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Dynamic stretching

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https://www.readbyqxmd.com/read/28634300/understanding-the-mechanical-response-of-double-stranded-dna-and-rna-under-constant-stretching-forces-using-all-atom-molecular-dynamics
#1
Alberto Marin-Gonzalez, J G Vilhena, Ruben Perez, Fernando Moreno-Herrero
Multiple biological processes involve the stretching of nucleic acids (NAs). Stretching forces induce local changes in the molecule structure, inhibiting or promoting the binding of proteins, which ultimately affects their functionality. Understanding how a force induces changes in the structure of NAs at the atomic level is a challenge. Here, we use all-atom, microsecond-long molecular dynamics to simulate the structure of dsDNA and dsRNA subjected to stretching forces up to 20 pN. We determine all of the elastic constants of dsDNA and dsRNA and provide an explanation for three striking differences in the mechanical response of these two molecules: the threefold softer stretching constant obtained for dsRNA, the opposite twist-stretch coupling, and its nontrivial force dependence...
June 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28632385/fatigue-resistant-bioinspired-composite-from-synergistic-two-dimensional-nanocomponents
#2
Sijie Wan, Qi Zhang, Xiaohang Zhou, Dechang Li, Baohua Ji, Lei Jiang, Qunfeng Cheng
Portable and wearable electronics require much more flexible graphene-based electrode with high fatigue life, which could repeatedly bend, fold, or stretch without sacrificing its mechanical properties and electrical conductivity. Herein, a kind of ultrahigh fatigue resistant graphene-based nanocomposite via tungsten disulfide (WS2) nanosheets is synthesized by introducing a synergistic effect with covalently cross-linking inspired by the orderly layered structure and abundant interfacial interactions of nacre...
June 20, 2017: ACS Nano
https://www.readbyqxmd.com/read/28632177/the-intersection-of-ngf-trka-signaling-and-amyloid-precursor-protein-processing-in-alzheimer-s-disease-neuropathology
#3
REVIEW
Nadia Canu, Giuseppina Amadoro, Viviana Triaca, Valentina Latina, Valentina Sposato, Veronica Corsetti, Cinzia Severini, Maria Teresa Ciotti, Pietro Calissano
Dysfunction of nerve growth factor (NGF) and its high-affinity Tropomyosin receptor kinase A (TrkA) receptor has been suggested to contribute to the selective degeneration of basal forebrain cholinergic neurons (BFCN) associated with the progressive cognitive decline in Alzheimer's disease (AD). The aim of this review is to describe our progress in elucidating the molecular mechanisms underlying the dynamic interplay between NGF/TrkA signaling and amyloid precursor protein (APP) metabolism within the context of AD neuropathology...
June 20, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28631401/a-polyacrylamide-hydrogel-electrolyte-enabled-intrinsically-1000-stretchable-and-50-compressible-supercapacitor
#4
Yan Huang, Ming Zhong, Fukuan Shi, Xiaoying Liu, Zijie Tang, Yukun Wang, Yang Huang, Haoqing Hou, Xuming Xie, Chunyi Zhi
Stretchability and compressibility of supercapacitors constitute essential elements of modern electronics such as flexible and wearable devices. Widely-used polyvinyl alcohol-based electrolytes are neither very stretchable nor compressible, which fundamentally limit the realization of high stretchability and compressibility of supercapacitors. We present a new electrolyte that is intrinsically super-stretchable and compressible. Vinyl hybrid silica nanoparticle cross-linkers are introduced into polyacrylamide hydrogel backbones to promote dynamic crosslinking of the polymer networks...
June 19, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28619447/similar-movements-are-associated-with-drastically-different-muscle-contraction-velocities
#5
Daniel A Hagen, Francisco J Valero-Cuevas
We investigated how kinematic redundancy interacts with the neurophysiological control mechanisms required for smooth and accurate, rapid limb movements. Biomechanically speaking, tendon excursions are over-determined because the rotation of few joints determines the lengths and velocities of many muscles. But how different are the muscle velocity profiles induced by various, equally valid hand trajectories? We used an 18-muscle sagittal-plane arm model to calculate 100,000 feasible shoulder, elbow, and wrist joint rotations that produced valid basketball free throws with different hand trajectories, but identical initial and final hand positions and velocities...
