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Thermodynamics

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https://www.readbyqxmd.com/read/28636006/copper-ion-interaction-with-the-rnase-catalytic-site-fragment-of-the-angiogenin-protein-an-experimental-and-theoretical-investigation
#1
Antonio Magrì, Giovanni Tabbì, Raffaella Breglia, Luca De Gioia, Piercarlo Fantucci, Maurizio Bruschi, Raffaele P Bonomo, Diego La Mendola
The angiogenin protein (Ang) is a member of the vertebrate-specific secreted ribonucleases and one of the most potent angiogenic factors known. Ang is a normal constituent of human plasma and its concentration increases under some physiological and pathological conditions to promote neovascularization. Ang was originally identified as an angiogenic tumour factor, but its biological activity has been found to extend from inducing angiogenesis to promoting cell survival in different neurodegenerative diseases...
June 21, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28634333/atomic-rearrangement-of-a-sputtered-mos2-film-from-amorphous-to-a-2d-layered-structure-by-electron-beam-irradiation
#2
Bong Ho Kim, Hyun Ho Gu, Young Joon Yoon
We synthesised a crystalline MoS2 film from as-sputtered amorphous film by applying an electron beam irradiation (EBI) process. A collimated electron beam (60 mm dia.) with an energy of 1 kV was irradiated for only 1 min to achieve crystallisation without an additional heating process. After the EBI process, we observed a two-dimensional layered structure of MoS2 about 4 nm thick and with a hexagonal atomic arrangement on the surface. A stoichiometric MoS2 film was confirmed to grow well on SiO2/Si substrates and include partial oxidation of Mo...
June 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28634126/biosorption-of-high-concentration-cu-ii-by-periphytic-biofilms-and-the-development-of-a-fiber-periphyton-bioreactor-fpbr
#3
Junzhuo Liu, Fengwu Wang, Wantong Wu, Juanjuan Wan, Jiali Yang, Sulin Xiang, Yonghong Wu
In this study, a kind of microbial aggregates: periphytic biofilms were used for Cu removal and immobilized onto fiber for developing a novel bioreactor. Results show that periphyton can effectively entrap Cu at initial concentrations of 2-20mgL(-1) due to the overproduction of EPS and porous structure of periphyton, and biosorption was the primary mechanism of Cu removal. Cu (mainly Cu3(OH)4(2+), Cu2(OH)2(2+) and Cu(2+)) adsorption onto periphytic biofilms followed the pseudo-second order kinetic model. The biosorption process fitted the Freundlich, Langmuir and Dubinin-Radushkevich Isotherm models well and was thermodynamically spontaneous...
June 10, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28633820/green-synthesis-of-ag-cr-ac-nanocomposites-by-azadirachta-indica-and-its-application-for-the-simultaneous-removal-of-binary-mixture-of-dyes-by-ultrasonicated-assisted-adsorption-process-using-response-surface-methodology
#4
Muhammad Saad, Hajira Tahir, Duaa Ali
In the present studies the Ag-Cr-AC nanocomposites were synthesized by Azadirachta indica leaves extract. They were inoculated on the amorphous surface of activated carbon. The surface morphology and structural identification was determined by SEM, FTIR and XRD techniques. The simultaneous removal of binary dye system of Reactive Red and Crystal Violet were performed by ultrasonicated assisted adsorption process utilizing Ag-Cr-AC nanocomposites. Central Composite Design (CCD) having 5 factors of time, pH, amount of Ag-Cr-AC (adsorbent), concentrations of Reactive Red (RR) and Crystal Violet (CV) was employed...
September 2017: Ultrasonics Sonochemistry
https://www.readbyqxmd.com/read/28633569/thermal-and-chemical-denaturation-of-colocasia-esculenta-tuber-agglutinin-from-%C3%AE-2%C3%AE-2-to-unfolded-state
#5
Himadri Biswas, Rajagopal Chattopadhyaya
The major tuber storage protein of Colocasia esculenta, is a monocot mannose-binding, widely used dietary lectin, containing two polypeptides of 12.0 and 12.4 kDa. By both gel filtration and dynamic light scattering at pH 7.2, the lectin has a α2β2 form of apparent molecular mass of 48.2 kDa and a hydrodynamic radius of 6.1±0.2 nm; however, at pH 3, it migrates as αβ and has a reduced hydrodynamic radius of 4.6±0.3 nm. Our circular dichroism spectroscopy studies show that the lectin retains approximately 100% of its secondary structure between pH 2-8, going down to ~90% for extreme acidic / alkaline conditions...
