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https://www.readbyqxmd.com/read/29166161/will-invertebrates-require-increasingly-carbon-rich-food-in-a-warming-world
#1
Thomas R Anderson, Dag O Hessen, Maarten Boersma, Jotaro Urabe, Daniel J Mayor
Elevated temperature causes metabolism and respiration to increase in poikilothermic organisms. We hypothesized that invertebrate consumers will therefore require increasingly carbon-rich diets in a warming environment because the increased energetic demands are primarily met using compounds rich in carbon, that is, carbohydrates and lipids. Here, we test this hypothesis using a new stoichiometric model that has carbon (C) and nitrogen (N) as currencies. Model predictions did not support the hypothesis, indicating instead that the nutritional requirements of invertebrates, at least in terms of food quality expressed as C∶N ratio, may change little, if at all, at elevated temperature...
December 2017: American Naturalist
https://www.readbyqxmd.com/read/29166154/predator-persistence-through-variability-of-resource-productivity-in-tritrophic-systems
#2
Floor H Soudijn, André M de Roos
The trophic structure of species communities depends on the energy transfer between trophic levels. Primary productivity varies strongly through time, challenging the persistence of species at higher trophic levels. Yet resource variability has mostly been studied in systems with only one or two trophic levels. We test the effect of variability in resource productivity in a tritrophic model system including a resource, a size-structured consumer, and a size-specific predator. The model complies with fundamental principles of mass conservation and the body-size dependence of individual-level energetics and predator-prey interactions...
December 2017: American Naturalist
https://www.readbyqxmd.com/read/29166116/theoretical-study-of-photodetachment-spectroscopy-of-hydrogenated-boron-cluster-anion-h2b7-and-its-deuterated-isotopomer
#3
Rudraditya Sarkar, S Mahapatra
Photodetachment spectroscopy of H2B7(-) and its deuterated isotopomer probing the energetically low-lying electronic states of the respective neutral cluster is theoretically investigated in this paper. The theoretical methodology is based on detailed quantum chemistry calculations of electronic state energies, construction of a vibronic coupling model in the diabatic electronic basis, and nuclear dynamics calculations from first principles using time-dependent and time-independent quantum mechanical methods...
November 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29166114/communication-recovering-the-flat-plane-condition-in-electronic-structure-theory-at-semi-local-dft-cost
#4
Akash Bajaj, Jon Paul Janet, Heather J Kulik
The flat-plane condition is the union of two exact constraints in electronic structure theory: (i) energetic piecewise linearity with fractional electron removal or addition and (ii) invariant energetics with change in electron spin in a half filled orbital. Semi-local density functional theory (DFT) fails to recover the flat plane, exhibiting convex fractional charge errors (FCE) and concave fractional spin errors (FSE) that are related to delocalization and static correlation errors. We previously showed that DFT+U eliminates FCE but now demonstrate that, like other widely employed corrections (i...
November 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29166086/focused-conformational-sampling-in-proteins
#5
Marco Bacci, Cassiano Langini, Jiří Vymětal, Amedeo Caflisch, Andreas Vitalis
A detailed understanding of the conformational dynamics of biological molecules is difficult to obtain by experimental techniques due to resolution limitations in both time and space. Computer simulations avoid these in theory but are often too short to sample rare events reliably. Here we show that the progress index-guided sampling (PIGS) protocol can be used to enhance the sampling of rare events in selected parts of biomolecules without perturbing the remainder of the system. The method is very easy to use as it only requires as essential input a set of several features representing the parts of interest sufficiently...
November 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29166064/interaction-component-analysis-of-the-effects-of-urea-and-its-alkylated-derivatives-on-the-structure-of-t4-lysozyme
#6
Yu Yamamori, Nobuyuki Matubayasi
The effects of urea and its alkylated derivatives on the structure of T4-lysozyme were analyzed from the standpoint of energetics. Molecular dynamics simulations were conducted with explicit solvent, and the energy-representation method was employed to compute the free energy of transfer of the protein from pure-water solvent to the mixed solvents of water with urea, methylurea, 1,1-dimethylurea, and isopropylurea. Through the decomposition of the transfer free energy into the cosolvent and water contributions, it was observed that the former is partially cancelled by the latter and governs the total free energy of transfer...
June 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29166061/modeling-hydroxylated-nanosilica-testing-the-performance-of-reaxff-and-ffsioh-force-fields
#7
Antoni Macià Escatllar, Piero Ugliengo, Stefan T Bromley
We analyze the performance of the FFSiOH force field and two parameterisations of the ReaxFF force field for modeling hydroxylated nanoscale silica (SiO2). Such nanosystems are fundamental in numerous aspects of geochemistry and astrochemistry and also play a key role during the hydrothermal synthesis of technologically important nanoporous silicas (e.g., catalysts, absorbents, and coatings). We consider four aspects: structure, relative energies, vibrational spectra, and hydroxylation energies, and compare the results with those from density functional calculations employing a newly defined dataset (HND: Hydroxylated Nanosilica Dataset)...