May 31, 2017: Journal of Biomechanics
https://www.readbyqxmd.com/read/28618613/describing-magnetorheology-under-a-colloidal-glass-approach
#6
J P Segovia-Gutiérrez, J de Vicente, Antonio M Puertas, R Hidalgo-Alvarez
The equilibrium structure and dynamics of magnetorheological (MR) fluids are studied in this work by simulations, where particles are modeled as dipoles with a quasihard spherical core. Upon increasing the interaction strength, controlled experimentally by the magnetic field, elongated clusters grow and, for intense fields, thick columns form, aligned with the field. The dynamics of the system is monitored by the mean-squared displacement and density correlation functions, which show an increasing slowing down with the attraction strength...
May 2017: Physical Review. E
https://www.readbyqxmd.com/read/28616984/oh-stretching-overtone-induced-dynamics-in-hso3f-from-reactive-molecular-dynamics-simulations
#7
Sebastian Brickel, Markus Meuwly
The OH-stretch induced dynamics in fluorosulfonic acid (HSO$_3$F) is characterized from a statistically significant number of trajectories using Multi-Surface Adiabatic Reactive Molecular Dynamics (MS-ARMD) simulations. The global reactive potential energy surface, which describes H-transfer and HF-elimination, is parametrized at the MP2/6-311G++(2p,2d) level of theory with an accuracy of better than 1 kcal/mol. Excitation along the OH-local mode leads to H-transfer dynamics but elimination of HF is only observed for excitations with $\nu \geq 6$ for 1 out of 5000 trajectories...
June 15, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28613274/experimental-neutron-scattering-evidence-for-proton-polaron-in-hydrated-metal-oxide-proton-conductors
#8
Artur Braun, Qianli Chen
Hydration of oxygen-deficient metal oxides causes filling of oxygen vacancies and formation of hydroxyl groups with interstitial structural protons, rotating around the oxygen in localized motion. Thermal activation from 500 to 800 K triggers delocalization of the protons by jumping to adjacent oxygen ions, constituting proton conductivity. We report quantitative analyses of proton and lattice dynamics by neutron-scattering data, which reveal the interaction of protons with the crystal lattice and proton-phonon coupling...
June 14, 2017: Nature Communications
https://www.readbyqxmd.com/read/28612067/stretch-dependent-changes-in-molecular-conformation-in-fibronectin-nanofibers
#9
John M Szymanski, Emily N Sevcik, Kairui Zhang, Adam W Feinberg
Fibronectin (FN) is an extracellular matrix (ECM) glycoprotein that plays an important role in a wide range of biological processes including embryonic development, wound healing, and fibrosis. Recent evidence has demonstrated that FN is mechanosensitive, where the application of force induces conformational changes within the FN molecule to expose otherwise cryptic binding domains. However, it has proven technically challenging to dynamically monitor how the nanostructure of FN fibers changes as a result of force-induced extension, due in part to the inherent complexity of FN networks within tissue and cell-generated extracellular matrix (ECM)...
June 14, 2017: Biomaterials Science
https://www.readbyqxmd.com/read/28611612/spasticity-measurement-based-on-tonic-stretch-reflex-threshold-in-children-with-cerebral-palsy-using-the-pedianklebot
#10
Marco Germanotta, Juri Taborri, Stefano Rossi, Flaminia Frascarelli, Eduardo Palermo, Paolo Cappa, Enrico Castelli, Maurizio Petrarca
Nowadays, objective measures are becoming prominent in spasticity assessment, to overcome limitations of clinical scales. Among others, Tonic Stretch Reflex Threshold (TSRT) showed promising results. Previous studies demonstrated the validity and reliability of TSRT in spasticity assessment at elbow and ankle joints in adults. Purposes of the present study were to assess: (i) the feasibility of measuring TSRT to evaluate spasticity at the ankle joint in children with Cerebral Palsy (CP), and (ii) the correlation between objective measures and clinical scores...
