Molecular sliding filament model for muscular contraction based on multiscale investigation

A multiscale approach that bridges the biophysics of the actin molecules at nanoscale and the biomechanics of actin filament at microscale level is developed and used to evaluate the mechanical performances of actin filament bundles. In order to investigate the contractile properties of skeletal muscle which is induced by the protein motor of myosin, a molecular model is proposed in the prediction of the dynamic behaviors of skeletal muscle based on classic sliding filament model. Randomly distributed myosin motors are applied on a 2.2 μm long sarcomere, whose principal components include actin and myosin filaments. It can be found that, the more myosin motors on the sarcomere, the faster the sarcomere contracts. The result demonstrates that the sarcomere shortening speed cannot increase infinitely by the modulation of myosin, thus providing insight into the self-protective properties of skeletal muscles. This molecular filament sliding model provides a theoretical way to evaluate the properties of skeletal muscles, and contributes to the understandings of the molecular mechanisms in the physiological phenomenon of muscular contraction.

Multiband photoluminescence from carbon nanoflakes synthesized by hot filament CVD: towards solid-state white light sources

Carbon nanoflakes (CNFLs) are synthesized on silicon substrates deposited with carbon islands in a methane environment using hot filament chemical vapor deposition. The structure and composition of the CNFLs are studied using field emission scanning electron microscopy, high-resolution transmission electron microscopy, micro-Raman spectroscopy, and X-ray photoelectron spectroscopy. The results indicate that the CNFLs are composed of multilayer graphitic sheets and the area and thickness of CNFs increase with the growth time. The photoluminescence (PL) of CNFLs excited by a 325 nm He-Cd laser exhibits three strong bands centered at 408, 526, and 699 nm, which are related to the chemical radicals terminated on the CNFLs and the associated interband transitions. The PL results indicate that the CNFLs are promising as an advanced nano-carbon material capable of generating white light emission. These outcomes are significant to control the electronic structure of CNFLs and contribute to the development of next-generation solid-state white light emission devices. © 2014 the Partner Organisations.

Formation and electron field emission of graphene films grown by hot filament chemical vapor deposition

Graphene films with different structures were catalytically grown on the silicon substrate pre-deposited with a gold film by hot filament chemical vapor deposition under different conditions, where methane, hydrogen and nitrogen were used as the reactive gases. The morphological and compositional properties of graphene films were studied using advanced instruments including field emission scanning electron microscopy, micro-Raman spectroscopy and X-ray photoelectron spectroscopy. The results indicate that the structure and composition of graphene films are changed with the variation of the growth conditions. According to the theory related to thermodynamics, the formation of graphene films was theoretically analyzed and the results indicate that the formation of graphene films is related to the fast incorporation and precipitation of carbon. The electron field emission (EFE) properties of graphene films were studied in a high vacuum system of ∼10-6 Pa and the EFE results show that the turn-on field is in a range of 5.2-5.64 V μm-1 and the maximum current density is about 63 μ A cm-2 at the field of 7.7 V μm-1. These results are important to control the structure of graphene films and have the potential applications of graphene in various nanodevices.

Carbon nanorods and graphene-like nanosheets by hot filament CVD : growth mechanisms and electron field emission

Carbon nanorods and graphene-like nanosheets are catalytically synthesized in a hot filament chemical vapor deposition system with and without plasma enhancement, with gold used as a catalyst. The morphological and structural properties of the carbon nanorods and nanosheets are investigated by field-emission scanning electron microscopy, transmission electron microscopy and micro-Raman spectroscopy. It is found that carbon nanorods are formed when a CH4 + H2 + N2 plasma is present while carbon nanosheets are formed in a methane environment without a plasma. The formation of carbon nanorods and carbon nanosheets are analyzed. The results suggest that the formation of carbon nanorods is primarily a precipitation process while the formation of carbon nanosheets is a complex process involving surface-catalysis, surface diffusion and precipitation influenced by the Gibbs–Thomson effect. The electron field emission properties of the carbon nanorods and graphene-like nanosheets are measured under high-vacuum; it is found that the carbon nanosheets have a lower field emission turn-on than the carbon nanorods. These results are important to improve the understanding of formation mechanisms of carbon nanomaterials and contribute to eventual applications of these structures in nanodevices.

