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https://www.readbyqxmd.com/read/28088149/collective-excitations-in-liquid-dimethyl-sulfoxide-dmso-fir-spectrum-low-frequency-vibrational-density-of-states-and-ultrafast-dipolar-solvation-dynamics
#1
Milan K Hazra, Biman Bagchi
Valuable dynamical and structural information about neat liquid DMSO at ambient conditions can be obtained through a study of low frequency vibrations in the far infrared (FIR), that is, terahertz regime. For DMSO, collective excitations as well as single molecule stretches and bends have been measured by different kinds of experiments such as OHD-RIKES and terahertz spectroscopy. In the present work, we investigate the intermolecular vibrational spectrum of DMSO through three different computational techniques namely (i) the far-infrared spectrum obtained through the Fourier transform of total dipole moment auto-time correlation function, (ii) from the Fourier transform of the translational and angular velocity time autocorrelation functions, and (iii) a quenched normal mode analysis of the parent liquid at 300 K...
January 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28088071/discrete-quasi-linear-viscoelastic-damping-analysis-of-connective-tissues-and-the-biomechanics-of-stretching
#2
Behzad Babaei, Aaron J Velasquez-Mao, Stavros Thomopoulos, Elliot L Elson, Steven D Abramowitch, Guy M Genin
The time- and frequency-dependent properties of connective tissue define their physiological function, but are notoriously difficult to characterize. Well-established tools such as linear viscoelasticity and the Fung quasi-linear viscoelastic (QLV) model impose forms on responses that can mask true tissue behavior. Here, we applied a more general discrete quasi-linear viscoelastic (DQLV) model to identify the static and dynamic time- and frequency-dependent behavior of rabbit medial collateral ligaments. Unlike the Fung QLV approach, the DQLV approach revealed that energy dissipation is elevated at a loading period of ∼10s...
December 22, 2016: Journal of the Mechanical Behavior of Biomedical Materials
https://www.readbyqxmd.com/read/28087342/myeloid-leukemia-factor-1-is-a-novel-modulator-of-neonatal-rat-cardiomyocyte-proliferation
#3
Ashraf Yusuf Rangrez, Jost Pott, Annika Kluge, Robert Frauen, Katharina Stiebeling, Phillip Hoppe, Samuel Sossalla, Norbert Frey, Derk Frank
The present study focuses on the identification of the gene expression profile of neonatal rat cardiomyocytes (NRVCMs) after dynamic mechanical stretch through microarrays of RNA isolated from cells stretched for 2, 6 or 24h. In this analysis, myeloid leukemia factor-1 (MLF1) was found to be significantly downregulated during the course of stretch. We found that MLF1 is highly expressed in the heart, however, its cardiac function is unknown yet. In line with microarray data, MLF1 was profoundly downregulated in in vivo mouse models of cardiomyopathy, and also significantly reduced in the hearts of human patients with dilated cardiomyopathy...
January 10, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28079374/ultrafast-dynamics-of-hydrogen-bond-breaking-and-making-in-the-excited-state-of-fluoren-9-one-time-resolved-visible-pump-ir-probe-spectroscopic-study
#4
Rajib Ghosh, Aruna K Mora, Sukhendu Nath, Dipak K Palit
Fluoren-9-one (FL) molecule with a single hydrogen bond accepting site (C=O group) has been used as a probe for investigation of the dynamics of hydrogen bond in its lowest excited singlet (S1) state using subpicosecond time-resolved visible pump - IR probe spectroscopic technique. In hexafluoroisopropanol (HFIP), a strong hydrogen bond donating solvent, formation of FL-alcohol hydrogen bonded complex in the ground electronic (S0) state is nearly complete with negligible concentration of FL molecule remaining free in solution...
January 12, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28075155/a-qualitative-study-exploring-community-yoga-practice-in-adults-with-rheumatoid-arthritis
#5
Heather M Greysen, S Ryan Greysen, Kathryn A Lee, Oi Saeng Hong, Patricia Katz, Heather Leutwyler
OBJECTIVE: Yoga may improve physical function and reduce disease symptoms in adults with rheumatoid arthritis (RA). However, little is known about how patients with RA are practicing yoga in the community. The objective of this qualitative study was to explore community yoga practice characteristics and thoughts about yoga practice for adults with RA. DESIGN: Participants completed a semi-structured telephone interview with open-ended questions. Thematic analysis was used to analyze interview transcripts...