2017: Frontiers in Human Neuroscience
https://www.readbyqxmd.com/read/28610839/fly-fishing-for-histones-catch-and-release-by-histone-chaperone-intrinsically-disordered-regions-and-acidic-stretches
#11
REVIEW
Christopher Warren, David Shechter
Chromatin is the complex of eukaryotic DNA and proteins required for the efficient compaction of the nearly two-meter long human genome into a roughly ten-micron diameter cell nucleus. The fundamental repeating unit of chromatin is the nucleosome: 147bp of DNA wrapped about an octamer of histone proteins. Nucleosomes are stable enough to organize the genome yet must be dynamically displaced and reassembled to allow access to the underlying DNA for transcription, replication, and DNA damage repair. Histone chaperones are a non-catalytic group of proteins that are central to the processes of nucleosome assembly and disassembly, and thus the fluidity of the ever-changing chromatin landscape...
June 10, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28608689/simulation-analysis-of-the-kinetic-exchange-of-copolymer-surfactants-in-micelles
#12
Fabián A García Daza, Josep Bonet Avalos, Allan D Mackie
The exchange of surfactants in micelles involves several processes which are difficult to characterize experimentally. Microscopic simulations have the potential to reveal some of the key aspects that take place when a surfactant spontaneously exits a micelle. We present a quantitative analysis of the kinetic exchange process over a large range of time. The study is based on a dynamic version of a single-chain mean field theory using a coarse-grained model for poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) triblock copolymer systems...
June 13, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28604867/how-seaweeds-release-the-excess-energy-from-sunlight-to-surrounding-sea-water
#13
Kenichi Koizumi, Makoto Hatakeyama, Mauro Boero, Katsuyuki Nobusada, Hirokazu Hori, Taku Misonou, Shinichiro Nakamura
We report an atomistic insight into the mechanism regulating the energy released by a porphyra-334 molecule, the ubiquitous photosensitive component of marine algae, in a liquid water environment upon an electron excitation. To quantify this rapidly occurring process, we resort to the Fourier analysis of the mass-weighted auto-correlation function, providing evidence for a remarkable dynamic change in the number of hydrogen bonds among water molecules and between the porphyra-334 and its surrounding hydrating water...
June 21, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28602716/tracking-the-amyloidogenic-core-of-iapp-amyloid-fibrils-insights-from-micro-raman-spectroscopy
#14
Nikolaos N Louros, Paraskevi L Tsiolaki, Fotis A Baltoumas, Georgios D Chryssikos, Vassilis Gionis, Stavros J Hamodrakas, Vassiliki A Iconomidou
Human islet amyloid polypeptide (hIAPP) is the major protein component of extracellular amyloid deposits, located in the islets of Langerhans, a hallmark of type II diabetes. The underlying mechanisms of IAPP aggregation have not yet been clearly defined, although the highly amyloidogenic sequence of the protein has been extensively studied. Several segments have been highlighted as aggregation-prone regions (APRs), with much attention focused on the central 8-17 and 20-29 stretches. In this work, we employ micro-Raman spectroscopy to identify specific regions that are contributing to or are excluded from the amyloidogenic core of IAPP amyloid fibrils...
June 5, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28595392/transient-raman-spectra-structure-and-thermochemistry-of-the-thiocyanate-dimer-radical-anion-in-water
#15
Ireneusz Janik, Ian Carmichael, G N R Tripathi
Time-resolved resonance-enhanced Stokes and anti-Stokes Raman spectra of the thiocyanate dimer radical anion, (SCN)2(•-), prepared by pulse radiolysis in water, have been obtained and interpreted in conjunction with theoretical calculations to provide detailed information on the molecular geometry and bond properties of the species. The structural properties of the radical are used to develop a molecular perspective on its thermochemistry in an aqueous solution. Twenty-nine Stokes Raman bands of the radical observed in the 120-4200 cm(-1) region are assigned in terms of the strongly enhanced 220 cm(-1) fundamental, weakly enhanced 721 cm(-1), and moderately enhanced 2073 cm(-1) fundamentals, their overtones, and combinations...
