7,518 research outputs found
Two-step ligand binding and cooperativity. A model to describe the cooperative binding of myosin subfragment 1 to regulated actin
No full textThe binding of actin to myosin subfragment 1 (S1) has been shown to occur as a two-step reaction. In the first step actin is weakly bound and then the complex isomerizes to the "rigor type" acto-S1 complex (Coates, J. H., A. H. Criddle, and M. A. Geeves, 1985 Biochem. J., 232:351–356). We propose here a model in which troponin/tropomyosin (Tn/Tm) controls the actin-S1 interaction by inhibiting the isomerization step. In this model the (actin)7 Tn/Tm unit is assumed to exist in two states: open and closed. S1 can bind to either of the two states but only the open form allows the isomerization reaction to take place. We demonstrate that this model can account for the cooperative binding of S1 and S1 nucleotide complexes to actin. The model provides a way of integrating both the effects of calcium and nucleotide on actin-S1 interactions
Kinetic Analysis of the Slow Skeletal Myosin MHC-1 Isoform from Bovine Masseter Muscle
No full textSeveral heavy chain isoforms of class II myosins are found in muscle fibres and show a large variety of different mechanical activities. Fast myosins (myosin heavy chain (MHC)-II-2) contract at higher velocities than slow myosins (MHC-II-1, also known as beta-myosin) and it has been well established that ADP binding to actomyosin is much tighter for MHC-II-1 than for MHC-II-2. Recently, we reported several other differences between MHC-II isoforms 1 and 2 of the rabbit. Isoform II-1 unlike II-2 gave biphasic dissociation of actomyosin by ATP, the ATP-cleavage step was significantly slower for MHC-II-1 and the slow isoforms showed the presence of multiple actomyosin-ADP complexes. These results are in contrast to published data on MHC-II-1 from bovine left ventricle muscle, which was more similar to the fast skeletal isoform. Bovine MHC-II-1 is the predominant isoform expressed in both the ventricular myocardium and slow skeletal muscle fibres such as the masseter and is an important source of reference work for cardiac muscle physiology. This work examines and extends the kinetics of bovine MHC-II-1. We confirm the primary findings from the work on rabbit soleus MHC-II-1. Of significance is that we show that the affinity of ADP for bovine masseter myosin in the absence of actin (represented by the dissociation constant K(D)) is weaker than originally described for bovine cardiac myosin and thus the thermodynamic coupling between ADP and actin binding to myosin is much smaller (K(AD)/K(D) approximately 5 instead of K(AD)/K(D) approximately 50). This may indicate a distinct type of mechanochemical coupling for this group of myosin motors. We also find that the ATP-hydrolysis rate is much slower for bovine MHC-II-1 (19 s(-1)) than reported previously (138 s(-1)). We discuss how this work fits into a broader characterisation of myosin motors from across the myosin family
Deep anisotropic dry etching of silicon microstructures by high-density plasmas
No full textThis thesis deals with the dry etching of deep anisotropic microstructures in monocrystalline silicon by high-density plasmas. High aspect ratio trenches are necessary in the fabrication of sensitive inertial devices such as accellerometers and gyroscopes. The etching of silicon in fluorine-based plasmas is isotropic. To obtain anisotropy the addition of sidewall passivation is necessary. This is achieved with both oxygen passivation at low temperatures and fluorocarbon passivation at room temperature. A quantitative approach was pursued to explain the etching mechanism. The etch results were analysed using the measured plasma species fluxes and the surface composition. Moreover, the transport of the plasma species in narrow anisotropic structures is a fundamental factor determining the etch rate and the profile evolution. The experimental methods such as the etching equipment, plasma diagnostics, surface analysis and sample preparation are described in chapter 2. Three etching processes were investigated: the cryogenic etching process with oxygen passivation at low temperatures, the Bosch process with fluorocarbon passivation at room temperature and the novel triple pulse process that was developed in our laboratory. The polymer deposition mechanism and the characteristic role of the ions are also explained. The cryogenic etching process is discussed in chapter 3. Fluorine radicals, oxygen radicals and ion bombardment are responsible for the three main sub-processes, that is, etching, sidewall passivation and depassivation of the trench bottom, respectively. Etching experiments with an extremely low ion-to-radical flux ratio were used to reveal the etching mechanism. Crystal orientation dependent etching leading to Si(111) crystal facets is observed in a surface kinetics controlled regime. By varying the plasma conditions it is possible to adjust the etching mechanism from fluorine-limited to ion-limited. Controlled etching is obtained because the etching is tuned from aspect ratio dependent in the fluorine-limited domain to aspect