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https://www.readbyqxmd.com/read/28992702/open-boundary-simulations-of-proteins-and-their-hydration-shells-by-hamiltonian-adaptive-resolution-scheme
#1
Thomas Tarenzi, Vania Calandrini, Raffaello Potestio, Alejandro Giorgetti, Paolo Carloni
The recently proposed Hamiltonian adaptive resolution scheme (H-AdResS) allows the performance of molecular simulations in an open boundary framework. It allows changing, on the fly, the resolution of specific subsets of molecules (usually the solvent), which are free to diffuse between the atomistic region and the coarse-grained reservoir. So far, the method has been successfully applied to pure liquids. Coupling the H-AdResS methodology to hybrid models of proteins, such as the molecular mechanics/coarse-grained (MM/CG) scheme, is a promising approach for rigorous calculations of ligand binding free energies in low-resolution protein models...
October 27, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28831903/think-drink-campaign-gets-national-attention
#2
Kat Keogh
A hospital's award-winning scheme - which helps patients recover faster from surgery side effects by keeping them hydrated pre-operation - is being shared nationwide.
August 23, 2017: Nursing Standard
https://www.readbyqxmd.com/read/28831152/different-route-of-hydroxide-incorporation-and-thermal-stability-of-new-type-of-water-clathrate-x-ray-single-crystal-and-raman-investigation
#3
Mateusz Dulski, Katarzyna M Marzec, Joachim Kusz, Irina Galuskina, Katarzyna Majzner, Evgeny Galuskin
Chlormayenite Ca12Al14O32[♦4Cl2] (♦-vacancy) is partially hydrated micro porouss mineral with hydroxide groups situated at various crystallographic sites. There are few mechanisms describing its hydration. The first one assumes Cl(-) substitution by OH(-) at the center of the structural cages (W-site). The second one determines the converting a T1O4 tetrahedron to a T1O3(OH)3 octahedron due to the replacement of oxygen at the O2 site by three OH-groups according to the scheme: ((O2)O(2-) +  (W) Cl(-)) → 3 ×  (O2a)OH...
August 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28731091/developing-force-fields-when-experimental-data-is-sparse-amber-gaff-compatible-parameters-for-inorganic-and-alkyl-oxoanions
#4
Sadra Kashefolgheta, Ana Vila Verde
We present a set of Lennard-Jones parameters for classical, all-atom models of acetate and various alkylated and non-alkylated forms of sulfate, sulfonate and phosphate ions, optimized to reproduce their interactions with water and with the physiologically relevant sodium, ammonium and methylammonium cations. The parameters are internally consistent and are fully compatible with the Generalized Amber Force Field (GAFF), the AMBER force field for proteins, the accompanying TIP3P water model and the sodium model of Joung and Cheatham...
August 9, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28707900/aerosol-fragmentation-driven-by-coupling-of-acid-base-and-free-radical-chemistry-in-the-heterogeneous-oxidation-of-aqueous-citric-acid-by-oh-radicals
#5
Matthew J Liu, Aaron A Wiegel, Kevin R Wilson, Frances A Houle
A key uncertainty in the heterogeneous oxidation of carboxylic acids by hydroxyl radicals (OH) in aqueous-phase aerosol is how the free-radical reaction pathways might be altered by acid-base chemistry. In particular, if acid-base reactions occur concurrently with acyloxy radical formation and unimolecular decomposition of alkoxy radicals, there is a possibility that differences in reaction pathways impact the partitioning of organic carbon between the gas and aqueous phases. To examine these questions, a kinetic model is developed for the OH-initiated oxidation of citric acid aerosol at high relative humidity...
August 1, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28636363/distinct-protein-hydration-water-species-defined-by-spatially-resolved-spectra-of-intermolecular-vibrations
#6
Viren Pattni, Tatiana Vasilevskaya, Walter Thiel, Matthias Heyden
In this molecular dynamics simulation study, we analyze intermolecular vibrations in the hydration shell of a solvated enyzme, the membrane type 1-matrix metalloproteinase, with high spatial resolution. Our approach allows us to characterize vibrational signatures of the local hydrogen bond network, the translational mobility of water molecules, as well as the molecular entropy, in specific local environments. Our study demonstrates the heterogeneity of water properties within the hydration shell of a complex biomolecule...
August 10, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28612358/%C3%AE-chymotrypsin-in-water-acetone-and-water-dimethyl-sulfoxide-mixtures-effect-of-preferential-solvation-and-hydration
#7
Vladimir A Sirotkin, Alexandra A Kuchierskaya
We investigated water/organic solvent sorption and residual enzyme activity to simultaneously monitor preferential solvation/hydration of protein macromolecules in the entire range of water content at 25°C. We applied this approach to estimate protein destabilization/stabilization due to the preferential interactions of bovine pancreatic α-chymotrypsin with water-acetone (moderate-strength H-bond acceptor) and water-DMSO (strong H-bond acceptor) mixtures. There are three concentration regimes for the dried α-chymotrypsin...
