymmetry is found to be strongly dependent on the adopted chemical abundance distribution. In general, models with a warm central region show higher values of blue asymmetry in optically thick HCO+ and CS lines than models with a starless core temperature profile. We find that in the formal context of Shu-type inside-out infall, and in the absence of rotation or outflows, the relative blue asymmetry of certain HCO+ and CS transitions is a function of time and, subject to the foregoing caveats, can act as a collapse chronometer. The sensitivity of simulated HCO+ line profiles to linear radial variations, subsonic or supersonic, of the internal turbulence field is investigated in the separate case of static cores.

We perform molecular dynamics simulations of a typical nanoporous-carbon based supercapacitors. The organic electrolyte consists in 1-ethyl-3-methyl--imidazolium and hexafluorophosphate ions dissolved in acetonitrile. We simulate systems at equilibrium, for various applied voltages. This allows us to determine the relevant thermodynamic (capacitance) and transport (in-pore resistivities) properties. These quantities are then injected in a transmission line model for testing its ability to predict the charging properties of the device. The results from this macroscopic model are in good agreement with non-equilibrium molecular dynamics simulations, which validates its use for interpreting electrochemical impedance experiments.

Physical damping, regarding the nonlinear Navier-Stokes viscous flow dynamics, refers to a tensorial turbulent dissipation term, attributed to adjacent moving macroscopic flow components. Mutual dissipation among these parts of fluid is described by a braking term in the momentum equation together with a heating term in the energy equation, both responsible of the damping of the momentum variation and of the viscous conversion of mechanical energy into heat. A macroscopic mixing scale length is currently the only characteristic length needed in the nonlinear modelling of viscous fluid dynamics describing the nonlinear eddy viscosity through the kinematic viscosity coefficient in the viscous stress tensor, without any reference to the chemical composition and to the atomic dimensions. Therefore, in this paper, we write a new formulation for the kinematic viscosity coefficient to the turbulent viscous physical dissipation in the Navier-Stokes equations, where molecular parameters are also included. Results of 2D tests are shown, where comparisons among flow structures are made on 2D shockless radial viscous transport and on 2D damping of collisional chaotic turbulence. An application to the 3D accretion disc modelling in low mass cataclysmic variables is also discussed. Consequences of the kinematic viscosity coefficient reformulation in a more strictly physical terms on the thermal conductivity coefficient for dilute gases are also discussed. The physical nature of the discussion here reported excludes any dependence by the pure mathematical aspect of the numerical modelling.

This article is from BMC Evolutionary Biology , volume 14 . Abstract Background: In East Asia, an increasing number of studies on temperate forest tree species find evidence for migration and gene exchange across the East China Sea (ECS) land bridge up until the last glacial maximum (LGM). However, it is less clear when and how lineages diverged in this region, whether in full isolation or in the face of post-divergence gene flow. Here, we investigate the effects of Quaternary changes in climate and sea level on the evolutionary and demographic history of Platycrater arguta, a rare temperate understorey shrub with disjunct distributions in East China (var. sinensis) and South Japan (var. arguta). Molecular data were obtained from 14 P. arguta populations to infer current patterns of molecular structure and diversity in relation to past (Last Interglacial and Last Glacial Maximum) and present distributions based on ecological niche modelling (ENM). A coalescent-based isolation-with-migration (IM) model was used to estimate lineage divergence times and population demographic parameters. Results: Combining information from nuclear/chloroplast sequence data with nuclear microsatellites, our IM analyses identify the two varieties as genetically distinct units that evolved in strict allopatry since the mid-Pleistocene, c. 0.89 (0.51–1.2) Ma. Together with Bayesian Skyeline Plots, our data further suggest that both lineages experienced post-divergence demographic growth, followed by refugial isolation, divergence, and in the case of var. arguta post-glacial admixture. However, past species distribution modelling indicates that the species’ overall distribution has not greatly changed over the last glacial cycles. Conclusions: Our findings highlight the important influence of ancient sea-level changes on the diversification of East Asia’s temperate flora. Implicitly, they challenge the notion of general temperate forest expansion across the ECS land bridge, demonstrating instead its ‘filter’ effect owing to an unsuitable environment for certain species and their biological (e.g., recruitment) properties.