ratio independent in the ion-limited domain. The transport of radicals in high aspect ratio trenches is an important limiting factor and was investigated with special structures. The etch results are described by an analytic model that is based on the surface site balance of fluorine and oxygen radicals. The results are further explained with a Monte Carlo simulation model. The Bosch process is clarified in chapter 4. The anisotropy of the etched structures is controlled by balancing the etching and passivation pulse. However, the maximal obtainable aspect ratio is limited by convergence of the trench sidewalls due to excessive passivation. The maximal obtainable aspect ratio increases if the ion-to-radical flux ratio increases. The transport of ions is an important limiting factor in the depassivation of the bottom of the trench. Divergence of the ion beam leads to a reduction of the ion flux, so that the fluorocarbon passivation is insufficiently removed near the base of the sidewalls. The average ion angle was measured and correlated to the maximal obtainable aspect ratio. The Bosch process was improved at the depassivation side with the triple pulse process and at the passivation side with preferential sidewall deposition. The triple pulse process that is described in chapter 5 has the aim to improve the depassivation in deep trenches. The three main sub-processes are decoupled using a separate depassivation pulse directly after the etching and passivation pulses. The fluorocarbon passivation is efficiently removed with low-pressure, high-density, oxygen-based plasmas. The investigated plasma chemistries include O2, CO2 and SO2. The triple pulse process leads to better profile control with a straight trench bottom. However, the maximal obtainable aspect ratio is comparable to the Bosch process because a larger etch depth and a small lateral etch cancel out. The polymer deposition mechanism is treated in chapter 6 with the aim to understand the fluorocarbon passivation in deep trenches. The deposition on plane surfaces and on special structures was investigated to distinguish between the radical-induced and ion-enhanced components. A simple analytical model, which explains the main deposition characteristics, was developed. Preferential sidewall deposition is obtained for higher ion fluxes and higher bias voltages where sputtering plays an important role. In this case no fluorocarbon passivation has to be removed from the bottom of the trench. The trench profile was optimised in the Bosch process by tuning the bias voltage during etching and passivation independently. It resulted in perfectly anisotropic trenches but the maximal obtainable aspect ratio was still limited by a small lateral etch. The characteristic role of the ions in the etching mechanism is explained in chapter 7. Ion-induced etching of both SiC in a SF6-O2 plasma and Si in a Cl2 plasma were investigated. The impact of the ions on the profile evolution can be examined more explicitly because spontaneous chemical reactions are absent for these plasma-material systems. The etching mechanism varies from fluorine-limited to ion-limited depending on the radical-to-ion flux ratio. Microtrenches are observed for an ion-limited etching mechanism. Fluorine-limited SiC etching is aspect ratio dependent in contrast to ion-limited SiC etching, which is aspect ratio independent. The etching of high aspect ratio SiC structures is limited by the positive sidewall taper. This is presumably caused by insufficient removal of the thin fluorocarbon layer on the surface. Si etching in a Cl2 plasma is always aspect ratio independent in contrast to SiC etching because of the low reaction probability. The conclusions and recommendations of this thesis are given in chapter 8.Applied Science
Cooperative regulation of myosin-actin interactions by a continuous flexible chain I: actin-tropomyosin systems
No full textWe present a model for cooperative myosin binding to the regulated actin filament, where tropomyosins are treated as a weakly-confined continuous flexible chain covering myosin binding sites. Thermal fluctuations in chain orientation are initially required for myosin binding, leaving kinked regions under which subsequent myosins may bind without further distortion of the chain. Statistical mechanics predicts the fraction of sites with bound myosin-S1 as a function of their affinities. Published S1 binding curves to regulated filaments with different tropomyosin isoforms are fitted by varying the binding constant, chain persistence length nu (in actin monomers), and chain kink energy A from a single bound S1. With skeletal tropomyosin, we find an S1 actin-binding constant of 2.2 x 10(7) M(-1), A = 1.6 k(B)T and nu = 2.7. Similar persistence lengths are found with yeast tropomyosin. Larger values are found for tropomyosin-troponin in the presence of calcium (nu = 3.7) and tropomyosins from smooth muscle and fibroblasts (nu = 4.5). The relationship of these results to structural information and the rigid-unit model of McKillop and Geeves is discussed
4.13 Thin Filament Regulation
