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https://www.readbyqxmd.com/read/27914048/geometric-potentials-for-computational-protein-sequence-design
#1
Jie Li, Patrice Koehl
Computational protein sequence design is the rational design based on computer simulation of new protein molecules to fold to target three-dimensional structures, with the ultimate goal of designing novel functions. It requires a good understanding of the thermodynamic equilibrium properties of the protein of interest. Here, we consider the contribution of the solvent to the stability of the protein. We describe implicit solvent models, focusing on approximations of their nonpolar components using geometric potentials...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27913958/the-effect-of-mass-transfer-parameterization-and-ice-retention-on-the-scavenging-and-redistribution-of-so2-by-a-deep-convective-cloud
#2
Vladan Vučković, Dragana Vujović
A chemistry module with the aqueous chemistry coupled with the complex 3D nonhydrostatic atmospheric model is used to investigate how the representation of gas-aqueous mass transfer and ice retention affect the SO2 redistribution in the presence of a convective cloud. Gas uptake to the liquid water is calculated using both Henry's law equilibrium (HE) and kinetic mass transport (KMT). The constant retention coefficients for SO2 (k ret = 0.46) and for H2O2 (k ret = 0.64) are used. It is shown that the amount of SO2 in the air at higher altitudes (10-12 km) is greater when partial retention (PR) is included...
December 2, 2016: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/27913901/3d-active-passive-response-of-human-knee-joint-in-gait-is-markedly-altered-when-simulated-as-a-planar-2d-joint
#3
H Marouane, A Shirazi-Adl, M Adouni
Musculoskeletal models of the lower extremity make a number of important assumptions when attempting to estimate muscle forces and tibiofemoral compartmental loads in activities such as gait. The knee is commonly idealized as a planar 2D joint in the sagittal plane with no consideration of motions and equilibrium in remaining planes. With muscle forces predicted, the static equilibrium in the frontal plane is then used to estimate compartmental loads neglecting also joint passive resistance and assuming condylar contact centers...
December 2, 2016: Biomechanics and Modeling in Mechanobiology
https://www.readbyqxmd.com/read/27913070/basagran-%C3%A2-induces-developmental-malformations-and-changes-the-bacterial-community-of-zebrafish-embryos
#4
Jacinta M M Oliveira, Victor Galhano, Isabel Henriques, Amadeu M V M Soares, Susana Loureiro
This study aimed to assess the effects of Basagran(®) on zebrafish (Danio rerio) embryos. The embryos were exposed to Basagran(®) at concentrations ranging from 120.0 to 480.6 mg/L, and the effects on embryo development (up to 96 h) and bacterial communities of 96 h-larvae were assessed. The embryo development response was time-dependent and concentration-dependent (106.35 < EC50 < 421.58 mg/L). The sensitivity of embryo-related endpoints decreased as follows: blood clotting in the head and/or around the yolk sac > delay or anomaly in yolk sac absorption > change in swimming equilibrium > development of pericardial and/or yolk sac oedema > scoliosis...
November 29, 2016: Environmental Pollution
https://www.readbyqxmd.com/read/27912966/structure-related-related-new-approach-in-the-gc-ms-analysis-of-cathinone-type-synthetic-drugs
#5
Borbála Molnár, Blanka Fodor, Antal Csámpai, Előd Hidvégi, Ibolya Molnár-Perl
A novel, structure-related derivatization principle has been developed in order to quantify cathinone-type synthetic drugs (CTSDs), focusing on the most common pentedrone (PENT), including also 4-fluoromethcathinone (4-FMC), methcathinone (MCTN), 4-methylethcathinone (4-MEC), 3,4-dimethylmethcathinone (3,4-DMMC), and 4-ethylmethcathinone (4-EMC). Firstly, oximated and, secondly, trimethylsilylated CTSD derivatives were characterized by mass fragmentation patterns using GC/MS that led to the development of a harmonized, quantitative, two-steps derivatization methodology...