October 2017: Proteins
https://www.readbyqxmd.com/read/28607681/hydration-stickers-improving-oral-hydration-in-vulnerable-patients
#8
Alysha Bhatti, Javier Ash, Shyam Gokani, Suveer Singh
Dehydration is a growing problem among elderly patients in hospital wards. Incidents such as those raised in the Francis Report highlight a problem that may not have been sufficiently addressed by current schemes. This improvement project aimed to identify the barriers faced by staff in improving oral hydration and to design and implement an effective solution. A 33 patient pilot study carried out at Chelsea & Westminster Hospital NHS Trust, United Kingdom, revealed that a significant proportion of patients were reported to be dehydrated on admission, with few having their hydration needs addressed...
2017: BMJ Quality Improvement Reports
https://www.readbyqxmd.com/read/28600826/tinker-openmm-absolute-and-relative-alchemical-free-energies-using-amoeba-on-gpus
#9
Matthew Harger, Daniel Li, Zhi Wang, Kevin Dalby, Louis Lagardère, Jean-Philip Piquemal, Jay Ponder, Pengyu Ren
The capabilities of the polarizable force fields for alchemical free energy calculations have been limited by the high computational cost and complexity of the underlying potential energy functions. In this work, we present a GPU-based general alchemical free energy simulation platform for polarizable potential AMOEBA. Tinker-OpenMM, the OpenMM implementation of the AMOEBA simulation engine has been modified to enable both absolute and relative alchemical simulations on GPUs, which leads to a ∼200-fold improvement in simulation speed over a single CPU core...
September 5, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28576085/lysozyme-in-water-acetonitrile-mixtures-preferential-solvation-at-the-inner-edge-of-excess-hydration
#10
Vladimir A Sirotkin, Alexandra A Kuchierskaya
Preferential solvation/hydration is an effective way for regulating the mechanism of the protein destabilization/stabilization. Organic solvent/water sorption and residual enzyme activity measurements were performed to monitor the preferential solvation/hydration of hen egg-white lysozyme at high and low water content in acetonitrile at 25 °C. The obtained results show that the protein destabilization/stabilization depends essentially on the initial hydration level of lysozyme and the water content in acetonitrile...
June 7, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28513645/electrode-potential-dependent-desolvation-and-resolvation-of-germanium-100-in-contact-with-aqueous-perchlorate-electrolytes
#11
Fang Niu, Rainer Schulz, Arcesio Castañeda Medina, Rochus Schmid, Andreas Erbe
The electrode potential dependence of the hydration layer on an n-Ge(100) surface was studied by a combination of in situ and operando electrochemical attenuated total reflection infrared (ATR-IR) spectroscopy and real space density functional theory (DFT) calculations. Constant-potential DFT calculations were coupled to a modified generalised Poisson-Boltzmann ion distribution model and applied within an ab initio molecular dynamics (AIMD) scheme. As a result, potential-dependent vibrational spectra of surface species and surface water were obtained, both experimentally and by simulations...
May 31, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28492328/inhibition-of-radiolytic-molecular-hydrogen-formation-by-quenching-of-excited-state-water
#12
Gregory P Horne, Simon M Pimblott, Jay A LaVerne
Comparison of experimental measurements of the yield of molecular hydrogen produced in the gamma radiolysis of water and aqueous nitrate solutions with predictions of a Monte Carlo track chemistry model shows that the nitrate anion scavenging of the hydrated electron, its precursor, and hydrogen atom cannot account for the observed decrease in the yield at high nitrate anion concentrations. Inclusion of the quenching of excited states of water (formed by either direct excitation or reaction of the water radical cation with the precursor to the hydrated electron) by the nitrate anion into the reaction scheme provides excellent agreement between the stochastic calculations and experiment demonstrating the existence of this short-lived species and its importance in water radiolysis...
May 23, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28300856/halobetasol-propionate-lotion-0-05-provides-superior-hydration-compared-to-halobetasol-propionate-cream-0-05-in-a-double-blinded-study-of-occlusivity-and-hydration
#13
Gary Grove, Charles Zerweck, Tim Houser, Anthony Andrasfay, Bob Gauthier, Charles Holland, Daniel Piacquadio
BACKGROUND: This study measured skin hydration and occlusivity of two test products [halobetasol propionate lotion, 0.05% (HBP Lotion) and Ultravate® (halobetasol propionate) cream, 0.05% (HBP Cream)] at 2, 4, and 6 hours after application to skin test sites previously challenged by dry shaving, which was performed to compromise the integrity of the stratum corneum barrier. METHODS: Trans-epidermal water loss (TEWL), an indicator of skin barrier function, was measured using cyberDERM, inc...
