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Dynamic stretching

Essam Hammam, Jalal Basahi, Iqbal Ismail, Ibrahim Hassan, Talal Almeelbi
The excited state hydrogen bonding dynamics of BBVN in hydrogen donating methanol solvent was explored at the TD-BMK/cc-pVDZ level of theory with accounting for the bulk environment effects at the polarizable continuum model (PCM). The heteroatoms of the BBVN laser dye form hydrogen bonds with four methanol molecules. In the formed BBVN-(MeOH)4 complex, the A-type hydrogen bond (N…HO), of an average strength of 25kJmol(-1), is twofold stronger than the B-type (O…HO) one. Upon photon absorption, the total HB binding energy increases from 78...
October 17, 2016: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
Long Liang, Christopher Jones, Shaohua Chen, Bo Sun, Yang Jiao
Collagen networks play an important role in coordinating and regulating collective cellular dynamics via a number of signaling pathways. Here, we investigate the transmission of forces generated by contractile cells in 3D collagen-I networks. Specifically, the graph (bond-node) representations of collagen networks with collagen concentrations of 1, 2 and 4 mg ml(-1) are derived from confocal microscopy data and used to model the network microstructure. Cell contraction is modeled by applying correlated displacements at specific nodes of the network, representing the focal adhesion sites...
October 25, 2016: Physical Biology
Hyun Jin Yang, Michael Trenary, Maki Kawai, Yousoo Kim
In contrast to conventional spectroscopic studies of adsorbates at high coverage that provide only spatially averaged information, we have characterized the laterally confined shuttling dynamics of a single molecule under the influence of intermolecular interactions by vibrational spectroscopy using a scanning tunneling microscope. The bridge sites on Pt(111) are only occupied by a CO molecule that is surrounded by four other CO molecules at on-top sites. The bridge-site CO undergoes laterally confined shuttling toward an adjacent on-top site to transiently occupy a metastable site, which is slightly displaced from the center of an on-top site through repulsive interaction with adjacent on-top CO molecules...
October 24, 2016: Journal of Physical Chemistry Letters
Bogdan I Costescu, Sebastian Sturm, Frauke Gräter
Protein unfolding often does not obey a simple two-state behavior. Previous single molecule force spectroscopy studies demonstrated stretched exponential kinetics of protein unfolding under a constant pulling force, the molecular origin of which remains subject to debate. We here set out to extensively sample the mechanical unfolding of ubiquitin and NuG2 by Molecular Dynamics (MD) simulations. Both proteins show kinetics best fit by stretched exponentials, with stretching exponents similar to those found in experiments, even though static disorder is absent in our short MD simulations...
October 19, 2016: Journal of Structural Biology
Alexis V Mickelson, Sampath K Gollapudi, Murali Chandra
The present study investigated the functional consequences of the human hypertrophic cardiomyopathy (HCM) mutation, A28V, in cardiac troponin T (TnT). The A28V mutation is located within the N-terminus of TnT, a region known to be important for full activation of cardiac thin filaments. The functional consequences of the A28V mutation in TnT remain unknown. Given how α- and β-myosin heavy chain (MHC) isoforms differently alter the effect of the N-terminus of TnT, we hypothesized that the A28V-induced effects would be differently modulated by α- and β-MHC isoforms...
October 21, 2016: American Journal of Physiology. Heart and Circulatory Physiology
Jonathan T Kaplan, Corey P Neu, Hicham Drissi, Nancy C Emery, David M Pierce
Osteoarthritis and articular cartilage injuries are common conditions in human joints and a frequent cause of pain and disability. Unfortunately, cartilage is avascular and has limited capabilities for self-repair. Despite the societal impact, there is little information on the dynamic process of cartilage degeneration. We performed a series of cyclic unconfined compression tests motivated by in vivo loading conditions and designed to generate mechanical fatigue. We examined the functional (both stress-stretch and creep) responses of the tissue after recovery from a specified number of loading cycles, as well as histology and second harmonic generation microscopy images...