June 20, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28633355/how-proteins-bind-to-dna-target-discrimination-and-dynamic-sequence-search-by-the-telomeric-protein-trf1
#6
Milosz Wieczór, Jacek Czub
Target search as performed by DNA-binding proteins is a complex process, in which multiple factors contribute to both thermodynamic discrimination of the target sequence from overwhelmingly abundant off-target sites and kinetic acceleration of dynamic sequence interrogation. TRF1, the protein that binds to telomeric tandem repeats, faces an intriguing variant of the search problem where target sites are clustered within short fragments of chromosomal DNA. In this study, we use extensive (>0.5 ms in total) MD simulations to study the dynamical aspects of sequence-specific binding of TRF1 at both telomeric and non-cognate DNA...
June 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28633093/fracture-resistance-of-ceramic-and-polymer-based-occlusal-veneer-restorations
#7
Majed Al-Akhali, Mohamed Sad Chaar, Adham Elsayed, Abdulaziz Samran, Matthias Kern
OBJECTIVES: The purpose of this in vitro study was to evaluate the influence of thermodynamic loading on the durability and fracture resistance behavior of occlusal veneers fabricated from different biomedical dental CAD/CAM materials. METHODS: The occlusal surfaces of 64 extracted premolars were prepared in the enamel layer and restored with occlusal veneers with a fissure/cusp thickness of 0.5/0.8mm made from four different dental CAD/CAM materials: group LD lithium disilicate (e...
June 13, 2017: Journal of the Mechanical Behavior of Biomedical Materials
https://www.readbyqxmd.com/read/28632318/-the-easier-the-better-preparation-of-efficient-photocatalysts-metastable-poly-heptazine-imide-salts
#8
Zupeng Chen, Aleksandr Savateev, Sergey Pronkin, Vasiliki Papaefthimiou, Christian Wolff, Marc Georg Willinger, Elena Willinger, Dieter Neher, Markus Antonietti, Dariya Dontsova
Cost-efficient, visible-light-driven hydrogen production from water is an attractive potential source of clean, sustainable fuel. Here, it is shown that thermal solid state reactions of traditional carbon nitride precursors (cyanamide, melamine) with NaCl, KCl, or CsCl are a cheap and straightforward way to prepare poly(heptazine imide) alkali metal salts, whose thermodynamic stability decreases upon the increase of the metal atom size. The chemical structure of the prepared salts is confirmed by the results of X-ray photoelectron and infrared spectroscopies, powder X-ray diffraction and electron microscopy studies, and, in the case of sodium poly(heptazine imide), additionally by atomic pair distribution function analysis and 2D powder X-ray diffraction pattern simulations...
June 20, 2017: Advanced Materials
https://www.readbyqxmd.com/read/28631123/modeling-solubility-of-co2-hydrocarbon-gas-in-ionic-liquid-emim-fap-using-aspen-plus-simulations
#9
Bishwadeep Bagchi, Sushmita Sati, Vidyasagar Shilapuram
The Peng-Robinson equation of state with quadratic van der Waals (vdW) mixing rule model was chosen to perform the thermodynamic calculations in Flash3 column of Aspen Plus to predict the solubility of CO2 or any one of the hydrocarbons (HCs) among methane, ethane, propane, and butane in an ionic liquid 1-ethyl-3-methylimidazolium tris(pentafluoroethyl)trifluorophosphate ([emim][FAP]). Bubble point pressure, solubility, bubble point temperature, fugacity, and partial molar volume at infinite dilution were obtained from the simulations, and enthalpy of absorption, Gibbs free energy of solvation, and entropy change of absorption were estimated by thermodynamic relations...
