Free energy surface reconstruction from umbrella samples using Gaussian process regression II: Multiple collective variables

We demonstrate how a prior assumption of smoothness can be used to enhance the reconstruction of free energy profiles from multiple umbrella sampling simulations using the Bayesian Gaussian process regression approach. The method we derive allows the concurrent use of histograms and free energy gradients and can easily be extended to include further data. In Part I we review the necessary theory and test the method for one collective variable. We demonstrate improved performance with respect to the weighted histogram analysis method and obtain meaningful error bars without any significant additional computation. In Part II we consider the case of multiple collective variables and compare to a reconstruction using least squares fitting of radial basis functions. We find substantial improvements in the regimes of spatially sparse data or short sampling trajectories. A software implementation is made available on www.libatoms.org.

Network reconstruction using knock-out and over-expression data

This paper outlines necessary and sufficient conditions for network reconstruction of linear, time-invariant systems using data from either knock-out or over-expression experiments. These structural system perturbations, which are common in biological experiments, can be formulated as unknown system inputs, allowing the network topology and dynamics to be found. We assume that only partial state measurements are available and propose an algorithm that can reconstruct the network at the level of the measured states using either time-series or steady-state data. A simulated example illustrates how the algorithm successfully reconstructs a network from data. © 2013 EUCA.

Reconfigurable predictive control for redundantly actuated systems with parameterised input constraints

A method is proposed for on-line reconfiguration of the terminal constraint used to provide theoretical nominal stability guarantees in linear model predictive control (MPC). By parameterising the terminal constraint, its complete reconstruction is avoided when input constraints are modified to accommodate faults. To enlarge the region of feasibility of the terminal control law for a certain class of input faults with redundantly actuated plants, the linear terminal controller is defined in terms of virtual commands. A suitable terminal cost weighting for the reconfigurable MPC is obtained by means of an upper bound on the cost for all feasible realisations of the virtual commands from the terminal controller. Conditions are proposed that guarantee feasibility recovery for a defined subset of faults. The proposed method is demonstrated by means of a numerical example. © 2013 Elsevier B.V. All rights reserved.

Rapid hologram generation utilizing layer-based approach and graphic rendering for realistic three-dimensional image reconstruction by angular tiling

An approach of rapid hologram generation for the realistic three-dimensional (3-D) image reconstruction based on the angular tiling concept is proposed, using a new graphic rendering approach integrated with a previously developed layer-based method for hologram calculation. A 3-D object is simplified as layered cross-sectional images perpendicular to a chosen viewing direction, and our graphics rendering approach allows the incorporation of clear depth cues, occlusion, and shading in the generated holograms for angular tiling. The combination of these techniques together with parallel computing reduces the computation time of a single-view hologram for a 3-D image of extended graphics array resolution to 176 ms using a single consumer graphics processing unit card. © 2014 SPIE and IS and T.

Applications of factor-criteria system reconstruction analysis in the reproduction research on grass carp, black carp, silver carp and bighead in the Yangtze River

The natural reproduction of grass carp, black carp, silver carp, and bighead will be affected adversely by the Three Gorges Project in the Yangtze River. One of the methods to save the fish is to regulate the water levels, keeping them suited for the species to spawn. Nine factors associated with the scale of larvae-flood of the four species are classified into five levels, and the ranges of these factors producing larvae-floods are given by using the "factor-criteria system reconstruction analysis" method. Moderate beginning water levels and flow, with high daily increases in the rate of water level and flow, and a long duration of water level rising are important for the production of a large larvae-flood.

Room temperature photoluminescence of tensile-strained Ge/Si0.13Ge0.87 quantum wells grown on silicon-based germanium virtual substrate

We report a room temperature study of the direct band gap photoluminescence of tensile-strained Ge/Si0.13Ge0.87 multiple quantum wells grown on Si-based germanium virtual substrates by ultrahigh vacuum chemical vapor deposition. Blueshifts of the luminescence peak energy from the Ge quantum wells in comparison with the Ge virtual substrate are in good agreement with the theoretical prediction when we attribute the luminescence from the quantum well to the c Gamma 1-HH1 direct band transition. The reduction in direct band gap in the tensile strained Ge epilayer and the quantum confinement effect in the Ge/Si0.13Ge0.87 quantum wells are directly demonstrated by room temperature photoluminescence.