Dr. EMan Esmat -tanta university

The adhesion of a series of organosilanes, with varying lengths of alkyl chain, adsorbed on different metal-oxide substrates have been modelled using a computational molecular dynamics (MD) approach. The silanes modelled were: (a) the fully hydrolysed version of gamma- glycidoxypropyltrimethoxysilane (GPMS), (b) the fully hydrolysed version of gamma- glycidoxydecyltrimethoxysilane (GDMS), and (c) the fully hydrolysed version of gamma- glycidoxyeicosyltrimethoxysilane (GEMS). The substrates were corundum (alpha-Al2O3), an amorphous form of aluminium oxide (amorphous alumna, Al2O3) and haematite (Fe2O3).

The adhesion of a series of organosilanes, with varying lengths of alkyl chain, adsorbed on different metal-oxide substrates have been modelled using a computational molecular dynamics (MD) approach. The silanes modelled were: (a) the fully hydrolysed version of gamma- glycidoxypropyltrimethoxysilane (GPMS), (b) the fully hydrolysed version of gamma- glycidoxydecyltrimethoxysilane (GDMS), and (c) the fully hydrolysed version of gamma- glycidoxyeicosyltrimethoxysilane (GEMS). The substrates were corundum (alpha-Al2O3), an amorphous form of aluminium oxide (amorphous alumna, Al2O3) and haematite (Fe2O3).

Molecular modelling and simulation of the surface tension of fluids with force fields is discussed. 29 real fluids are studied, including nitrogen, oxygen, carbon dioxide, carbon monoxide, fluorine, chlorine, bromine, iodine, ethane, ethylene, acetylene, propyne, propylene, propadiene, carbon disulfide, sulfur hexafluoride, and many refrigerants. The fluids are represented by two-centre Lennard-Jones plus point quadrupole models from the literature. These models were adjusted only to experimental data of the vapour pressure and saturated liquid density so that the results for the surface tension are predictions. The deviations between the predictions and experimental data for the surface tension are of the order of 20 percent. The surface tension is usually overestimated by the models. For further improvements, data on the surface tension can be included in the model development. A suitable strategy for this is multi-criteria optimization based on Pareto sets. This is demonstrated using the model for carbon dioxide as an example.

viii, 196p. ; 23 cm

A main aim of the present work is to use computational molecular dynamics (MD) modelling to study the adsorption of both short- and long-chained organosilane primers on different types of metal oxides. Of particular interest will be the verification of the predictions from the modelling, wherever possible, using the existing experimental data to be found in the literature.

This article is from BMC Developmental Biology , volume 13 . Abstract Background: Cells in some tissues acquire a polarisation in the plane of the tissue in addition to apical-basal polarity. This polarisation is commonly known as planar cell polarity and has been found to be important in developmental processes, as planar polarity is required to define the in-plane tissue coordinate system at the cellular level. Results: We have built an in-silico functional model of cellular polarisation that includes cellular asymmetry, cell-cell signalling and a response to a global cue. The model has been validated and parameterised against domineering non-autonomous wing hair phenotypes in Drosophila. Conclusions: We have carried out a systematic comparison of in-silico polarity phenotypes with patterns observed in vivo under different genetic manipulations in the wing. This has allowed us to classify the specific functional roles of proteins involved in generating cell polarity, providing new hypotheses about their specific functions, in particular for Pk and Dsh. The predictions from the model allow direct assignment of functional roles of genes from genetic mosaic analysis of Drosophila wings.

This article is from BMC Developmental Biology , volume 13 . Abstract Background: Cells in some tissues acquire a polarisation in the plane of the tissue in addition to apical-basal polarity. This polarisation is commonly known as planar cell polarity and has been found to be important in developmental processes, as planar polarity is required to define the in-plane tissue coordinate system at the cellular level. Results: We have built an in-silico functional model of cellular polarisation that includes cellular asymmetry, cell-cell signalling and a response to a global cue. The model has been validated and parameterised against domineering non-autonomous wing hair phenotypes in Drosophila. Conclusions: We have carried out a systematic comparison of in-silico polarity phenotypes with patterns observed in vivo under different genetic manipulations in the wing. This has allowed us to classify the specific functional roles of proteins involved in generating cell polarity, providing new hypotheses about their specific functions, in particular for Pk and Dsh. The predictions from the model allow direct assignment of functional roles of genes from genetic mosaic analysis of Drosophila wings.