June 19, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28630928/novel-phase-diagram-behavior-and-materials-design-in-heterostructural-semiconductor-alloys
#10
Aaron M Holder, Sebastian Siol, Paul F Ndione, Haowei Peng, Ann M Deml, Bethany E Matthews, Laura T Schelhas, Michael F Toney, Roy G Gordon, William Tumas, John D Perkins, David S Ginley, Brian P Gorman, Janet Tate, Andriy Zakutayev, Stephan Lany
Structure and composition control the behavior of materials. Isostructural alloying is historically an extremely successful approach for tuning materials properties, but it is often limited by binodal and spinodal decomposition, which correspond to the thermodynamic solubility limit and the stability against composition fluctuations, respectively. We show that heterostructural alloys can exhibit a markedly increased range of metastable alloy compositions between the binodal and spinodal lines, thereby opening up a vast phase space for novel homogeneous single-phase alloys...
June 2017: Science Advances
https://www.readbyqxmd.com/read/28630679/molecular-interactions-of-amyloid-nanofibrils-with-biological-aggregation-modifiers-implications-for-cytotoxicity-mechanisms-and-biomaterial-design
#11
REVIEW
Durga Dharmadana, Nicholas P Reynolds, Charlotte E Conn, Céline Valéry
Amyloid nanofibrils are ubiquitous biological protein fibrous aggregates, with a wide range of either toxic or beneficial activities that are relevant to human disease and normal biology. Protein amyloid fibrillization occurs via nucleated polymerization, through non-covalent interactions. As such, protein nanofibril formation is based on a complex interplay between kinetic and thermodynamic factors. The process entails metastable oligomeric species and a highly thermodynamically favoured end state. The kinetics, and the reaction pathway itself, can be influenced by third party moieties, either molecules or surfaces...
August 6, 2017: Interface Focus
https://www.readbyqxmd.com/read/28630473/impact-of-antigen-density-on-the-binding-mechanism-of-igg-antibodies
#12
Maya Hadzhieva, Anastas D Pashov, Srinivas Kaveri, Sébastien Lacroix-Desmazes, Hugo Mouquet, Jordan D Dimitrov
The density and distribution pattern of epitopes at the surface of pathogens have a profound impact on immune responses. Although multiple lines of evidence highlight the significance of antigen surface density for antibody binding, a quantitative description of its effect on recognition mechanisms is missing. Here, we analyzed binding kinetics and thermodynamics of six HIV-1 neutralizing antibodies as a function of the surface density of envelope glycoprotein gp120. Antibodies that recognize gp120 with low to moderate binding affinity displayed the most pronounced sensitivity to variation in antigen density, with qualitative and substantial quantitative changes in the energetics of the binding process as revealed by non-equilibrium and equilibrium thermodynamic analyses...
June 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28629809/theoretical-modeling-of-the-subject-western-and-eastern-types-of-human-reflexion
#13
REVIEW
Vladimir A Lefebvre
The author put forth the hypothesis that mental phenomena are connected with thermodynamic properties of large neural network. A model of the subject with reflexion and capable for meditation is constructed. The processes of reflexion and meditation are presented as the sequence of heat engines. Each subsequent engine compensates for the imperfectness of the preceding engine by performing work equal to the lost available work of the preceding one. The sequence of heat engines is regarded as a chain of the subject's mental images of the self...
June 16, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28629618/conditioning-and-robustness-of-rna-boltzmann-sampling-under-thermodynamic-parameter-perturbations
#14
Emily Rogers, David Murrugarra, Christine Heitsch
Understanding how RNA secondary structure prediction methods depend on the underlying nearest-neighbor thermodynamic model remains a fundamental challenge in the field. Minimum free energy (MFE) predictions are known to be "ill conditioned" in that small changes to the thermodynamic model can result in significantly different optimal structures. Hence, the best practice is now to sample from the Boltzmann distribution, which generates a set of suboptimal structures. Although the structural signal of this Boltzmann sample is known to be robust to stochastic noise, the conditioning and robustness under thermodynamic perturbations have yet to be addressed...
June 16, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28628903/functional-kaolin-supported-nanoscale-zero-valent-iron-as-a-fenton-like-catalyst-for-the-degradation-of-direct-black-g
#15
Jiajiang Lin, Mengqiang Sun, Xinwen Liu, Zuliang Chen
Kaolin supported nanoscale zero-valent iron (K-nZVI) is synthesized and applied as the Fenton-like oxidation catalyst to degrade a model azo dye, Direct Black G (DBG). The characterization of K-nZVI by the high resolution transmission electronmicroscopy (HRTEM), X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM), Energy Diffraction Spectrum (EDS) and X-ray diffraction (XRD) show that kaolin as a support material not only reduces the aggregation of zero-valent iron (nZVI) but also facilitates the Fenton-like oxidation by increasing the local concentration of DBG in the vicinity of nZVI...
