995 research outputs found

    AutoClickChem: Click Chemistry in Silico

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    Academic researchers and many in industry often lack the financial resources available to scientists working in “big pharma.” High costs include those associated with high-throughput screening and chemical synthesis. In order to address these challenges, many researchers have in part turned to alternate methodologies. Virtual screening, for example, often substitutes for high-throughput screening, and click chemistry ensures that chemical synthesis is fast, cheap, and comparatively easy. Though both in silico screening and click chemistry seek to make drug discovery more feasible, it is not yet routine to couple these two methodologies. We here present a novel computer algorithm, called AutoClickChem, capable of performing many click-chemistry reactions in silico. AutoClickChem can be used to produce large combinatorial libraries of compound models for use in virtual screens. As the compounds of these libraries are constructed according to the reactions of click chemistry, they can be easily synthesized for subsequent testing in biochemical assays. Additionally, in silico modeling of click-chemistry products may prove useful in rational drug design and drug optimization. AutoClickChem is based on the pymolecule toolbox, a framework that may facilitate the development of future python-based programs that require the manipulation of molecular models. Both the pymolecule toolbox and AutoClickChem are released under the GNU General Public License version 3 and are available for download from http://autoclickchem.ucsd.edu

    Studying the effects of thalamic interneurons in a thalamocortical neural mass model

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    Neural mass models of the thalamocortical circuitry are often used to mimic brain activity during sleep and wakefulness as observed in scalp electroencephalogram (EEG) signals [1]. It is understood that alpha rhythms (8-13 Hz) dominate the EEG power-spectra in the resting-state [2] as well as the period immediately before sleep [3]. Literature review shows that the thalamic interneurons (IN) are often ignored in thalamocortical population models; the emphasis is on the connections between the thalamo cortical relay (TCR) and the thalamic reticular nucleus (TRN). In this work, we look into the effects of the IN cell population on the behaviour of an existing thalamocortical model containing the TCR and TRN cell populations [4]. A schematic of the extended model used in this work is shown in Fig.1. The model equations are solved in Matlab using the Runge-Kutta method of the 4th/5th order. The model shows high sensitivity to the forward and reverse rates of reactions during synaptic transmission as well as on the membrane conductance of the cell populations. The input to the model is a white noise signal simulating conditions of resting state with eyes closed, a condition well known to be associated with dominant alpha band oscillations in EEG e.g. [5]. Thus, the model parameters are calibrated to obtain a set of basal parameter values when the model oscillates with a dominant frequency within the alpha band. The time series plots and the power spectra of the model output are compared with those when the IN cell population is disconnected from the circuit (by setting the inhibitory connectivity parameter from the IN to the TCR to zero). We observe (Fig. 2 inset) a significant difference in time series output of the TRN cell population with and without the IN cell population in the model; this in spite of the IN having no direct connectivity to and from the TRN cell population (Fig. 1). A comparison of the power spectra behaviour of the model output within the delta (1-3.5Hz), theta (3.75-7.5Hz), alpha (7.75-13.5Hz) and beta (13.75-30.5Hz) bands is shown in Fig. 2. Disconnecting the IN cell population shows a significant drop in the alpha band power and the dominant frequency of oscillation now lies within the theta band. An overall ‘slowing’ (left-side shift) of the power spectra is observed with an increase within the delta and theta bands and a decrease in the alpha and beta bands. Such a slowing of EEG is a signature of slow wave sleep in healthy individuals, and this suggests that the IN cell population may be centrally involved in the phase transition to slow wave sleep [6]. It is also characteristic of the waking EEG in Alzheimer’s disease, and may help us to understand the role of the IN cell population in modulating TCR and TRN cell behaviour in pathological brain conditions

    Molecular dynamics simulations and drug discovery

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    This review discusses the many roles atomistic computer simulations of macromolecular (for example, protein) receptors and their associated small-molecule ligands can play in drug discovery, including the identification of cryptic or allosteric binding sites, the enhancement of traditional virtual-screening methodologies, and the direct prediction of small-molecule binding energies. The limitations of current simulation methodologies, including the high computational costs and approximations of molecular forces required, are also discussed. With constant improvements in both computer power and algorithm design, the future of computer-aided drug design is promising; molecular dynamics simulations are likely to play an increasingly important role

    Influence of climatic variables on crown condition in pine forests of Northern Spain

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    ProducciĂłn CientĂ­ficaThe aim of this study was to find relationships between crown condition and some climatic parameters to identify which are those having a main influence on crown condition, and how this influence is shown in the tree (crown transparency), and to contribute to the understanding of how these parameters will affect under future climate change scenarios