June 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29166050/plane-wave-pseudopotential-implementation-and-performance-of-scan-meta-gga-exchange-correlation-functional-for-extended-systems
#8
Yi Yao, Yosuke Kanai
We present the implementation and performance of the strongly constrained and appropriately normed, SCAN, meta-GGA exchange-correlation (XC) approximation in the planewave-pseudopotential (PW-PP) formalism using the Troullier-Martins pseudopotential scheme. We studied its performance by applying the PW-PP implementation to several practical applications of interest in condensed matter sciences: (a) crystalline silicon and germanium, (b) martensitic phase transition energetics of phosphorene, and (c) a single water molecule physisorption on a graphene sheet...
June 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29166027/nanoscale-detection-of-intermediate-solid-solutions-in-equilibrated-lixfepo4-microcrystals
#9
Brian M May, Young-Sang Yu, Martin Holt, Fiona C Strobridge, Ulrike Bösenberg, Clare P Grey, Jordi Cabana
Redox-driven phase transformations in solids determine the performance of lithium-ion batteries, crucial in the technological transition from fossil fuels. Couplings between chemistry and strain define reversibility and fatigue of an electrode. The accurate definition of all phases in the transformation, their energetics and nanoscale location within a particle produces fundamental understanding of these couplings needed to design materials with ultimate performance. Here we demonstrate that scanning X-ray diffraction microscopy (SXDM) extends our ability to image battery processes in single particles...
November 22, 2017: Nano Letters
https://www.readbyqxmd.com/read/29166011/a-cooperative-folding-unit-as-the-structural-link-for-energetic-coupling-within-a-protein
#10
Nathan W Gardner, Sarah M McGinness, Jainik Panchal, Elizabeth M Topp, Chiwook Park
Previously, we demonstrated that ligand binding to Escherichia coli cofactor-dependent phosphoglycerate mutase (dPGM), a homodimeric protein, is energetically coupled with dimerization. The equilibrium unfolding of dPGM occurs with a stable, monomeric intermediate. Binding of several non-substrate metabolites stabilizes the dimeric native form over the monomeric intermediate, reducing the population of the intermediate. Both the active site and the dimer interface appear to be unfolded in the intermediate. We hypothesized that a loop containing residues 118-152 was responsible for the energetic coupling between the dimer interface and the distal active site and was unfolded in the intermediate...
November 22, 2017: Biochemistry
https://www.readbyqxmd.com/read/29165455/isomer-specific-detection-in-the-uv-photodissociation-of-the-propargyl-radical-by-chirped-pulse-mm-wave-spectroscopy-in-a-pulsed-quasi-uniform-flow
#11
Bernadette M Broderick, Nicolas Suas-David, Nureshan Dias, Arthur G Suits
Isomer-specific detection and product branching fractions in the UV photodissociation of the propargyl radical is achieved through the use of chirped-pulse Fourier-transform mm-wave spectroscopy in a pulsed quasi-uniform flow (CPUF). Propargyl radicals are produced in the 193 nm photodissociation of 1,2-butadiene. Absorption of a second photon leads to H atom elimination giving three possible C3H2 isomers: singlets cyclopropenylidene (c-C3H2) and propadienylidene (l-C3H2), and triplet propargylene ((3)HCCCH)...
November 22, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29165360/dynamic-docking-a-paradigm-shift-in-computational-drug-discovery
#12
REVIEW
Dario Gioia, Martina Bertazzo, Maurizio Recanatini, Matteo Masetti, Andrea Cavalli
Molecular docking is the methodology of choice for studying in silico protein-ligand binding and for prioritizing compounds to discover new lead candidates. Traditional docking simulations suffer from major limitations, mostly related to the static or semi-flexible treatment of ligands and targets. They also neglect solvation and entropic effects, which strongly limits their predictive power. During the last decade, methods based on full atomistic molecular dynamics (MD) have emerged as a valid alternative for simulating macromolecular complexes...
November 22, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29164898/ionic-solution-what-goes-right-and-wrong-with-continuum-solvation-modeling
#13
Changhao Wang, Pengyu Ren, Ray Luo
Solvent-mediated electrostatic interactions were well recognized to be important in the structure and function of molecular systems. Ionic interaction is an important component in electrostatic interactions, especially in highly charged molecules, such as nucleic acids. Here we focus on the quality of the widely used PBSA continuum models in modeling ionic interactions by comparing with both explicit solvent simulations and experiment. In this work, the molality-dependent chemical potentials for sodium chloride (NaCl) electrolyte were first simulated in the SPC/E explicit solvent...
November 22, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29164478/excited-state-and-non-linear-optical-properties-of-nir-absorbing-%C3%AE-thiophene-fused-bf2-azadipyrromethene-dyes-computational-investigation
#14
Yogesh Gawale, Lydia Rhyman, Mohamed I Elzagheid, Ponnadurai Ramasami, Nagaiyan Sekar
Density functional theory and time-dependent density functional theory computations were used to understand the electronic and photophysical parameters of NIR β-thiophene-fused BF2-azadipyrromethene dyes. The computed data are in good agreement with those obtained experimentally and they provide insights into the origin of red shifted optical spectra compared to the parent aza-BODIPY, low Stokes shift, non-linear optical responses and quantitative description of the singlet-triplet energy gap. The resultant decrease in the HOMO - LUMO energy gap is responsible for the red shift...