The work described here was carried out at the European Lab. for Non-Linear Spectroscopy (LENS) to achieve a better understanding of molecular vibrations employing computer simulations. H-bonds are the main intermolecular interactions affecting vibrational spectra and here it’s shown how they usually induce a (red or blue) shift on the vibrational frequencies of the groups engaged in them, and how this shift nicely correlates with structural properties. H-bonds can be present also in a bifurcated arrangement. In systems such as confined water, this bifurcated configuration has long lifetimes, allowing it to be studied by both spectroscopic and computational means. The computational protocols implemented and adopted here allow for a direct comparison between structural features and vibrational spectra.

We report on two recent advances in the modelling of viscoelastic polymers: (i) a new constitutive model which combines the virtual stick-slip continuum molecular-based ideas of Johnson and Stacer with the Rouse bead chain ideas; (ii) a two-dimensional version of a model that accounts for stenosis-driven shear wave propagation in biotissue.

We report on two recent advances in the modelling of viscoelastic polymers: (i) a new constitutive model which combines the virtual stick-slip continuum molecular-based ideas of Johnson and Stacer with the Rouse bead chain ideas; (ii) a two-dimensional version of a model that accounts for stenosis-driven shear wave propagation in biotissue.

This article is from International Journal of Molecular Sciences , volume 15 . Abstract Fevicordin-A (FevA) isolated from Phaleria macrocarpa (Scheff) Boerl. seeds was evaluated for its potential anticancer activity by in vitro and in silico approaches. Cytotoxicity studies indicated that FevA was selective against cell lines of human breast adenocarcinoma (MCF-7) with an IC50 value of 6.4 μM. At 11.2 μM, FevA resulted in 76.8% cell death of T-47D human breast cancer cell lines. Critical pharmacophore features amongst human Estrogen Receptor-α (hERα) antagonists were conserved in FevA with regard to a hypothesis that they could make notable contributions to its pharmacological activity. The binding stability as well as the dynamic behavior of FevA towards the hERα receptor in agonist and antagonist binding sites were probed using molecular dynamics (MD) simulation approach. Analysis of MD simulation suggested that the tail of FevA was accountable for the repulsion of the C-terminal of Helix-11 (H11) in both agonist and antagonist receptor forms. The flexibility of loop-534 indicated the ability to disrupt the hydrogen bond zipper network between H3 and H11 in hERα. In addition, MM/GBSA calculation from the molecular dynamic simulations also revealed a stronger binding affinity of FevA in antagonistic action as compared to that of agonistic action. Collectively, both the experimental and computational results indicated that FevA has potential as a candidate for an anticancer agent, which is worth promoting for further preclinical evaluation.

This article is from Organic and Medicinal Chemistry Letters , volume 2 . Abstract Background: The endocannabinoid system is involved in many physiological and pathological processes. Two receptors (cannabinoid receptor type 1 (CB1) and type 2 (CB2)) are known so far. Many unwanted psychotic side effects of inhibitors of this system can be addressed to the interaction with CB1. While CB1 is one of the most abundant neuroreceptors, CB2 is expressed in the brain only at very low levels. Thus, highly potent and selective compounds for CB2 are desired. N-aryl-((hetero)aromatic)-oxadiazolyl-propionamides represent a promising class of such selective ligands for the human CB2. Here, a library of various derivatives is studied for suitable routes for labelling with 18F. Such 18F-labelled compounds can then be employed as CB2-selective radiotracers for molecular imaging studies employing positron emission tomography (PET). Results: By varying the N-arylamide substructure, we explored the binding pocket of the human CB2 receptor and identified 9-ethyl-9H-carbazole amide as the group with optimal size. Radioligand replacement experiments revealed that the modification of the (hetero)aromatic moiety in 3-position of the 1,2,4-oxadiazoles shows only moderate impact on affinity to CB2 but high impact on selectivity towards CB2 with respect to CB1. Further, we could show by autoradiography studies that the most promising compounds bind selectively on CB2 receptors in mouse spleen tissue. Molecular docking studies based on a novel three-dimensional structural model of the human CB2 receptor in its activated form indicate that the compounds bind with the N-arylamide substructure in the binding pocket. 18F labelling at the (hetero)aromatic moiety at the opposite site of the compounds via radiochemistry was carried out. Conclusions: The synthesized CB2-selective compounds have high affinity towards CB2 and good selectivity against CB1. The introduction of labelling groups at the (hetero)aromatic moiety shows only moderate impact on CB2 affinity, indicating the introduction of potential labelling groups at this position as a promising approach to develop CB2-selective ligands suitable for molecular imaging with PET. The high affinity for human CB2 and selectivity against human CB1 of the herein presented compounds renders them as suitable candidates for molecular imaging studies.