October 1, 2016: Journal of the Mechanical Behavior of Biomedical Materials
Pengyun Yu, Yan Zhao, Fan Yang, Huifen Pan, Jianru Wang, Juan Zhao, Wenming Wang, Hongfei Wang, Jianping Wang
The [Ru(II)-NO(+)] group affects the structure and chemical reactivity of nitrosylruthenium(II) complexes. A characteristic infrared absorption band due to the nitrosyl (NO) stretching motion is shown in the frequency region of 1800-1900 cm(-1). In this work, linear infrared (IR) and nonlinear IR methods, including pump-probe and two-dimensional (2D) IR, were utilized to study the structures and dynamics of two isomeric nitrosylruthenium complexes [Ru(OAc)(2mqn)2NO] (H2mqn= 2-methyl-8-quinolinol) in cis and trans isomeric configurations in a weak polar solvent (CDCl3)...
October 18, 2016: Journal of Physical Chemistry. B
N Bavi, O Bavi, M Vossoughi, R Naghdabadi, A P Hill, B Martinac, Y Jamali
Gating of mechanosentive (MS) channels is driven by a hierarchical cascade of movements and deformations of transmembrane helices in response to bilayer tension. Determining the intrinsic mechanical properties of the individual transmembrane helices is therefore central to understanding the intricacies of the gating mechanism of MS channels. We used a constant-force steered molecular dynamics (SMD) approach to perform unidirectional pulling tests on all the helices of MscL in M. tuberculosis and E. coli homologs...
October 18, 2016: Channels
Daniel Pelaez, Zenith Acosta Torres, Tsz Kin Ng, Kwong Wai Choy, Chi Pui Pang, Herman S Cheung
Cellular therapies for the treatment of myocardial infarction have proven to be an invaluable tool in recent years and provide encouraging evidence for the possibility to restore normal heart function. However, questions still remain as to the optimal cell source, pre-conditioning methods and delivery techniques for such an application. This study explores the use of a population of stem cells arising from the neural crest and isolated from adult human periodontal ligament along with short-term mechanical strain as an inducer of cardiomyogenesis and possibly pre-conditioning stimulus for cellular cardiomyoplasty...
October 17, 2016: Cell and Tissue Research
F M Gilles, R Llubaroff, C Pastorino
We characterize the fluctuation properties of a polymer chain under external tension and the fluctuation-induced forces between two ring molecules threaded around the chain. The problem is relevant in the context of fluctuation-induced forces in soft-matter systems, features of liquid interfaces, and to describe the properties of polyrotaxanes and slide-ring materials. We perform molecular-dynamics simulations of the Kremer-Grest bead-spring model for the polymer and a simple ring-molecule model in the canonical ensemble...
September 2016: Physical Review. E
Zhen Zhang, I Koroleva, L I Manevitch, L A Bergman, A F Vakakis
We study the dynamics and acoustics of a nonlinear lattice with fixed boundary conditions composed of a finite number of particles coupled by linear springs, undergoing in-plane oscillations. The source of the strongly nonlinearity of this lattice is geometric effects generated by the in-plane stretching of the coupling linear springs. It has been shown that in the limit of low energy the lattice gives rise to a strongly nonlinear acoustic vacuum, which is a medium with zero speed of sound as defined in classical acoustics...
September 2016: Physical Review. E
C Dietz, M H Thoma
In this work, existing methods for plasma crystal analysis are investigated using artificial and simulated calibration data, which reproduce a multiphase system consisting of fcc, hcp, and bcc crystal data. Disturbances of the artificial data including Gaussian noise, stretching, and randomly missing particles are used to investigate the methods thoroughly. A popular method, called bond order parameter, has been repeatedly criticized as a structure analysis tool and will be improved with the help of a recent development...
September 2016: Physical Review. E
T Mizuno, Y Umemura
No abstract text is available yet for this article.
October 13, 2016: International Journal of Sports Medicine
Hsuan Su, Nai-Jen Chang, Wen-Lan Wu, Lan-Yuen Guo, I-Hua Chu
CONTEXT: Foam rolling has been proposed to improve muscle function, performance, and joint range of motion (ROM). However, whether a foam rolling protocol can be adopted as a warm-up to improve flexibility and muscle strength is unclear. OBJECTIVE: To examine and compare the acute effects of foam rolling, static stretching, and dynamic stretching used as part of warm-up on flexibility and muscle strength of knee flexion and extension. DESIGN: Crossover study...