Experimental demonstration of distributed feedback semiconductor lasers based on reconstruction-equivalent-chirp technology

In this paper we report, to the best of our knowledge, the first experimental realization of distributed feedback (DFB) semiconductor lasers based on reconstruction-equivalent-chirp (REC) technology. Lasers with different lasing wavelengths are achieved simultaneously on one chip, which shows a potential for the REC technology in combination with the photonic integrated circuits (PIC) technology to be a possible method for monolithic integration, in that its fabrication is as powerful as electron beam technology and the cost and time-consuming are almost the same as standard holographic technology. (C) 2009 Optical Society of America

co-creativepen toolkit: a pen-based 3d toolkit for children cooperatly designing virtual environment

Co-CreativePen Toolkit is a pen-based 3D toolkit for children cooperatly designing virtual environment. This toolkit is used to construct different applications involved with distributedpen-based 3D interaction. In this toolkit,sketch method is encapsulated as kinds of interaction techniques. Children can use pen to construct 3D and IBR objects, to navigate in the virtual world, to select and manipulate virtual objects, and to communicate with other children. Children can use pen to select other children in the virtual world, and use pen to write message to children selected The distributed architecture of Co-CreativePen Toolkit is based on the CORBA. A common scene graph is managed in the server with several copies of this graph are managed in every client.Every changes of the scene graph in client will cause the change in the server and other client.

construction of feature-matching perception in virtual assembly

An important characteristic of virtual assembly is interaction. Traditional di-rect manipulation in virtual assembly relies on dynamic collision detection, which is very time-consuming and even impossible in desktop virtual assembly environment. Feature-matching isa critical process in harmonious virtual assembly, and is the premise of assembly constraint sens-ing. This paper puts forward an active object-based feature-matching perception mechanism and afeature-matching interactive computing process, both of which make the direct manipulation in vir-tual assembly break away from collision detection. They also help to enhance virtual environmentunderstandability of user intention and promote interaction performance. Experimental resultsshow that this perception mechanism can ensure that users achieve real-time direct manipulationin desktop virtual environment.

Effect of reconstruction beam polarization on the kinetics of anisotropic gratings in bacteriorhodopsin

Anisotropic gratings are recorded on bacteriorhodopsin films by two parallelly polarized beams, and the effect of the polarization orientation of the reconstructing beam on the diffraction efficiency kinetics is studied. A theoretical model for the diffraction efficiency kinetics of the anisotropic grating is developed by combining Jones-matrix and photochromic two-state theory. It is found that the polarization azimuth of the reconstructing beam produces a cosine modulation on the kinetics of the diffraction efficiency, being positive at the peak efficiency and negative for steady state. By adding auxiliary violet light during grating formation, the saturation of the grating can be restrained. As a result, the negative cosine modulation for the steady-state diffraction efficiency changes to a positive one. In addition, the steady-state diffraction efficiency is increased appreciably for all reconstructing polarization orientations. (c) 2008 Optical Society of America.

Phase and amplitude reconstruction from a single carrier-frequency interferogram without phase unwrapping

A rapid algorithm for phase and amplitude reconstruction from a single spatial-carrier interferogram is proposed by bringing a phase-shifting mechanism into reconstruction of a carrier-frequency interferogram. The algorithm reconstructs phase through directly obtaining and integrating its real-value derivatives, avoiding a phase unwrapping process. The proposed method is rapid and easy to implement and is made insensitive to the profile of the interferogram boundaries by choosing a suitable integrating path. Moreover, the algorithm can also be used to reconstruct the amplitude of the object wave expediently without retrieving the phase profile in advance. The feasibility of this algorithm is demonstrated by both numerical simulation and experiment. (c) 2008 Optical Society of America.

Phase reconstruction from three interferograms based on integral of phase gradient

A novel algorithm of phase reconstruction based on the integral of phase gradient is presented. The algorithm directly derives two real-valued partial derivatives from three phase-shifted interferograms. Through integrating the phase derivatives, the desired phase is reconstructed. During the phase reconstruction process, there is no need for an extra rewrapping manipulation to ensure values of the phase derivatives lie in the interval [-pi, pi] as before, thus this algorithm can prevent error or distortion brought about by the phase unwrapping operation. Additionally, this algorithm is fast and easy to implement, and insensitive to the nonuniformity of the intensity distribution of the interferogram. The feasibility of the algorithm is demonstrated by both computer simulation and experiment.