Two peculiar stars showing an apparent extremely broadened and strong NaI D absorption have been discovered in surveys for cool white dwarfs by Oppenheimer et al. (2001) and Harris et al. (SDSS, 2003). We discuss the nature of these objects using PHOENIX atmosphere models for metal-poor brown dwarfs/very low mass stars, and new white dwarf LTE and NLTE models for hydrogen- and helium-dominated atmospheres with metals. These include complete molecular formation in chemical equilibrium and a model for the alkali resonance line broadening based on the damping profiles of Allard et al. (2003), as well as new molecular line opacities for metal hydrides. First results of our calculations indicate good agreement with a hydrogen-dominated WD atmosphere with a Na abundance roughly consistent with a state of high accretion. We analyse deviations of the abundances of Na, K, Mg and Ca from the cosmic pattern and comment on implications of these results for standard accretion scenarios.

The atmospheric structure of Mira variables is considerably influenced by pulsation. Molecular absorption lines in the near-infrared (NIR), especially second overtone CO lines, show therefore a characteristic behaviour in time-series of high-resolution spectra. We computed synthetic CO line profiles based on a new dynamic model atmosphere and derived radial velocities (RVs) from the Doppler shifted lines. For the first time, we could quantitatively reproduce observations of the very typical, discontinuous RV curves.

Edge Cloud 2 (EC2) is a molecular cloud, about 35 pc in size, with one of the largest galactocentric distances known to exist in the Milky Way. We present observations of a peak CO emission region in the cloud and use these to determine its physical characteristics. We calculate a gas temperature of 20 K and a density of n(H2) ~ 10^4 cm^-3. Based on our CO maps, we estimate the mass of EC2 at around 10^4 M_sun and continuum observations suggest a dust-to-gas mass ratio as low as 0.001. Chemical models have been developed to reproduce the abundances in EC2 and they indicate that: heavy element abundances may be reduced by a factor of five relative to the solar neighbourhood (similar to dwarf irregular galaxies and damped Lyman alpha systems); very low extinction (Av < 4 mag) due to a very low dust-to-gas ratio; an enhanced cosmic ray ionisation rate; and a higher UV field compared to local interstellar values. The reduced abundances may be attributed to the low level of star formation in this region and are probably also related to the continuing infall of primordial (or low metallicity) halo gas since the Milky Way formed. Finally, we note that shocks from the old supernova remnant GSH 138-01-94 may have determined the morphology and dynamics of EC2.

We present a dynamical model of DNA mechanical unzipping under the action of a force. The model includes the motion of the fork in the sequence-dependent landscape, the trap(s) acting on the bead(s), and the polymeric components of the molecular construction (unzipped single strands of DNA, and linkers). Different setups are considered to test the model, and the outcome of the simulations is compared to simpler dynamical models existing in the literature where polymers are assumed to be at equilibrium.

We present a dynamical model of DNA mechanical unzipping under the action of a force. The model includes the motion of the fork in the sequence-dependent landscape, the trap(s) acting on the bead(s), and the polymeric components of the molecular construction (unzipped single strands of DNA, and linkers). Different setups are considered to test the model, and the outcome of the simulations is compared to simpler dynamical models existing in the literature where polymers are assumed to be at equilibrium.

Advancement in science and technology has brought a remarkable change in the field of drug discovery. Earlier it was very difficult to predict the target for receptor but nowadays, it is easy and robust task to dock the target protein with ligand and binding affinity is calculated. Docking helps in the virtual screening of drug along with its hit identification. There are two approaches through which docking can be carried out, shape complementary and stimulation approach. There are many procedures involved in carrying out docking and all require different software's and algorithms. Molecular docking serves as a good platform to screen a large number of ligands and is useful in Drug-DNA studies. This review mainly focuses on the general idea of molecular docking and discusses its major applications, different types of interaction involved and types of docking. By Rishabh Jain "Review on Computational Bioinformatics and Molecular Modelling: Novel Tool for Drug Discovery" Published in International Journal of Trend in Scientific Research and Development (ijtsrd), ISSN: 2456-6470, Volume-3 | Issue-1 , December 2018, URL: http://www.ijtsrd.com/papers/ijtsrd18914.pdf Direct URL: http://www.ijtsrd.com/pharmacy/pharmacoinformatics/18914/review-on-computational-bioinformatics-and-molecular-modelling-novel-tool-for-drug-discovery/rishabh-jain international journals of computer science , call for paper engineering , indexed journal