November 22, 2016: Journal of Chromatography. A
https://www.readbyqxmd.com/read/27912737/hcv-prevalence-can-predict-hiv-epidemic-potential-among-people-who-inject-drugs-mathematical-modeling-analysis
#6
Vajiheh Akbarzadeh, Ghina R Mumtaz, Susanne F Awad, Helen A Weiss, Laith J Abu-Raddad
BACKGROUND: Hepatitis C virus (HCV) and HIV are both transmitted through percutaneous exposures among people who inject drugs (PWID). Ecological analyses on global epidemiological data have identified a positive association between HCV and HIV prevalence among PWID. Our objective was to demonstrate how HCV prevalence can be used to predict HIV epidemic potential among PWID. METHODS: Two population-level models were constructed to simulate the evolution of HCV and HIV epidemics among PWID...
December 3, 2016: BMC Public Health
https://www.readbyqxmd.com/read/27912123/synthesis-of-hierarchical-porous-zinc-oxide-zno-microspheres-with-highly-efficient-adsorption-of-congo-red
#7
Chunsheng Lei, Meng Pi, Chuanjia Jiang, Bei Cheng, Jiaguo Yu
Hierarchical porous zinc oxide (ZnO) was successfully synthesized via a facile hydrothermal method followed by calcination, and characterized by X-ray diffraction, field-emission scanning electron microscopy, transmission electron microscopy, nitrogen adsorption-desorption, and Fourier transform infrared spectroscopy analyses. The as-prepared porous ZnO exhibits microsphere morphologies with diameters of 6-8μm, which are assembled from two-dimensional nanosheets. The as-prepared hierarchical porous ZnO microspheres possessed high specific surface areas (57m(2)/g), and were evaluated for adsorption of Congo red (CR) in aqueous solution...
November 15, 2016: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/27912114/remediation-of-cr-vi-by-inorganic-organic-clay
#8
Suramya I Rathnayake, Wayde N Martens, Yunfei Xi, Ray L Frost, Godwin A Ayoko
Application of inorganic-organic clays (IOCs) for the remediation of hexavalent chromium (Cr (VI)) and the effect of bisphenol-A (BPA) were investigated. IOCs were better adsorbents for the removal of Cr (VI) than organoclay. Solution pH significantly affected the surface charge of IOCs and speciation of Cr in the solution; hence, the adsorption of Cr onto IOCs. Pseudo-second order model and Langmuir model were the best fit for the kinetics and equilibrium data, indicating chemisorption and formation of monolayer on homogenous adsorption sites, respectively...
November 21, 2016: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/27912099/citrate-enhanced-release-of-arsenic-during-pyrite-oxidation-at-circumneutral-conditions
#9
Peng Zhang, Weiyu Yao, Songhu Yuan
The release of arsenic (As) from the oxidation of As-rich pyrite is an important source of the high arsenic in groundwater. As a widespread low-molecular-weight organic acid, citrate plays an important role on the cycling of Fe(II)/Fe(III) through complexation in circumneutral subsurface environments, while the influence of citrate on the release of As from the oxidation of As-rich pyrite is poorly understood. In this study, As was loaded onto pyrite particles under anoxic conditions, and its release was investigated in the presence of 0-1 mM citrate at pH 7...
November 24, 2016: Water Research
https://www.readbyqxmd.com/read/27911944/specific-stimuli-induce-specific-adaptations-sensorimotor-training-vs-reactive-balance-training
#10
Kathrin Freyler, Anne Krause, Albert Gollhofer, Ramona Ritzmann
Typically, balance training has been used as an intervention paradigm either as static or as reactive balance training. Possible differences in functional outcomes between the two modalities have not been profoundly studied. The objective of the study was to investigate the specificity of neuromuscular adaptations in response to two balance intervention modalities within test and intervention paradigms containing characteristics of both profiles: classical sensorimotor training (SMT) referring to a static ledger pivoting around the ankle joint vs...