January 11, 2017: Journal of Alternative and Complementary Medicine: Research on Paradigm, Practice, and Policy
https://www.readbyqxmd.com/read/28074204/surfactants-adsorption-on-crossing-stripes-and-steps
#6
Manaswee Suttipong, Brian P Grady, Alberto Striolo
Using coarse-grained dissipative particle dynamics (DPD) simulations, we systematically study the effect of surface heterogeneity on surfactant adsorption. Here we investigate the adsorption and aggregation of surfactants on hydrophobic stripes crossing each other perpendicularly (i.e., crossing stripes) and on hydrophobic steps. The results are compared with those obtained for isolated stripes. We find that on crossing stripes of moderate stripe widths (e.g., L = 0.61LS, 1.22LS and 1.83LS, where LS is the length of one surfactant molecule) the crossing region hinders the formation of defect-free adsorbed surfactant structures...
January 11, 2017: Soft Matter
https://www.readbyqxmd.com/read/28068771/perturbation-approach-for-computing-infrared-spectra-of-the-local-mode-of-probe-molecules
#7
Rui-Jie Xue, Adam Grofe, He Yin, Zexing Qu, Jiali Gao, Hui Li
Linear and two-dimensional infrared (IR) spectroscopy of site-specific probe molecules provides an opportunity to gain a molecular-level understanding of the local hydrogen-bonding network, conformational dynamics, and long-range electrostatic interactions in condensed-phase and biological systems. A challenge in computation is to determine the time-dependent vibrational frequencies that incorporate explicitly both nuclear quantum effects of vibrational motions and an electronic structural representation of the potential energy surface...
January 10, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28067863/dynamic-features-of-the-highly-excited-vibrational-states-of-the-hocl-non-integrable-system-based-on-the-dynamic-potential-and-lyapunov-exponent-approaches
#8
Aixing Wang, Chao Fang, Yibao Liu
In this article the dynamic features of the highly excited vibrational states of the hypochlorous acid (HOCl) non-integrable system are studied using the dynamic potential and Lyapunov exponent approaches. On the condition that the 3:1 resonance between the H-O stretching and H-O-Cl bending modes accompany the 2:1 Fermi resonance between the O-Cl stretching and H-O-Cl bending modes, it is found that the dynamic potentials of the highly excited vibrational states vary regularly with different Polyad numbers (P numbers)...
January 7, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28064404/heterogeneous-nanomechanical-properties-of-type-i-collagen-in-longitudinal-direction
#9
Ming Tang, Tong Li, Neha S Gandhi, Kevin Burrage, YuanTong Gu
Collagen is an abundant structural biopolymer in mammal vertebrates, providing structural support as well as mechanical integrity for connective tissues such as bone, ligament, and tendon. The mechanical behaviours of these tissues are determined by the nanomechanics of their structures at different hierarchies and the role of collagen structures in the extracellular matrix. Some studies revealed that there is significant microstructural difference in the longitudinal direction of the collagen fibril, which challenges the conventional rod-like assumption prevalently adopted in the existing studies...
January 7, 2017: Biomechanics and Modeling in Mechanobiology
https://www.readbyqxmd.com/read/28059762/highly-stretchable-polymer-semiconductor-films-through-the-nanoconfinement-effect
#10
Jie Xu, Sihong Wang, Ging-Ji Nathan Wang, Chenxin Zhu, Shaochuan Luo, Lihua Jin, Xiaodan Gu, Shucheng Chen, Vivian R Feig, John W F To, Simon Rondeau-Gagné, Joonsuk Park, Bob C Schroeder, Chien Lu, Jin Young Oh, Yanming Wang, Yun-Hi Kim, He Yan, Robert Sinclair, Dongshan Zhou, Gi Xue, Boris Murmann, Christian Linder, Wei Cai, Jeffery B-H Tok, Jong Won Chung, Zhenan Bao
Soft and conformable wearable electronics require stretchable semiconductors, but existing ones typically sacrifice charge transport mobility to achieve stretchability. We explore a concept based on the nanoconfinement of polymers to substantially improve the stretchability of polymer semiconductors, without affecting charge transport mobility. The increased polymer chain dynamics under nanoconfinement significantly reduces the modulus of the conjugated polymer and largely delays the onset of crack formation under strain...