November 21, 2017: Journal of Fluorescence
https://www.readbyqxmd.com/read/29163923/size-and-charge-effect-of-guest-cations-in-the-formation-of-polyoxopalladates-a-theoretical-and-experimental-study
#15
Zhongling Lang, Peng Yang, Zhengguo Lin, Likai Yan, Ming-Xing Li, Jorge J Carbó, Ulrich Kortz, Josep M Poblet
The development of rational synthetic procedures with desired nuclearity and high selectivity is a critical issue in inorganic chemistry. Here we demonstrate a comprehensive understanding of the template effect induced by metal cations in the formation mechanism of the class of polyoxopalladates ({MPd12L8} nanocube and {MPd15L10} nanostar) by combining computational and experimental techniques. The capture of a M (n+) guest ion by a peripheral palladium(ii)-oxo shell leads to a competition between the parent Pd(2+) addenda ion and the respective guest metal ion...
November 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/29163921/the-short-device-lifetimes-of-blue-pholeds-insights-into-the-photostability-of-blue-ir-iii-complexes
#16
Denis Jacquemin, Daniel Escudero
Using Ir(iii) complexes as dopants in phosphorescent organic light-emitting diodes (PhOLEDs) is the most successful strategy to attain long-lasting and highly-performant electroluminescent devices. Whilst highly efficient blue PhOLEDs are accessible, their limited operational lifetimes still restraint their practical use in lighting and displays. These short lifetimes are directly related to the low intrinsic photostability of blue Ir(iii) complexes. This work uses first principles to unveil the mechanisms of degradation of blue phosphors arising from energetically hot excited states (≅6...
November 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/29163431/camelina-seed-supplementation-at-two-dietary-fat-levels-change-ruminal-bacterial-community-composition-in-a-dual-flow-continuous-culture-system
#17
Xiaoxia Dai, Paul J Weimer, Kimberly A Dill-McFarland, Virginia L N Brandao, Garret Suen, Antonio P Faciola
This experiment aimed to determine the effects of camelina seed (CS) supplementation at different dietary fat levels on ruminal bacterial community composition and how it relates to changes in ruminal fermentation in a dual-flow continuous culture system. Diets were randomly assigned to 8 fermenters (1,200-1,250 mL) in a 2 × 2 factorial arrangement of treatments in a replicated 4 × 4 Latin square with four 10-day experimental periods that consisted of 7 days for diet adaptation and 3 days for sample collection...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29162371/the-role-of-caveolin-1-in-lipid-droplets-and-their-biogenesis
#18
Weria Pezeshkian, Guillaume Chevrot, Himanshu Khandelia
We address unresolved questions of the energetics and mechanism of Lipid Droplet (LD) biogenesis, and of the role of Caveolins in the endoplasmic reticulum (ER) and in mature LDs. LDs are eukaryotic repositories of neutral lipids, which are believed to be synthesised in the ER. We investigate the effects of a curvature-inducing protein, caveolin-1, on the formation and structure of a spontaneously aggregated triolein (TO) lipid lens in a flat lipid bilayer using Molecular Dynamics (MD) simulations. A truncated form of Caveolin-1 (Cav1) localises on the interface between the spontaneously formed TO aggregate and the bulk bilayer, and thins the bilayer at the edge of the aggregate, which may contribute to lowering the energy barrier for pinching off the aggregate from the host bilayer...
November 18, 2017: Chemistry and Physics of Lipids
https://www.readbyqxmd.com/read/29161982/the-effects-of-musical-training-on-speech-detection-in-the-presence-of-informational-and-energetic-masking
#19
Charlotte Morse-Fortier, Mary M Parrish, Jane A Baran, Richard L Freyman
Recent research has suggested that musicians have an advantage in some speech-in-noise paradigms, but not all. Whether musicians outperform nonmusicians on a given speech-in-noise task may well depend on the type of noise involved. To date, few groups have specifically studied the role that informational masking plays in the observation of a musician advantage. The current study investigated the effect of musicianship on listeners' ability to overcome informational versus energetic masking of speech. Monosyllabic words were presented in four conditions that created similar energetic masking but either high or low informational masking...
January 2017: Trends in Hearing
https://www.readbyqxmd.com/read/29161042/conformational-dynamics-of-matrix-metalloproteinase-1%C3%A2-triple-helical-peptide-complexes
#20
Tatyana G Karabencheva-Christova, Christo Z Christov, Gregg B Fields
Matrix metalloproteinase-1 (MMP-1) is a zinc-dependent protease that catalyzes hydrolysis of interstitial collagens. A previously reported X-ray crystallographic structure revealed specific interactions between a triple-helical peptide (THP) model of interstitial collagen and the hemopexin-like (HPX) and catalytic (CAT) domains of MMP-1. An NMR-based structure of MMP-1 in complex with a different THP was also solved, where docking was used to model the MMP-1•THP interactions and develop a mechanism for the early stages of collagenolysis...
November 21, 2017: Journal of Physical Chemistry. B
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