2016: PloS One
https://www.readbyqxmd.com/read/27911906/adsorptive-removal-of-toxic-chromium-from-waste-water-using-wheat-straw-and-eupatorium-adenophorum
#11
Dagang Song, Kaiwen Pan, Akash Tariq, Azizullah Azizullah, Feng Sun, Zilong Li, Qinli Xiong
Environmental pollution with heavy metals is a serious issue worldwide posing threats to humans, animals and plants and to the stability of overall ecosystem. Chromium (Cr) is one of most hazardous heavy metals with a high carcinogenic and recalcitrant nature. Aim of the present study was to select low-cost biosorbent using wheat straw and Eupatorium adenophorum through simple carbonization process, capable of removing Cr (VI) efficiently from wastewater. From studied plants a low cost adsorbent was prepared for removing Cr (VI) from aqueous solution following very simple carbonization method excluding activation process...
2016: PloS One
https://www.readbyqxmd.com/read/27911881/low-energy-ne-ion-beam-induced-modifications-of-magnetic-properties-in-mnas-thin-films
#12
M Trassinelli, L Bernard Carlsson, S Cervera, M Eddrief, V H Etgens, E V Gafton, E Lacaze, E Lamour, A Lévy, S Macé, C Prigent, J-P Rozet, S Steydli, M Marangolo, D Vernhet
Investigations of the complex behavior of the magnetization of manganese arsenide thin films due to defects induced by irradiation of slow heavy ions are presented. In addition to the thermal hysteresis suppression already highlighted in Trassinelli et al (2014 Appl. Phys. Lett. 104 081906), we report here on new local magnetic features recorded by a magnetic force microscope at different temperatures close to the characteristic sample phase transition. Complementary measurements of the global magnetization in different conditions (applied magnetic field and temperatures) enable the film characterization to be completed...
December 2, 2016: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/27911789/design-principles-for-nonequilibrium-self-assembly
#13
Michael Nguyen, Suriyanarayanan Vaikuntanathan
We consider an important class of self-assembly problems, and using the formalism of stochastic thermodynamics, we derive a set of design principles for growing controlled assemblies far from equilibrium. The design principles constrain the set of configurations that can be obtained under nonequilibrium conditions. Our central result provides intuition for how equilibrium self-assembly landscapes are modified under finite nonequilibrium drive.
November 22, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27911787/data-driven-parameterization-of-the-generalized-langevin-equation
#14
Huan Lei, Nathan A Baker, Xiantao Li
We present a data-driven approach to determine the memory kernel and random noise in generalized Langevin equations. To facilitate practical implementations, we parameterize the kernel function in the Laplace domain by a rational function, with coefficients directly linked to the equilibrium statistics of the coarse-grain variables. We show that such an approximation can be constructed to arbitrarily high order and the resulting generalized Langevin dynamics can be embedded in an extended stochastic model without explicit memory...
November 29, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27911563/codecaying-dark-matter
#15
Jeff Asaf Dror, Eric Kuflik, Wee Hao Ng
We propose a new mechanism for thermal dark matter freeze-out, called codecaying dark matter. Multicomponent dark sectors with degenerate particles and out-of-equilibrium decays can codecay to obtain the observed relic density. The dark matter density is exponentially depleted through the decay of nearly degenerate particles rather than from Boltzmann suppression. The relic abundance is set by the dark matter annihilation cross section, which is predicted to be boosted, and the decay rate of the dark sector particles...
November 18, 2016: Physical Review Letters
https://www.readbyqxmd.com/read/27911547/parametric-symmetry-breaking-in-a-nonlinear-resonator
#16
Anina Leuch, Luca Papariello, Oded Zilberberg, Christian L Degen, R Chitra, Alexander Eichler
Much of the physical world around us can be described in terms of harmonic oscillators in thermodynamic equilibrium. At the same time, the far-from-equilibrium behavior of oscillators is important in many aspects of modern physics. Here, we investigate a resonating system subject to a fundamental interplay between intrinsic nonlinearities and a combination of several driving forces. We have constructed a controllable and robust realization of such a system using a macroscopic doubly clamped string. We experimentally observe a hitherto unseen double hysteresis in both the amplitude and the phase of the resonator's response function and present a theoretical model that is in excellent agreement with the experiment...