Room-temperature photoluminescence from nitrogenated carbon nanotips grown by plasma-enhanced hot filament chemical vapor deposition

Nitrogenated carbon nanotips with a low atomic concentration of nitrogen have been synthesized by using a custom-designed plasma-enhanced hot-filament plasma chemical vapor deposition system. The properties (including morphology, structure, composition, photoluminescence, etc.) of the synthesized nitrogenated carbon nanotips are investigated using advanced characterization tools. The room-temperature photoluminescence measurements show that the nitrogenated carbon nanotips can generate two distinct broad emissions located at ∼405 and ∼507 nm, respectively. Through the detailed analysis, it is shown that these two emission bands are attributed to the transition between the lone pair valence and bands, which are related to the sp3 and sp2 C-N bonds, respectively. These results are highly relevant to advanced applications of nitrogenated carbon nanotips in light emitting optoelectronic devices.

Comprehensive contribution of filament thickness and crosslinker failure to the rheological property of F-actin cytoskeleton

Rheological property of F-actin cytoskeleton is significant to the restructuring of cytoskeleton under a variety of cell activities. This study numerically validates the rheological property of F-actin cytoskeleton is not only a result of kinetic energy dissipation of F-actin, but also greatly depends on the configuration remodeling of networks structure. Both filament geometry and crosslinker properties can affect the remodeling of F-actin cytoskeleton. The crosslinker unbinding is found to dissipate energy and induce prominent stress relaxation in the F-actin adjacent to cross-linkages. Coupled with F-actin elasticity, the energy dissipation and stress relaxation are more significant in bundled F-actin networks than in single F-actin networks.

Effect of substrate roughness on growth of diamond by hot filament CVD

Polycrystalline diamond coatings are grown on Si (100) substrate by hot filament CVD technique. We investigate here the effect of substrate roughening on the substrate temperature and methane concentration required to maintain high quality, high growth rate and faceted morphology of the diamond coatings. It has been shown that as we increase the substrate roughness from 0.05 mu m to 0.91 mu m (centre line average or CLA) there is enhancement in deposited film quality (Raman peak intensity ratio of sp (3) to non-sp (3) content increases from 1.65 to 7.13) and the substrate temperature can be brought down to 640A degrees C without any additional substrate heating. The coatings grown at adverse conditions for sp (3) deposition has cauliflower morphology with nanocrystalline grains and coatings grown under favourable sp (3) condition gives clear faceted grains.

Force and ATP hydrolysis dependent regulation of RecA nucleoprotein filament by single-stranded DNA binding protein

In Escherichia coli, the filament of RecA formed on single-stranded DNA (ssDNA) is essential for recombinational DNA repair. Although ssDNA-binding protein (SSB) plays a complicated role in RecA reactions in vivo, much of our understanding of the mechanism is based on RecA binding directly to ssDNA. Here we investigate the role of SSB in the regulation of RecA polymerization on ssDNA, based on the differential force responses of a single 576-nucleotide-long ssDNA associated with RecA and SSB. We find that SSB outcompetes higher concentrations of RecA, resulting in inhibition of RecA nucleation. In addition, we find that pre-formed RecA filaments de-polymerize at low force in an ATP hydrolysis- and SSB-dependent manner. At higher forces, re-polymerization takes place, which displaces SSB from ssDNA. These findings provide a physical picture of the competition between RecA and SSB under tension on the scale of the entire nucleoprotein SSB array, which have broad biological implications particularly with regard to competitive molecular binding.

Carbon nanoflake growth from carbon nanotubes by hot filament chemical vapor deposition

We report the growth of carbon nanoflakes (CNFs) on Si substrate by the hot filament chemical vapor deposition without the substrate bias or the catalyst. CNFs were grown using the single wall carbon nanotubes and the multiwall carbon nanotubes as the nucleation center, in the Ar-rich CH4-H-2-Ar precursor gas mixture with 1% CH4, at the chamber pressure and the substrate temperature of 7.5 Ton and 840 degrees C, respectively. In the H-2-rich condition, CNF synthesis failed due to severe etch-removal of carbon nanotubes (CNTs) while it was successful at the optimized Ar-rich condition. Other forms of carbon such as nano-diamond or mesoporous carbon failed to serve as the nucleation centers for the CNF growth. We proposed a mechanism of the CNF synthesis from the CNTs, which involved the initial unzipping of CNTs by atomic hydrogen and subsequent nucleation and growth of CNFs from the unzipped portion of the graphene layers. (C) 2013 Elsevier Ltd. All rights reserved.