October 13, 2016: Journal of Sport Rehabilitation
Mike Reppert, Anish R Roy, Jeremy O B Tempkin, Aaron R Dinner, Andrei Tokmakoff
The characterization of intrinsically disordered protein (IDP) ensembles is complicated both by inherent heterogeneity and by the fact that many common experimental techniques function poorly when applied to IDPs. For this reason, the development of alternative structural tools for probing IDP ensembles has attracted considerable attention. Here we describe our recent work in developing experimental and computational tools for characterizing IDP ensembles using Amide I (backbone carbonyl stretch) vibrational spectroscopy...
October 13, 2016: Journal of Physical Chemistry. B
Carien C M Groot, Krassimir P Velikov, Huib J Bakker
Though it is commonly known that a small amount of water can be present in triglyceride oil, a molecular picture of how water molecules organize in the oil phase is lacking. We investigate the hydrogen-bond configuration and dynamics of water in triacetin, tributyrin and trioctanoin using linear infrared and time-resolved two-dimensional infrared (2DIR) spectroscopy of the water hydroxyl stretch vibration. We identify water molecules with a single strong hydrogen bond to the triglyceride, water molecules with two weaker hydrogen bonds to the triglycerides, and water clusters...
October 13, 2016: Physical Chemistry Chemical Physics: PCCP
Chiara H Giammanco, Patrick L Kramer, Daryl B Wong, Michael D Fayer
The effects of water concentration and varying alkyl chain length on the dynamics of water in 1-alkyl-3-methylimidazolium tetrafluoroborate room temperature ionic liquids (RTILs) were characterized using two dimensional infrared (2D IR) vibrational echo spectroscopy and polarization-selective IR pump-probe experiments to study the water hydroxyl (OD) stretching mode of dilute HOD in H2O. Three imidazolium cation alkyl chain lengths, ethyl (Emim), butyl (Bmim), and decyl (Dmim), were investigated. Both the Bmim and Dmim cations have sufficiently long chains that the liquids exhibit polar-apolar segregation, while the Emim ionic liquid has no significant apolar aggregation...
October 11, 2016: Journal of Physical Chemistry. B
Karina Hoher, Piercarlo F Cardoso, Luiz F Lepre, Rômulo A Ando, Leonardo J A Siqueira
An investigation comprising experimental techniques (absorption capacity of SO2 and vibrational spectroscopy) and molecular simulations (thermodynamics, structure, and dynamics) has been performed for the polymer poly(ethylene oxide) (PEO), the ionic liquid butyltrimethylammonium bis(trifluoromethylsulfonyl)imide ([N4111][Tf2N]) and their mixtures as sulfur dioxide (SO2) absorbing materials. The polymer PEO has higher capacity to absorb SO2 than the neat ionic liquid, whereas the mixtures presented intermediary absorption capacities...
October 10, 2016: Physical Chemistry Chemical Physics: PCCP
Sandipa Indra, Ranjit Biswas
Heterogeneity and molecular motions in representative cryoprotectant mixtures made of trehalose and glycerol are investigated in the temperature range, , via time-resolved fluorescence Stokes shift and anisotropy measurements, and molecular dynamics simulations of four-point density-time correlations and H-bond relaxations. Mixtures containing 5 wt% and 20 wt% of trehalose along with neat glycerol are studied. Viscosity coefficients for these systems lie in the range, . Measured solute (Coumarin 153) rotation and solvation times reveal a substantial departure from the hydrodynamic viscosity dependence, suggesting strong micro-heterogeneous nature of these systems...
October 10, 2016: Journal of Physical Chemistry. B
Kunpeng Cui, Tao Lin Sun, Takayuki Kurokawa, Tasuku Nakajima, Takayuki Nonoyama, Liang Chen, Jian Ping Gong
Recently, we have developed a series of charge balanced polyampholyte (PA) physical hydrogels by random copolymerization in water, which show extraordinarily high toughness, self-healing ability and viscoelasticity. The excellent performance of PA hydrogels is ascribed to dynamic ionic bond formation through inter- and intra-chain interactions. The randomness results in ionic bonds of wide strength distribution, the strong bonds, which serve as permanent crosslinking, imparting the elasticity, while the weak bonds reversibly break and re-form, dissipating energy...
October 7, 2016: Soft Matter
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