January 6, 2017: Science
https://www.readbyqxmd.com/read/28049327/molecular-simulation-of-flow-enhanced-nucleation-in-n-eicosane-melts-under-steady-shear-and-uniaxial-extension
#11
David A Nicholson, Gregory C Rutledge
Non-equilibrium molecular dynamics is used to study crystal nucleation of n-eicosane under planar shear and, for the first time, uniaxial extension. A method of analysis based on the mean first-passage time is applied to the simulation results in order to determine the effect of the applied flow field type and strain rate on the steady-state nucleation rate and a characteristic growth rate, as well as the effects on kinetic parameters associated with nucleation: the free energy barrier, critical nucleus size, and monomer attachment pre-factor...
December 28, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28049324/relaxation-pathways-of-the-od-stretch-fundamental-of-hod-in-liquid-h2o
#12
Beatriz Miguel, José Zúñiga, Alberto Requena, Adolfo Bastida
The molecular dynamics with quantum transitions method is used to study the vibrational relaxation of the OD stretching mode of HOD dissolved in liquid H2O water at 303 K. All the vibrational modes of the solute and solvent molecules that participate in the relaxation process are described by quantum mechanics, while the rotational and translational degrees of freedom are treated classically. A modification of the water intramolecular SPC/E (Simple Point Charge/Extended) force field providing vibrational frequencies in solution closer to the experimental values is proposed to analyze the influence of the vibrational energy gaps on the relaxation channels...
December 28, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28049314/internal-dynamics-of-microgels-a-mesoscale-hydrodynamic-simulation-study
#13
Ali Ghavami, Hideki Kobayashi, Roland G Winkler
We analyze the dynamics of polymers in a microgel system under different swelling conditions. A microgel particle consists of coarse-grained linear polymers which are tetra-functionally crosslinked and undergoes conformational changes in response to the external stimuli. Here, a broad range of microgel sizes, extending from tightly collapsed to strongly swollen particles, is considered. In order to account for hydrodynamic interactions, the microgel is embedded in a multiparticle collision dynamics fluid while hydrophobic attraction is modelled by an attractive Lennard-Jones potential and swelling of ionic microgels is described through the Debye-Hückel potential...
December 28, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28036175/modeling-carbon-dioxide-vibrational-frequencies-in-ionic-liquids-i-ab-initio-calculations
#14
Eric J Berquist, Clyde A Daly, Thomas Brinzer, Krista K Bullard, Zachary M Campbell, Steven A Corcelli, Sean Garrett-Roe, Daniel S Lambrecht
This work elucidates the molecular binding mechanism of CO2 in [C4C1IM][PF6] ionic liquid (IL) and its interplay with the CO2 asymmetric stretch frequency ν3, and establishes computational protocols for the reliable construction of spectroscopic maps for simulating ultrafast 2D-IR data of CO2 solvated in ILs. While charge transfer drives the static frequency shift between different ionic liquids ( J. Chem. Phys. 2015 , 142 , 212425 ), we find here that electrostatic and Pauli repulsion effects dominate the dynamical frequency shift between different geometries sampled from the finite-temperature dynamics within a single ionic liquid...
December 30, 2016: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28034301/mechanistic-differences-between-hiv-1-and-siv-nucleocapsid-proteins-and-cross-species-hiv-1-genomic-rna-recognition
#15
Klara Post, Erik D Olson, M Nabuan Naufer, Robert J Gorelick, Ioulia Rouzina, Mark C Williams, Karin Musier-Forsyth, Judith G Levin
BACKGROUND: The nucleocapsid (NC) domain of HIV-1 Gag is responsible for specific recognition and packaging of genomic RNA (gRNA) into new viral particles. This occurs through specific interactions between the Gag NC domain and the Psi packaging signal in gRNA. In addition to this critical function, NC proteins are also nucleic acid (NA) chaperone proteins that facilitate NA rearrangements during reverse transcription. Although the interaction with Psi and chaperone activity of HIV-1 NC have been well characterized in vitro, little is known about simian immunodeficiency virus (SIV) NC...