No full textThe review summarizes the current state of knowledge of the calcium regulation of striated muscle contraction via the thin filament proteins, tropomyosin and troponin. The description focuses on in vitro studies of the thin filament and covers structural, biochemical and dynamic aspects of the thin filament's response to calcium binding. A reductionist approach has allowed many of the transitions to be defined at the level of a single structural unit. Here an emphasis is placed on the co-operative nature of the structural and biochemical transitions of the thin filament and the allosteric relationship between calcium and myosin binding to the thin filament
Assessment of Models for Near Wall Behavior and Swirling Flows in Nuclear Reactor Sub-system Simulations
No full textAccurate simulation of turbulence remains one of the most challenging problems in nuclear reactor analysis and design. Due to limitations in computing resources, Reynolds averaged Navier Stokes models (RANS) continue to play an important role in reactor simulations. The Consortium for advanced simulations of light water reactors (CASL) is a Department of Energy technology hub that is investing in research and developmentof a state-of-the-art computational fluid dynamics capabilityto meet the challenges of turbulent simulation of nuclear reactors. In this presentation, we assess several RANS eddy viscosity models appropriate for single-phase incompressible turbulent flows. Specifically, we compare the single equation Splalart-Allmaras to several variations of the model. The assessment takes into consideration elements of full system reactor cores such as complex geometries, heterogeneous meshes, swirling flow, near wall flow behavior, heat transfer and robustness issues. The goal of this strategically oriented assessment is to provide an accurate and robust turbulent simulation capability for the CASL community. Metrics of performance will be constructed by comparing different models on a strategically chosen set of problems that represent reactor core sub-systems
O zarubežnoj dejatel'nosti professora M.A. Kumaxova
No full textOn professor M.A. Kumakhov's work and research abroad (in Russian)
Professor Mukhadin A. Kumakhov and the author collaborated in the area of Northwest Caucasian languages under a period from 1991 to 2008. The fruitful collaboration at Lund and Malmö universities resulted in three joint monographs and a number of articles, which is outlined in the article. Mukhadin A. Kumakhov became Honorary Doctor of the Philosophical Faculty of Lund University in 1998
Bringing clouds into our lab!: The influence of turbulence on early stage rain droplets
No full textWe are investigating a droplet-laden flow in an air-filled turbulence chamber, forced by speaker-driven air jets. The speakers are running in a random manner; yet they allow us to control and define the statistics of the turbulence. We study the motion of droplets with tunable size in a turbulent flow, mimicking the early stages of raindrop formation. 3D Particle Tracking Velocimetry (PTV) is chosen as the experimental method to track the droplets and collect data for statistical analysis. Thereby it is possible to study the spatial distribution of the droplets in turbulence using the so-called Radial Distribution Function (RDF), a statistical measure to quantify the clustering of particles. Additionally, this technique allows us to measure velocity statistics of the droplets and the influence of the turbulence on droplet trajectories, both individually and collectively. In this contribution, we will present velocity statistics of the droplets and quantify their clustering using the RDF for different turbulence conditions
Cooperative regulation of myosin-actin interactions by a continuous flexible chain II: actin-tropomyosin-troponin and regulation by calcium
No full textThe model of myosin regulation by a continuous tropomyosin chain is generalized to a chain of tropomyosin-troponin units. Myosin binding to regulated actin is cooperative and initially inhibited by the chain as before. In the absence of calcium, myosin is further inhibited by the binding of troponin-I to actin, which through the whole of troponin pins the tropomyosin chain in a blocking position; myosin and TnI compete for actin and induce oppositely-directed chain kinks. The model predicts equilibrium binding curves for myosin-S1 and TnI as a function of their first-order affinities K(S1) and L(TI). Myosin is detached by the actin binding of TnI, but TnI is more efficiently detached by myosin when the kink size (typically nine to ten actin sites) spans the seven-site spacing between adjacent TnI molecules. An allosteric mechanism is used for coupling the detachment of TnI to calcium binding by TnC. With thermally activated TnI kinks (kink energy B approximately k(B)T), TnI also binds cooperatively to actin, producing cooperative detachment of myosin and biphasic myosin-calcium Hill plots, with Hill coefficients of 2 at high calcium and 4-6 at low calcium as observed in striated muscle. The theory also predicts the cooperative effects observed in the calcium loading of TnC
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