June 7, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28593765/formation-of-annular-protofibrillar-assembly-by-cysteine-tripeptide-unravelling-the-interactions-with-nmr-ftir-and-molecular-dynamics
#16
Biswadip Banerji, Moumita Chatterjee, Uttam Pal, Nakul Chandra Maiti
Both the hydrogen bonding and hydrophobic interactions play a significant role in molecular assembly including self assembly of proteins and peptides. In this investigation, we reported formation of annular protofibrillar structure (diameter ~500 nm) made of a newly synthesized s-benzyl-protected cysteine tripeptide which was primarily stabilized by hydrogen bonding and hydrophobic interactions. AFM and FESEM analyses found small oligomers (~ 60 nm in diameter) to bigger annular (~ 300 nm) with an inner diameter of 100 nm and protofibrillar structure after 1-2 days incubation...
June 8, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28593083/dynamic-oscillatory-stretching-efficacy-on-hamstring-extensibility-and-stretch-tolerance-a-randomized-controlled-trial
#17
Arie Michaeli, Jason Cameron Tee, Aimee Stewart
BACKGROUND: While static stretch (SS), proprioceptive neuromuscular facilitation (PNF) and oscillatory physiological mobilization techniques are documented to have positive effects on a range of motion (ROM), there are no reports on the effect of dynamic oscillatory stretching (DOS), a technique that combines these three techniques, on hamstring extensibility. PURPOSE: To determine whether DOS improves hamstring extensibility and stretch tolerance to a greater degree than SS in asymptomatic young participants...
June 2017: International Journal of Sports Physical Therapy
https://www.readbyqxmd.com/read/28589977/fingerprints-of-inter-and-intramolecular-hydrogen-bonding-in-saligenin-water-clusters-revealed-by-mid-and-far-infrared-spectroscopy
#18
Daniël J Bakker, Arghya Dey, Daniel P Tabor, Qin Ong, Jérôme Mahé, Marie-Pierre Gaigeot, Edwin L Sibert, Anouk M Rijs
Saligenin (2-(hydroxymethyl)phenol) exhibits both strong and weak intramolecular electrostatic interactions. The bonds that result from these interactions compete with intermolecular hydrogen bonds once saligenin binds to one or more water molecules. Infrared (IR) ultraviolet (UV) ion-dip spectroscopy was used to study isolated saligenin-(H2O)n clusters (n = 1-3) in the far- and mid-IR regions of the spectrum. Both harmonic and anharmonic (coupled local modes and Born-Oppenheimer molecular dynamics) quantum chemical calculations were applied to assign cluster geometries to the measured spectra, and to assign vibrational modes to all spectral features measured for each cluster...
June 7, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28561592/pressure-dependence-of-the-boson-peak-of-glassy-glycerol
#19
Muhtar Ahart, Dilare Aihaiti, Russell J Hemley, Seiji Kojima
The pressure dependence of the Boson peak (BP) of glycerol, including its behavior across the liquid-glass transition, has been studied under pressure using Raman scattering. A significant hardening of the BP was observed with increasing pressure up to 11 GPa at room temperature. The pressure dependence of BP frequency νBP is proportional to (1+P/P0)(1/3), where P and P0 are the pressure and a constant, respectively, the spectra are consistent with a soft potential model that differs from the behavior of most inorganic glasses...
May 31, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28560321/directional-mechanical-stability-of-bacteriophage-%C3%AF-29-motor-s-3wj-prna-extraordinary-robustness-along-portal-axis
#20
Zhonghe Xu, Yang Sun, Jeffrey K Weber, Yi Cao, Wei Wang, Daniel Jasinski, Peixuan Guo, Ruhong Zhou, Jingyuan Li
The molecular motor exploited by bacteriophage φ29 to pack DNA into its capsid is regarded as one of the most powerful mechanical devices present in viral, bacterial, and eukaryotic systems alike. Acting as a linker element, a prohead RNA (pRNA) effectively joins the connector and ATPase (adenosine triphosphatase) components of the φ29 motor. During DNA packing, this pRNA needs to withstand enormous strain along the capsid's portal axis-how this remarkable stability is achieved remains to be elucidated. We investigate the mechanical properties of the φ29 motor's three-way junction (3WJ)-pRNA using a combined steered molecular dynamics and atomic force spectroscopy approach...
May 2017: Science Advances
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