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https://www.readbyqxmd.com/read/27760249/multidirectional-in-vivo-characterization-of-skin-using-wiener-nonlinear-stochastic-system-identification-techniques
#1
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
#2
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
#3
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
#4
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
#5
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
https://www.readbyqxmd.com/read/27365866/numerical-treatment-of-stokes-solvent-flow-and-solute-solvent-interfacial-dynamics-for-nonpolar-molecules
#6
Hui Sun, Shenggao Zhou, David K Moore, Li-Tien Cheng, Bo Li
We design and implement numerical methods for the incompressible Stokes solvent flow and solute-solvent interface motion for nonpolar molecules in aqueous solvent. The balance of viscous force, surface tension, and van der Waals type dispersive force leads to a traction boundary condition on the solute-solvent interface. To allow the change of solute volume, we design special numerical boundary conditions on the boundary of a computational domain through a consistency condition. We use a finite difference ghost fluid scheme to discretize the Stokes equation with such boundary conditions...
May 2016: Journal of Scientific Computing
https://www.readbyqxmd.com/read/27112404/accurate-measurement-of-liquid-transport-through-nanoscale-conduits
#7
Mohammad Amin Alibakhshi, Quan Xie, Yinxiao Li, Chuanhua Duan
Nanoscale liquid transport governs the behaviour of a wide range of nanofluidic systems, yet remains poorly characterized and understood due to the enormous hydraulic resistance associated with the nanoconfinement and the resulting minuscule flow rates in such systems. To overcome this problem, here we present a new measurement technique based on capillary flow and a novel hybrid nanochannel design and use it to measure water transport through single 2-D hydrophilic silica nanochannels with heights down to 7 nm...
2016: Scientific Reports
https://www.readbyqxmd.com/read/26993234/a-two-dimensional-microscale-model-of-gas-exchange-during-photosynthesis-in-maize-zea-mays-l-leaves
#8
Moges Retta, Quang Tri Ho, Xinyou Yin, Pieter Verboven, Herman N C Berghuijs, Paul C Struik, Bart M Nicolaï
CO2 exchange in leaves of maize (Zea mays L.) was examined using a microscale model of combined gas diffusion and C4 photosynthesis kinetics at the leaf tissue level. Based on a generalized scheme of photosynthesis in NADP-malic enzyme type C4 plants, the model accounted for CO2 diffusion in a leaf tissue, CO2 hydration and assimilation in mesophyll cells, CO2 release from decarboxylation of C4 acids, CO2 fixation in bundle sheath cells and CO2 retro-diffusion from bundle sheath cells. The transport equations were solved over a realistic 2-D geometry of the Kranz anatomy obtained from light microscopy images...
May 2016: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/26957601/energy-landscape-in-protein-folding-and-unfolding
#9
Francesco Mallamace, Carmelo Corsaro, Domenico Mallamace, Sebastiano Vasi, Cirino Vasi, Piero Baglioni, Sergey V Buldyrev, Sow-Hsin Chen, H Eugene Stanley
We use (1)H NMR to probe the energy landscape in the protein folding and unfolding process. Using the scheme ⇄ reversible unfolded (intermediate) → irreversible unfolded (denatured) state, we study the thermal denaturation of hydrated lysozyme that occurs when the temperature is increased. Using thermal cycles in the range 295 < T < 365 K and following different trajectories along the protein energy surface, we observe that the hydrophilic (the amide NH) and hydrophobic (methyl CH3 and methine CH) peptide groups evolve and exhibit different behaviors...
March 22, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/26896984/isotopomer-selective-spectra-of-a-single-intact-h2o-molecule-in-the-cs-d2o-5h2o-isotopologue-going-beyond-pattern-recognition-to-harvest-the-structural-information-encoded-in-vibrational-spectra
#10
Conrad T Wolke, Joseph A Fournier, Evangelos Miliordos, Shawn M Kathmann, Sotiris S Xantheas, Mark A Johnson
We report the vibrational signatures of a single H2O molecule occupying distinct sites of the hydration network in the Cs(+)(H2O)6 cluster. This is accomplished using isotopomer-selective IR-IR hole-burning on the Cs(+)(D2O)5(H2O) clusters formed by gas-phase exchange of a single, intact H2O molecule for D2O in the Cs(+)(D2O)6 ion. The OH stretching pattern of the Cs(+)(H2O)6 isotopologue is accurately recovered by superposition of the isotopomer spectra, thus establishing that the H2O incorporation is random and that the OH stretching manifold is largely due to contributions from decoupled water molecules...