February 1, 2017: Journal of Drugs in Dermatology: JDD
https://www.readbyqxmd.com/read/28138128/understanding-and-preventing-contrast-induced-acute-kidney-injury
#14
REVIEW
Michael Fähling, Erdmann Seeliger, Andreas Patzak, Pontus B Persson
Contrast-induced acute kidney injury (CIAKI) occurs in up to 30% of patients who receive iodinated contrast media and is generally considered to be the third most common cause of hospital-acquired AKI. Accurate assessment of the incidence of CIAKI is obscured, however, by the use of various definitions for diagnosis, the different populations studied and the prophylactic measures put in place. A deeper understanding of the mechanisms that underlie CIAKI is required to enable reliable risk assessment for individual patients, as their medical histories will determine the specific pathways by which contrast media administration might lead to kidney damage...
March 2017: Nature Reviews. Nephrology
https://www.readbyqxmd.com/read/27992815/molecular-dynamics-study-of-micelles-properties-according-to-their-size
#15
S Lebecque, J M Crowet, M N Nasir, M Deleu, L Lins
Surfactants are molecules able to spontaneously self-assemble to form aggregates with well-defined properties, such as spherical micelles, planar bilayers, cylindrical micelles or vesicles. Micelles have notably several applications in many domains, such as drug delivery or membrane protein solubilization. In this context, the study of micelle formation in relation with the structural and physico-chemical properties of surfactants is of great interest to better control their use in the different application fields...
March 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/27760249/multidirectional-in-vivo-characterization-of-skin-using-wiener-nonlinear-stochastic-system-identification-techniques
#16
Matthew D Parker, Lynette A Jones, Ian W Hunter, A J Taberner, M P Nash, P M F Nielsen
A triaxial force-sensitive microrobot was developed to dynamically perturb skin in multiple deformation modes, in vivo. Wiener static nonlinear identification was used to extract the linear dynamics and static nonlinearity of the force-displacement behavior of skin. Stochastic input forces were applied to the volar forearm and thenar eminence of the hand, producing probe tip perturbations in indentation and extension. Wiener static nonlinear approaches increased the variance accounted for by 0.1 % to 3.4 % over linear approaches, to 94 % to 97 %...
October 19, 2016: Journal of Biomechanical Engineering
https://www.readbyqxmd.com/read/27699855/a-multi-resolution-model-to-capture-both-global-fluctuations-of-an-enzyme-and-molecular-recognition-in-the-ligand-binding-site
#17
Aoife C Fogarty, Raffaello Potestio, Kurt Kremer
In multi-resolution simulations, different system components are simultaneously modeled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is needed in the active site to capture the chemistry of ligand binding. Global properties of the rest of the protein also play an essential role, determining the structure and fluctuations of the binding site; however, these can be modeled on a coarser level. Similarly, in the most computationally efficient scheme only the solvent hydrating the active site requires atomistic detail...
December 2016: Proteins
https://www.readbyqxmd.com/read/27598945/understanding-protein-diffusion-in-polymer-solutions-a-hydration-with-depletion-model
#18
Xiaoqing Feng, Anpu Chen, Juan Wang, Nanrong Zhao, Zhonghuai Hou
Understanding the diffusion of proteins in polymer solutions is of ubiquitous importance for modeling processes in vivo. Here, we present a theoretical framework to analyze the decoupling of translational and rotational diffusion of globular proteins in semidilute polymer solutions. The protein is modeled as a spherical particle with an effective hydrodynamic radius, enveloped by a depletion layer. Based on the scaling formula of macroscopic viscosity for polymer solutions as well as the mean-field theory for the depletion effect, we specify the space-dependent viscosity profile in the depletion zone...
September 6, 2016: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/27409458/dft-calculations-with-van-der-waals-interactions-of-hydrated-calcium-carbonate-crystals-caco3%C3%A2-h2o-6h2o-structural-electronic-optical-and-vibrational-properties
#19
Stefane N Costa, Valder N Freire, Ewerton W S Caetano, Francisco F Maia, Carlos A Barboza, Umberto L Fulco, Eudenilson L Albuquerque
The role of hydration on the structural, electronic, optical, and vibrational properties of monohydrated (CaCO3·H2O, hexagonal, P31, Z = 9) and hexahydrated (CaCO3·6H2O, monoclinic, C2/c, Z = 4) calcite crystals is assessed with the help of published experimental and theoretical data applying density functional theory within the generalized gradient approximation and a dispersion correction scheme. We show that the presence of water increases the main band gap of monohydrocalcite by 0.4 eV relative to the anhydrous structure, although practically not changing the hexahydrocalcite band gap...
July 21, 2016: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/27367817/small-molecule-hydration-energy-and-entropy-from-3d-rism
#20
J Johnson, D A Case, T Yamazaki, S Gusarov, A Kovalenko, T Luchko
Implicit solvent models offer an attractive way to estimate the effects of a solvent environment on the properties of small or large solutes without the complications of explicit simulations. One common test of accuracy is to compute the free energy of transfer from gas to liquid for a variety of small molecules, since many of these values have been measured. Studies of the temperature dependence of these values (i.e. solvation enthalpies and entropies) can provide additional insights into the performance of implicit solvent models...
September 1, 2016: Journal of Physics. Condensed Matter: An Institute of Physics Journal
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