262 research outputs found

    Langevin Thermostat for Rigid Body Dynamics

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    We present a new method for isothermal rigid body simulations using the quaternion representation and Langevin dynamics. It can be combined with the traditional Langevin or gradient (Brownian) dynamics for the translational degrees of freedom to correctly sample the NVT distribution in a simulation of rigid molecules. We propose simple, quasi-symplectic second-order numerical integrators and test their performance on the TIP4P model of water. We also investigate the optimal choice of thermostat parameters.Comment: 15 pages, 13 figures, 1 tabl

    Co-operative binding of human fibronectin to Sfbl protein triggers streptococcal invasion into respiratory epithelial cells.

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    Streptococcal fibronectin binding protein I (SfbI) mediates adherence to and invasion of Streptococcus pyogenes into human epithelial cells. In this study, we analysed the binding activity of distinct domains of SfbI protein towards its ligand, the extracellular matrix component fibronectin, as well as the biological implication of the binding events during the infection process. By using purified recombinant SfbI derivatives as well as in vivo expressed SfbI domains on the surface of heterologous organism Streptococcus gordonii, we were able to dissociate the two major streptococcal target domains on the human fibronectin molecule. The SfbI repeat region exclusively bound to the 30 kDa N-terminal fragment of fibronectin, whereas the SfbI spacer region exclusively bound to the 45 kDa collagen-binding fragment of fibronectin. In the case of native surface-expressed SfbI protein, an induced fit mode of bacteria-fibronectin interaction was identified. We demonstrate that binding of the 30 kDa fibronectin fragment to the repeat region of SfbI protein co-operatively activates the adjacent SfbI spacer domain to bind the 45 kDa fibronectin fragment. The biological consequence arising from this novel mode of fibronectin targeting was analysed in eukaryotic cell invasion assays. The repeat region of SfbI protein is mediating adherence and constitutes a prerequisite for subsequent invasion, whereas the SfbI spacer domain efficiently triggers the invasion process of streptococci into the eukaryotic cell. Thus, we were able to dissect bacterial adhesion from invasion by manipulating one protein. SfbI protein therefore represents a highly evolved prokaryotic molecule that exploits the host factor fibronectin not only for extracellular targeting but also for its subsequent activation that leads to efficient cellular invasion

    A generic materials and operations planning approach for inventory turnover optimization in the chemical industry

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    Chemical industries usually involve continuous and large-scale production processes that require demanding inventory control systems. This paper aims to show the results of the implementation of a mixed-integer programming model (MIP) based on the Generic Materials and Operations Planning Problem (GMOP) for optimizing the inventory turnover in a fertilizer company. Results showed significant improvements for Inventory Turnover Ratios and overall costs when compared with an empirical production planning method

    Performance assessment of aero-assisted orbital transfer vehicles

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    Aero-assisted orbital transfer vehicles are analyzed. The aerodynamic characteristics over the flight profile and three- and six-degree-of-freedom performance analyses were determined. The important results, to date, are: (1) the aerodynamic preliminary analysis system, an interactive computer program, used to predict the aerodynamics (performance, stability, and control) for these vehicles; (2) the performance capability, e.g., maximum inclination change, maximum heating rate, and maximum sensed acceleration, can be determined using continuum aerodynamics only; (3) guidance schemes can be developed that allow for errors in atmospheric density prediction, mispredicted trim angle of attack, and off-nominal atmospheric interface conditions, even for vehicles with a low lift-to-drag ratio; and (4) multiple pass trajectories can be used to reduce the maximum heating rate

    Ergodic properties of quasi-Markovian generalized Langevin equations with configuration dependent noise and non-conservative force

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    We discuss the ergodic properties of quasi-Markovian stochastic differential equations, providing general conditions that ensure existence and uniqueness of a smooth invariant distribution and exponential convergence of the evolution operator in suitably weighted LL^{\infty} spaces, which implies the validity of central limit theorem for the respective solution processes. The main new result is an ergodicity condition for the generalized Langevin equation with configuration-dependent noise and (non-)conservative force
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