November 18, 2016: Physical Review Letters
https://www.readbyqxmd.com/read/27911295/efficacy-and-safety-of-plasma-exchange-with-5-albumin-to-modify-cerebrospinal-fluid-and-plasma-amyloid-%C3%AE-concentrations-and-cognition-outcomes-in%C3%A2-alzheimer-s-disease-patients-a%C3%A2-multicenter-randomized-controlled-clinical-trial
#17
Mercè Boada, Fernando Anaya, Pilar Ortiz, Javier Olazarán, Joshua R Shua-Haim, Thomas O Obisesan, Isabel Hernández, Joan Muñoz, Mar Buendia, Montserrat Alegret, Asunción Lafuente, Lluís Tárraga, Laura Núñez, Mireia Torres, Joan Ramon Grifols, Isidre Ferrer, Oscar L Lopez, Antonio Páez
BACKGROUND: Studies conducted in animal models and humans suggest the presence of a dynamic equilibrium of amyloid-β (Aβ) peptide between cerebrospinal fluid (CSF) and plasma compartments. OBJECTIVE: To determine whether plasma exchange (PE) with albumin replacement was able to modify Aβ concentrations in CSF and plasma as well as to improve cognition in patients with mild-moderate Alzheimer's disease (AD). METHODS: In a multicenter, randomized, patient- and rater-blind, controlled, parallel-group, phase II study, 42 AD patients were assigned (1 : 1) to PE treatment or control (sham) groups...
November 28, 2016: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/27910991/structural-fingerprints-of-yielding-mechanisms-in-attractive-colloidal-gels
#18
Arman Boromand, Safa Jamali, João M Maia
Core-Modified Dissipative Particle Dynamics (CM-DPD) with a modified depletion potential and full hydrodynamics description is used to study non-equilibrium properties of colloidal gels with short range attraction potentials at an intermediate volume fraction (ϕ = 0.2) under start-up shear deformation. Full structural and rheological analysis using the stress fabric tensor complemented by bond number and bond distribution evolution under flow reveals that similarly to dilute colloidal gels, flow-induced anisotropy and strain-induced stretching of bonds are present during the first yielding transition...
December 2, 2016: Soft Matter
https://www.readbyqxmd.com/read/27910657/time-dependent-analysis-of-visible-helium-line-ratios-for-electron-temperature-and-density-diagnostic-using-synthetic-simulations-on-nstx-u
#19
J M Muñoz Burgos, T Barbui, O Schmitz, D Stutman, K Tritz
Helium line-ratios for electron temperature (Te) and density (ne) plasma diagnostic in the Scrape-Off-Layer (SOL) and edge regions of tokamaks are widely used. Due to their intensities and proximity of wavelengths, the singlet, 667.8 and 728.1 nm, and triplet, 706.5 nm, visible lines have been typically preferred. Time-dependency of the triplet line (706.5 nm) has been previously analyzed in detail by including transient effects on line-ratios during gas-puff diagnostic applications. In this work, several line-ratio combinations within each of the two spin systems are analyzed with the purpose of eliminating transient effects to extend the application of this powerful diagnostic to high temporal resolution characterization of plasmas...
November 2016: Review of Scientific Instruments
https://www.readbyqxmd.com/read/27910649/upgrades-to-improve-the-usability-reliability-and-spectral-range-of-the-mst-thomson-scattering-diagnostic
#20
S Z Kubala, M T Borchardt, D J Den Hartog, D J Holly, C M Jacobson, L A Morton, W C Young
The Thomson scattering diagnostic on MST records both equilibrium and fluctuating electron temperature with a range capability of 10 eV-5 keV. Standard operation with two modified commercial Nd:YAG lasers allows measurements at rates of 1 kHz-25 kHz. Several subsystems of the diagnostic are being improved. The power supplies for the avalanche photodiode detectors (APDs) that record the scattered light are being replaced to improve usability, reliability, and maintainability. Each of the 144 APDs will have an individual rack mounted switching supply, with bias voltage adjustable to match the APD...
November 2016: Review of Scientific Instruments
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