February 21, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/26841516/-on-two-opposing-bio-surfaces-as-comprehended-in-terms-of-an-extension-of-the-coulomb-amontons-law-of-friction-with-its-virtual-usefulness-for-biotribology-in-nanoscale
#11
A Gadomski, J Hladyszowski
An extension of the Coulomb-Amontons law is proposed in terms of an interaction-detail involving renormalization (simplified) n-th level scheme. The coefficient of friction is obtained in a general exponential (nonlinear) form, characteristic of virtually infinite (or, many body) level of the interaction map. Yet, its application for a hydration repulsion bilayered system, prone to facilitated lubrication, is taken as linearly confined, albeit with an inclusion of a decisive repelling force/pressure factor...
November 2015: Biofizika
https://www.readbyqxmd.com/read/26829851/-effectiveness-of-fullerene-tris-aminocapronic-acid-hydrate-in-the-model-of-experimental-viral-bacterial-pneumonia-of-mice
#12
I N Falynskova, E I Leonova, I T Fedyakina, N R Makhmudova, L N Lepekha, N A Mikhailova, L D Rasnetsov, V V Zverev, I A Leneva
AIM: Study the effectiveness of the substance and various drug formulations of fullerene-(tris-aminocapronic acid) hydrate (FTAAH onwards) in the model of experimental viral-bacterial pneumonia of mice. MATERIALS AND METHODS: BALB/c mice were infected with influenza virus A/California/04/2009 and subsequently infected with Staphylococcus aureus. The animals were treated after viral infection with the substance and various drug forms of FTAAH, as well as comparative preparations--oseltamivir and arbidol...
September 2015: Zhurnal Mikrobiologii, Epidemiologii, i Immunobiologii
https://www.readbyqxmd.com/read/26805183/-a-case-of-advanced-breast-cancer-in-which-marked-improvement-of-joint-pain-was-obtained-with-stepwise-dose-reduction-of-trastuzumab-emtansine-t-dm1
#13
Nobushige Yabe, Shinji Murai, Yoko Harada, Takahiro Yokose, Takamichi Yokoe, Ippei Oto, Takahisa Yoshikawa, Kenjiro Kitasato, Hirotomo Shimizu, Hiromitsu Jinno, Yuko Kitagawa
A 51-year-old woman had previously received treatment for breast cancer at another hospital but had refused early and aggressive treatment. Therefore, she was treated with symptomatic therapy. As her disease progressed, the patient wished to receive palliative care, and was transferred to a palliative care hospital. However, based on her general condition, it was determined that aggressive treatment should not be abandoned, and she was referred to our hospital for treatment. During her initial visit, the patient was found to have left breast cancer with chest wall invasion, right breast metastasis, multiple liver and lung metastases, left pleural effusion accompanied by pleural dissemination, and left upper limb edema...
November 2015: Gan to Kagaku Ryoho. Cancer & Chemotherapy
https://www.readbyqxmd.com/read/26742826/the-dangerous-new-synthetic-drug-%C3%AE-pvp-as-the-hydrated-chloride-salt-%C3%AE-pyrrolidinopentiophenone-hydrochloride-0-786-hydrate
#14
Matthew R Wood, Ivan Bernal, Roger A Lalancette
α-Pyrrolidinovalerophenone (α-PVP), a dangerous designer drug, is now being marketed around the world as a harmless `bath salt', when in reality it is a powerful β-ketone phenethylamine stimulant. A sample of the free base from a recent law-enforcement seizure was crystallized as the HCl salt [systematic name: 1-(1-oxo-1-phenylpentan-2-yl)pyrrolidin-1-ium chloride 0.786-hydrate], C15H22NO(+)·Cl(-)·0.786H2O. In the crystal structure, the propyl chain is nearly perpendicular to both the phenyl ring and the carbonyl group...