    Resonant nonlinear magneto-optical effects in atoms

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    In this article, we review the history, current status, physical mechanisms, experimental methods, and applications of nonlinear magneto-optical effects in atomic vapors. We begin by describing the pioneering work of Macaluso and Corbino over a century ago on linear magneto-optical effects (in which the properties of the medium do not depend on the light power) in the vicinity of atomic resonances, and contrast these effects with various nonlinear magneto-optical phenomena that have been studied both theoretically and experimentally since the late 1960s. In recent years, the field of nonlinear magneto-optics has experienced a revival of interest that has led to a number of developments, including the observation of ultra-narrow (1-Hz) magneto-optical resonances, applications in sensitive magnetometry, nonlinear magneto-optical tomography, and the possibility of a search for parity- and time-reversal-invariance violation in atoms.Comment: 51 pages, 23 figures, to appear in Rev. Mod. Phys. in Oct. 2002, Figure added, typos corrected, text edited for clarit

    Orientation dependent molecular electrostatics drives efficient charge generation in homojunction organic solar cells

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    Organic solar cells usually utilise a heterojunction between electron-donating (D) and electron-accepting (A) materials to split excitons into charges. However, the use of D-A blends intrinsically limits the photovoltage and introduces morphological instability. Here, we demonstrate that polycrystalline films of chemically identical molecules offer a promising alternative and show that photoexcitation of α-sexithiophene (α-6T) films results in efficient charge generation. This leads to α-6T based homojunction organic solar cells with an external quantum efficiency reaching up to 44% and an open-circuit voltage of 1.61 V. Morphological, photoemission, and modelling studies show that boundaries between α-6T crystalline domains with different orientations generate an electrostatic landscape with an interfacial energy offset of 0.4 eV, which promotes the formation of hybridised exciton/charge-transfer states at the interface, dissociating efficiently into free charges. Our findings open new avenues for organic solar cell design where material energetics are tuned through molecular electrostatic engineering and mesoscale structural control

    Size-dependent response of foraminiferal calcification to seawater carbonate chemistry

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    Michael J. Henehan acknowledges financial support from the Yale Peabody Museum.The response of the marine carbon cycle to changes in atmospheric CO2 concentrations will be determined, in part, by the relative response of calcifying and non-calcifying organisms to global change. Planktonic foraminifera are responsible for a quarter or more of global carbonate production, therefore understanding the sensitivity of calcification in these organisms to environmental change is critical. Despite this, there remains little consensus as to whether, or to what extent, chemical and physical factors affect foraminiferal calcification. To address this, we directly test the effect of multiple controls on calcification in culture experiments and core-top measurements of Globigerinoides ruber. We find that two factors, body size and the carbonate system, strongly influence calcification intensity in life, but that exposure to corrosive bottom waters can overprint this signal post mortem. Using a simple model for the addition of calcite through ontogeny, we show that variable body size between and within datasets could complicate studies that examine environmental controls on foraminiferal shell weight. In addition, we suggest that size could ultimately play a role in determining whether calcification will increase or decrease with acidification. Our models highlight that knowledge of the specific morphological and physiological mechanisms driving ontogenetic change in calcification in different species will be critical in predicting the of foraminiferal calcification to future change in atmospheric pCO2.Publisher PDFPeer reviewe

    Dependence of spin pumping and spin transfer torque upon Ni81Fe19 thickness in Ta/Ag/Ni81Fe19/Ag/Co2MnGe/Ag/Ta spin-valve structures

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    This is the final version of the article. Available from American Physical Society via the DOI in this record.Spin pumping has been studied within Ta / Ag / Ni 81 Fe 19 (0–5 nm) / Ag (6 nm) / Co 2 MnGe (5 nm) / Ag / Ta large-area spin-valve structures, and the transverse spin current absorption of Ni 81 Fe 19 sink layers of different thicknesses has been explored. In some circumstances, the spin current absorption can be inferred from the modification of the Co 2 MnGe source layer damping in vector network analyzer ferromagnetic resonance (VNA-FMR) experiments. However, the spin current absorption is more accurately determined from element-specific phase-resolved x-ray ferromagnetic resonance (XFMR) measurements that directly probe the spin transfer torque (STT) acting on the sink layer at the source layer resonance. Comparison with a macrospin model allows the real part of the effective spin mixing conductance to be extracted. We find that spin current absorption in the outer Ta layers has a significant impact, while sink layers with thicknesses of less than 0.6 nm are found to be discontinuous and superparamagnetic at room temperature, and lead to a noticeable increase of the source layer damping. For the thickest 5-nm sink layer, increased spin current absorption is found to coincide with a reduction of the zero frequency FMR linewidth that we attribute to improved interface quality. This study shows that the transverse spin current absorption does not follow a universal dependence upon sink layer thickness but instead the structural quality of the sink layer plays a crucial role.The authors gratefully acknowledge the support of EPSRC Grant No. EP/J018767/1, and the award of the Exeter-Brown Scholarship in High Frequency Spintronics to C.J.D
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