We use detailed numerical simulations of the coupled chemical, thermal and dynamical evolution of the gas in a turbulent molecular cloud to study the usefulness of the [CI] 609 micron and 370 micron fine structure emission lines as tracers of cloud structure. Emission from these lines is observed throughout molecular clouds, and yet the question of what we can learn from them about the physics of the clouds remains largely unexplored. We show that the fact that [CI] emission is widespread within molecular clouds is a simple consequence of the fact that the clouds are dominated by turbulent motions. Turbulence creates large density inhomogeneities, allowing radiation to penetrate deeply into the clouds. As a result, [CI] emitting gas is found throughout the cloud, rather than being concentrated at the edges. We examine how well we can use [CI] emission to trace the structure of the cloud, and show that the integrated intensity of the 609 micron line traces column density accurately over a wide range of visual extinctions. For extinctions greater than a few, [CI] and 13CO both perform well, but [CI] becomes a superior tracer of column densities for visual extinctions A_V

Anthrax protective antigen (PA) is one of the three proteins produced by the gram positive bacteria Bacillus anthracis collectively known as the anthrax toxin. The role played by PA in anthrax intoxication is to transport the two enzymes lethal factor (LF) and edema factor (EF) into the cell. Collier and co-workers reported the isolation of two peptides via phage display that bind to the PA63 heptamer and inhibit its interaction with LF and EF, and thereby prevent the transport of LF and EF into the cell. One of these peptides was selected for structural investigation on the basis of its ability to prevent the binding of LF to the PA63 heptamer bundle. Two dimensional trNOESY experiments coupled with NOE restrained simulated annealing calculations were used to determine the PA63-bound conformation of P1. On binding to PA63, P1 adopts a helical conformation involving residues 3-9 while the C- and N-terminal residues exhibit dynamic fraying.

We present a model for describing the general structure of molecular clouds (MCs) at early evolutionary stages in terms of their mass-size relationship. Sizes are defined through threshold levels at which equipartitions between gravitational, turbulent and thermal energy $|W| \sim f(E_{\rm kin} + E_{\rm th})$ take place, adopting interdependent scaling relations of velocity dispersion and density and assuming a lognormal density distribution at each scale. Variations of the equipartition coefficient $1\le f\le 4$ allow for modelling of star-forming regions at scales within the size range of typical MCs ($\gtrsim$4 pc). Best fits are obtained for regions with low or no star formation (Pipe, Polaris) as well for such with star-forming activity but with nearly lognormal distribution of column density (Rosette). An additional numerical test of the model suggests its applicability to cloud evolutionary times prior to the formation of first stars.

S-type AGB stars have a C/O ratio which suggests that they are transition objects between oxygen-rich M-type stars and carbon-rich C-type stars. As such, their circumstellar compositions of gas and dust are thought to be sensitive to their precise C/O ratio, and it is therefore of particular interest to examine their circumstellar properties. We present new Herschel HIFI and PACS sub-millimetre and far-infrared line observations of several molecular species towards the S-type AGB star W Aql. We use these observations, which probe a wide range of gas temperatures, to constrain the circumstellar properties of W Aql, including mass-loss rate and molecular abundances. We used radiative transfer codes to model the circumstellar dust and molecular line emission to determine circumstellar properties and molecular abundances. We assumed a spherically symmetric envelope formed by a constant mass-loss rate driven by an accelerating wind. Our model includes fully integrated H2O line cooling as part of the solution of the energy balance. We detect circumstellar molecular lines from CO, H2O, SiO, HCN, and, for the first time in an S-type AGB star, NH3. The radiative transfer calculations result in an estimated mass-loss rate for W Aql of 4.0e-6 Msol yr-1 based on the 12CO lines. The estimated 12CO/13CO ratio is 29, which is in line with ratios previously derived for S-type AGB stars. We find an H2O abundance of 1.5e-5, which is intermediate to the abundances expected for M and C stars, and an ortho/para ratio for H2O that is consistent with formation at warm temperatures. We find an HCN abundance of 3e-6, and, although no CN lines are detected using HIFI, we are able to put some constraints on the abundance, 6e-6, and distribution of CN in W Aql's circumstellar envelope using ground-based data. We find an SiO abundance of 3e-6, and an NH3 abundance of 1.7e-5, confined to a small envelope.