December 29, 2016: Retrovirology
https://www.readbyqxmd.com/read/28032999/dynamic-flexibility-of-hydrogenase-active-site-models-studied-with-2d-ir-spectroscopy
#16
Peter A Eckert, Kevin J Kubarych
Hydrogenase enzymes enable organisms to use H2 as an energy source, having evolved extremely efficient biological catalysts for the reversible oxidation of molecular hydrogen. Small-molecule mimics of these enzymes provide both simplified models of the catalysis reactions and potential artificial catalysts that might be used to facilitate a hydrogen economy. We have studied two diiron hydrogenase mimics, μ-pdt-[Fe(CO)3]2 and μ-edt-[Fe(CO)3]2 (pdt = propanedithiolate, edt = ethanedithiolate), in a series of alkane solvents and have observed significant ultrafast spectral dynamics using two-dimensional infrared (2D-IR) spectroscopy...
January 12, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28028244/origin-of-hydrophobicity-and-enhanced-water-hydrogen-bond-strength-near-purely-hydrophobic-solutes
#17
Joze Grdadolnik, Franci Merzel, Franc Avbelj
Hydrophobicity plays an important role in numerous physicochemical processes from the process of dissolution in water to protein folding, but its origin at the fundamental level is still unclear. The classical view of hydrophobic hydration is that, in the presence of a hydrophobic solute, water forms transient microscopic "icebergs" arising from strengthened water hydrogen bonding, but there is no experimental evidence for enhanced hydrogen bonding and/or icebergs in such solutions. Here, we have used the redshifts and line shapes of the isotopically decoupled IR oxygen-deuterium (O-D) stretching mode of HDO water near small purely hydrophobic solutes (methane, ethane, krypton, and xenon) to study hydrophobicity at the most fundamental level...
December 27, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28018663/geohistorical-records-indicate-no-impact-of-the-deepwater-horizon-oil-spill-on-oyster-body-size
#18
Gregory P Dietl, Stephen R Durham
Documentation of the near- and long-term effects of the Deepwater Horizon (DWH) oil spill, one of the largest environmental disasters in US history, is still ongoing. We used a novel before-after-control-impact analysis to test the hypothesis that average body size of intertidal populations of the eastern oyster (Crassostrea virginica) inhabiting impacted areas in Louisiana decreased due to increased stress/mortality related to the oil spill. Time-averaged death assemblages of oysters were used to establish a pre-spill baseline of body-size structure for four impacted and four control locations along a 350 km stretch of Louisiana's coastline...
November 2016: Royal Society Open Science
https://www.readbyqxmd.com/read/28010074/effect-of-sequence-dispersity-on-morphology-of-tapered-diblock-copolymers-from-molecular-dynamics-simulations
#19
William G Levine, Youngmi Seo, Jonathan R Brown, Lisa M Hall
Tapered diblock copolymers are similar to typical AB diblock copolymers but have an added transition region between the two blocks which changes gradually in composition from pure A to pure B. This tapered region can be varied from 0% (true diblock) to 100% (gradient copolymer) of the polymer length, and this allows some control over the microphase separated domain spacing and other material properties. We perform molecular dynamics simulations of linearly tapered block copolymers with tapers of various lengths, initialized from fluids density functional theory predictions...
December 21, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28002739/hydrogen-bond-network-of-water-around-protein-investigated-with-terahertz-and-infrared-spectroscopy
#20
Keiichiro Shiraga, Yuichi Ogawa, Naoshi Kondo
The dynamical and structural properties of water at protein interfaces were characterized on the basis of the broadband complex dielectric constant (0.25 to 400 THz) of albumin aqueous solutions. Our analysis of the dielectric responses between 0.25 and 12 THz first revealed hydration water with retarded reorientational dynamics extending ∼8.5 Å (corresponding to three to four layers) out from the albumin surface. Second, the number of nonhydrogen-bonded water was decreased in the presence of the albumin solute, indicating protein inhibits the fragmentation of the water hydrogen-bond network...
December 20, 2016: Biophysical Journal
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