June 12, 2017: Chemosphere
https://www.readbyqxmd.com/read/28628873/complexation-thermodynamics-of-%C3%AE-cyclodextrin-with-ionic-surfactants-in-water
#16
Daniel Ondo, Miguel Costas
The interaction of α-cyclodextrin (α-CD) with ten ionic surfactants (S) in water was systematically examined using isothermal titration calorimetry. The S comprised cationic and anionic head groups while the hydrocarbon alkyl chain length varied from eight to fourteen carbon atoms. The heat data were measured at five temperatures ranging from 283.15K to 318.15K and were treated simultaneously allowing the estimation of a thermodynamically consistent temperature dependence of the equilibrium constant, as well as the enthalpy and heat capacity for the sequential formation of the [α-CD·S] and the [α-CD2·S] inclusion complexes...
June 8, 2017: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/28628859/structural-and-functional-effects-of-nucleotide-variation-on-the-human-tb-drug-metabolizing-enzyme-arylamine-n-acetyltransferase-1
#17
Ruben Cloete, Wisdom A Akurugu, Cedric J Werely, Paul D van Helden, Alan Christoffels
The human arylamine N-acetyltransferase 1 (NAT1) enzyme plays a vital role in determining the duration of action of amine-containing drugs such as para-aminobenzoic acid (PABA) by influencing the balance between detoxification and metabolic activation of these drugs. Recently, four novel single nucleotide polymorphisms (SNPs) were identified within a South African mixed ancestry population. Modeling the effects of these SNPs within the structural protein was done to assess possible structure and function changes in the enzyme...
June 10, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28628248/kinetic-selectivity-and-thermodynamic-features-of-competitive-imine-formation-in-dynamic-covalent-chemistry
#18
Jean-Marie Lehn, Sirinan Kulchat, Manuel N Chaur
The kinetic and thermodynamic selectivities of imine formation have been investigated for several dynamic covalent libraries of aldehydes and amines. Two systems were examined, involving the reaction of different types of primary amino groups (aliphatic amines, alkoxy-amines, hydrazides and hydrazines) with two types of aldehydes, sulfobenzaldehyde and pyridoxal phosphate in aqueous solution at different pD (5.0, 8.5, 11.4) on one hand, 2-pyridinecarboxaldehyde and salicylaldehyde in organic solvents on the other hand...
June 19, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28628124/emergence-of-an-enslaved-phononic-bandgap-in-a-non-equilibrium-pseudo-crystal
#19
Nicolas Bachelard, Chad Ropp, Marc Dubois, Rongkuo Zhao, Yuan Wang, Xiang Zhang
Material systems that reside far from thermodynamic equilibrium have the potential to exhibit dynamic properties and behaviours resembling those of living organisms. Here we realize a non-equilibrium material characterized by a bandgap whose edge is enslaved to the wavelength of an external coherent drive. The structure dynamically self-assembles into an unconventional pseudo-crystal geometry that equally distributes momentum across elements. The emergent bandgap is bestowed with lifelike properties, such as the ability to self-heal to perturbations and adapt to sudden changes in the drive...
June 19, 2017: Nature Materials
https://www.readbyqxmd.com/read/28627561/a-promising-single-atom-catalyst-for-co-oxidation-ag-on-boron-vacancies-of-h-bn-sheets
#20
Zhansheng Lu, Peng Lv, Zongxian Yang, Shuo Li, Dongwei Ma, Ruqian Wu
Single atom catalysts (SACs) have attracted broad research interest in recent years due to their importance in various fields, such as environmental protection and energy conversion. Here, we discuss the mechanisms of CO oxidation to CO2 over single Ag atoms supported on hexagonal boron-nitride sheets (Ag1/BN) through systematic van der Waals inclusive density functional theory (DFT-D) calculations. The Ag adatom can be anchored onto a boron defect (VB), as suggested by the large energy barrier of 3.12 eV for Ag diffusion away from the VB site...
June 19, 2017: Physical Chemistry Chemical Physics: PCCP
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