January 2016: Acta Crystallographica. Section C, Structural Chemistry
https://www.readbyqxmd.com/read/26742824/hydrogen-bonding-patterns-in-bis-2-4-6-triazaniumylcyclohexane-1-3-5-tris-olate-%C3%AE%C2%BA-3-o-o-o-germanium-iv-tetrachloride-hexahydrate
#15
Christian Neis, Bernd Morgenstern, Kaspar Hegetschweiler
A first preliminary report on the crystal structure of a hydrated salt formulated as [Ge(taci)2]Cl4·13H2O (taci is 1,3,5-triamino-1,3,5-trideoxy-cis-inositol) appeared more than 20 years ago [Ghisletta (1994). PhD thesis, ETH Zürich. Switzerland]. At that time it was not possible to discriminate unambiguously between the positions of some of the chloride ions and water O atoms, and disorder was thus postulated. In a new determination, a conclusive scheme of hydrogen bonding proves to be a particularly appealing aspect of the structure...
January 2016: Acta Crystallographica. Section C, Structural Chemistry
https://www.readbyqxmd.com/read/26633230/toward-the-prediction-of-organic-hydrate-crystal-structures
#16
Ashley T Hulme, Sarah L Price
Lattice energy minimization studies on four ordered crystal structures of ice and 22 hydrates of approximately rigid organic molecules (along with 11 corresponding anhydrate structures) were used to establish a model potential scheme, based on the use of a distributed multipole electrostatic model, that can reasonably reproduce the crystal structures. Transferring the empirical repulsion-dispersion potentials for organic oxygen and polar hydrogen atoms to water appears more successful for modeling ice phases than using common water potentials derived from liquid properties...
July 2007: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/26616769/a-graphics-processing-unit-implementation-of-coulomb-interaction-in-molecular-dynamics
#17
Prateek K Jha, Rastko Sknepnek, Guillermo Iván Guerrero-García, Monica Olvera de la Cruz
We report a GPU implementation in HOOMD Blue of long-range electrostatic interactions based on the orientation-averaged Ewald sum scheme, introduced by Yakub and Ronchi (J. Chem. Phys. 2003, 119, 11556). The performance of the method is compared to an optimized CPU version of the traditional Ewald sum available in LAMMPS, in the molecular dynamics of electrolytes. Our GPU implementation is significantly faster than the CPU implementation of the Ewald method for small to a sizable number of particles (∼10(5))...
October 12, 2010: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/26613484/practically-efficient-qm-mm-alchemical-free-energy-simulations-the-orthogonal-space-random-walk-strategy
#18
Donghong Min, Lianqing Zheng, William Harris, Mengen Chen, Chao Lv, Wei Yang
The difference between free energy changes occurring at two chemical states can be rigorously estimated via alchemical free energy (AFE) simulations. Traditionally, most AFE simulations are carried out under the classical energy potential treatment; then, accuracy and applicability of AFE simulations are limited. In the present work, we integrate a recent second-order generalized ensemble strategy, the orthogonal space random walk (OSRW) method, into the combined quantum mechanical/molecular mechanical (QM/MM) potential based AFE simulation scheme...
August 10, 2010: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/26609601/computations-of-absolute-solvation-free-energies-of-small-molecules-using-explicit-and-implicit-solvent-model
#19
Devleena Shivakumar, Yuqing Deng, Benoît Roux
Accurate determination of absolute solvation free energy plays a critical role in numerous areas of biomolecular modeling and drug discovery. A quantitative representation of ligand and receptor desolvation, in particular, is an essential component of current docking and scoring methods. Furthermore, the partitioning of a drug between aqueous and nonpolar solvents is one of the important factors considered in pharmacokinetics. In this study, the absolute hydration free energy for a set of 239 neutral ligands spanning diverse chemical functional groups commonly found in drugs and drug-like candidates is calculated using the molecular dynamics free energy perturbation method (FEP/MD) with explicit water molecules, and compared to experimental data as well as its counterparts obtained using implicit solvent models...
April 14, 2009: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/26606339/linear-scaling-constrained-density-functional-theory-in-conquest
#20
Alex M P Sena, Tsuyoshi Miyazaki, David R Bowler
The constrained density functional theory (cDFT) formalism is implemented in the linear scaling density functional theory (DFT) code CONQUEST. This will enable the simulation of electron-transfer processes in large biologically and technologically relevant systems. The Becke weight population scheme is chosen to define the constraint, as it enables force components to be calculated both analytically and efficiently in a linear scaling code. It is demonstrated that the imposition of a constraint is not affected by the truncation of the density matrix...
April 12, 2011: Journal of Chemical Theory and Computation
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