Local stability of a gravitating filament: a dispersion relation

Filamentary structures are ubiquitous in astrophysics and are observed at various scales. On a cosmological scale, matter is usually distributed along filaments, and filaments are also typical features of the interstellar medium. Within a cosmic filament, matter can contract and form galaxies, whereas an interstellar gas filament can clump into a series of bead-like structures that can then turn into stars. To investigate the growth of such instabilities, we derive a local dispersion relation for an idealized self-gravitating filament and study some of its properties. Our idealized picture consists of an infinite self-gravitating and rotating cylinder with pressure and density related by a polytropic equation of state. We assume no specific density distribution, treat matter as a fluid, and use hydrodynamics to derive the linearized equations that govern the local perturbations. We obtain a dispersion relation for axisymmetric perturbations and study its properties in the (kR, kz) phase space, where kR and kz are the radial and longitudinal wavenumbers, respectively. While the boundary between the stable and unstable regimes is symmetrical in kR and kz and analogous to the Jeans criterion, the most unstable mode displays an asymmetry that could constrain the shape of the structures that form within the filament. Here the results are applied to a fiducial interstellar filament, but could be extended for other astrophysical systems, such as cosmological filaments and tidal tails.

Mechanical force antagonizes the inhibitory effects of RecX on RecA filament formation in Mycobacterium tuberculosis

Efficient bacterial recombinational DNA repair involves rapid cycles of RecA filament assembly and disassembly. The RecX protein plays a crucial inhibitory role in RecA filament formation and stability. As the broken ends of DNA are tethered during homologous search, RecA filaments assembled at the ends are likely subject to force. In this work, we investigated the interplay between RecX and force on RecA filament formation and stability. Using magnetic tweezers, at single molecular level, we found that Mycobacterium tuberculosis (Mt) RecX could catalyze stepwise de-polymerization of preformed MtRecA filament in the presence of ATP hydrolysis at low forces (<7 pN). However, applying larger forces antagonized the inhibitory effects of MtRecX, and a partially de-polymerized MtRecA filament could repolymerize in the presence of MtRecX, which cannot be explained by previous models. Theoretical analysis of force-dependent conformational free energies of naked ssDNA and RecA nucleoprotein filament suggests that mechanical force stabilizes RecA filament, which provides a possible mechanism for the observation. As the antagonizing effect of force on the inhibitory function of RecX takes place in a physiological range; these findings broadly suggest a potential mechanosensitive regulation during homologous recombination.

Molecular Mechanism Underlying ATP-Induced Conformational Changes in the Nucleoprotein Filament of Mycobacterium smegmatis RecA

RecA plays a central role in bacterial DNA repair, homologous recombination, and restoration of stalled replication forks by virtue of its active extended nucleoprotein filament. Binding of ATP and its subsequent recognition by the carboxamide group of a highly conserved glutamine (GIn196 in MsRecA) have been implicated in the formation of active RecA nucleoprotein filaments. Although the mechanism of ATP-dependent structural transitions in RecA has been proposed on the basis of low-resolution electron microscopic reconstructions, the precise sequence of events that constitute these transitions is poorly understood. On the basis of biochemical and crystallographic analyses of MsRecA variants carrying mutations in highly conserved Gln196 and Arg198 residues, we propose that the disposition of the interprotomer interface is the structural basis of allosteric activation of RecA. Furthermore, this study accounts, for the contributions of several conserved amino acids to ATP hydrolysis and to the transition from collapsed to extended filament forms in Mycobacterium smegmatis RecA (MsRecA). In addition to their role in the inactive compressed state, the study reveals a role for GIn196 and Arg198 along with Phe219 in ATP hydrolysis in the active extended nucleoprotein filament. Finally, our data suggest that the primary, but not secondary, nucleotide binding site in MsRecA isomerizes into the ATP binding site present in the extended nucleoprotein filament.