Iterative Linearized Density Matrix Propagation for Modeling Coherent Energy Transfer in Photosynthetic Light Harvesting

We present results of calculations [1] that employ a new mixed quantum classical iterative density matrix propagation approach (ILDM , or so called Is‐Landmap) [2] to explore the survival of coherence in different photo synthetic models. Our model studies confirm the long lived quantum coherence , while conventional theoretical tools (such as Redfield equation) fail to describe these phenomenon [3,4]. Our ILDM method is a numerical exactly propagation scheme and can be served as a bench mark calculation tools[2]. Result get from ILDM and from other recent methods have been compared and show agreement with each other[4,5]. Long lived coherence plateau has been attribute to the shift of harmonic potential due to the system bath interaction, and the harvesting efficiency is a balance between the coherence and dissipation[1]. We use this approach to investigate the excitation energy transfer dynamics in various light harvesting complex include Fenna‐Matthews‐Olsen light harvesting complex[1] and Cryptophyte Phycocyanin 645 [6]. [1] P.Huo and D.F.Coker ,J. Chem. Phys. 133, 184108 (2010) . [2] E.R. Dunkel, S. Bonella, and D.F. Coker, J. Chem. Phys. 129, 114106 (2008). [3] A. Ishizaki and G.R. Fleming, J. Chem. Phys. 130, 234111 (2009). [4] A. Ishizaki and G.R. Fleming, Proc. Natl. Acad. Sci. 106, 17255 (2009). [5] G. Tao and W.H. Miller, J. Phys. Chem. Lett. 1, 891 (2010). [6] P.Huo and D.F.Coker in preparation

Gene selection using iterative feature elimination random forests for survival outcomes.

Although many feature selection methods for classification have been developed, there is a need to identify genes in high-dimensional data with censored survival outcomes. Traditional methods for gene selection in classification problems have several drawbacks. First, the majority of the gene selection approaches for classification are single-gene based. Second, many of the gene selection procedures are not embedded within the algorithm itself. The technique of random forests has been found to perform well in high-dimensional data settings with survival outcomes. It also has an embedded feature to identify variables of importance. Therefore, it is an ideal candidate for gene selection in high-dimensional data with survival outcomes. In this paper, we develop a novel method based on the random forests to identify a set of prognostic genes. We compare our method with several machine learning methods and various node split criteria using several real data sets. Our method performed well in both simulations and real data analysis.Additionally, we have shown the advantages of our approach over single-gene-based approaches. Our method incorporates multivariate correlations in microarray data for survival outcomes. The described method allows us to better utilize the information available from microarray data with survival outcomes.

Regularized iterative and noniterative procedures for object restoration in the presence of noise :an error analysis

An analysis is carried out, using the prolate spheroidal wave functions, of certain regularized iterative and noniterative methods previously proposed for the achievement of object restoration (or, equivalently, spectral extrapolation) from noisy image data. The ill-posedness inherent in the problem is treated by means of a regularization parameter, and the analysis shows explicitly how the deleterious effects of the noise are then contained. The error in the object estimate is also assessed, and it is shown that the optimal choice for the regularization parameter depends on the signal-to-noise ratio. Numerical examples are used to demonstrate the performance of both unregularized and regularized procedures and also to show how, in the unregularized case, artefacts can be generated from pure noise. Finally, the relative error in the estimate is calculated as a function of the degree of superresolution demanded for reconstruction problems characterized by low space–bandwidth products.

Nested heuristic methods for the location-routeing problem

The concept of 'nested methods' is adopted to solve the location-routeing problem. Unlike the sequential and iterative approaches, in this method we treat the routeing element as a sub-problem within the larger problem of location. Efficient techniques that take into account the above concept and which use a neighbourhood structure inspired from computational geometry are presented. A simple version of tabu search is also embedded into our methods to improve the solutions further. Computational testing is carried out on five sets of problems of 400 customers with five levels of depot fixed costs, and the results obtained are encouraging.

A scalable strategy for the parallelization of multiphysics unstructured mesh-iterative codes on distributed-memory systems

Realizing scalable performance on high performance computing systems is not straightforward for single-phenomenon codes (such as computational fluid dynamics [CFD]). This task is magnified considerably when the target software involves the interactions of a range of phenomena that have distinctive solution procedures involving different discretization methods. The problems of addressing the key issues of retaining data integrity and the ordering of the calculation procedures are significant. A strategy for parallelizing this multiphysics family of codes is described for software exploiting finite-volume discretization methods on unstructured meshes using iterative solution procedures. A mesh partitioning-based SPMD approach is used. However, since different variables use distinct discretization schemes, this means that distinct partitions are required; techniques for addressing this issue are described using the mesh-partitioning tool, JOSTLE. In this contribution, the strategy is tested for a variety of test cases under a wide range of conditions (e.g., problem size, number of processors, asynchronous / synchronous communications, etc.) using a variety of strategies for mapping the mesh partition onto the processor topology.

Numerical experiments of some Krylov subspace methods for black oil model

This paper discusses preconditioned Krylov subspace methods for solving large scale linear systems that originate from oil reservoir numerical simulations. Two types of preconditioners, one being based on an incomplete LU decomposition and the other being based on iterative algorithms, are used together in a combination strategy in order to achieve an adaptive and efficient preconditioner. Numerical tests show that different Krylov subspace methods combining with appropriate preconditioners are able to achieve optimal performance.

An algorithm for total variation inpainting based on nonlinear multi-grid methods

Image inpainting refers to restoring a damaged image with missing information. The total variation (TV) inpainting model is one such method that simultaneously fills in the regions with available information from their surroundings and eliminates noises. The method works well with small narrow inpainting domains. However there remains an urgent need to develop fast iterative solvers, as the underlying problem sizes are large. In addition one needs to tackle the imbalance of results between inpainting and denoising. When the inpainting regions are thick and large, the procedure of inpainting works quite slowly and usually requires a significant number of iterations and leads inevitably to oversmoothing in the outside of the inpainting domain. To overcome these difficulties, we propose a solution for TV inpainting method based on the nonlinear multi-grid algorithm.

Automated Methods for Aircraft Design Integrated with Manufacturing

Aircraft design is a complex, long and iterative process that requires the use of various specialties and optimization tools. However these tools and specialities do not include manufacturing, which is often considered later in the product development process leading to higher cost and time delays. This work focuses on the development of an automated design tool that accounts for manufacture during the design process focusing on early geometry definition which in turn informs assembly planning. To accomplish this task the design process needs to be open to any variation in structural configuration while maintaining the design intent. Redefining design intent as a map which links a set of requirements to a set of functions using a numerical approach enables the design process itself to be considered as a mathematical function. This definition enables the design process to utilise captured design knowledge and translate it into a set of mathematical equations that design the structure. This process is articulated in this paper using the structural design and definition for an aircraft fuselage section as an exemplar.

An iterative longest matching segment approach to speech enhancement with additive noise and channel distortion

This paper presents a new approach to speech enhancement from single-channel measurements involving both noise and channel distortion (i.e., convolutional noise), and demonstrates its applications for robust speech recognition and for improving noisy speech quality. The approach is based on finding longest matching segments (LMS) from a corpus of clean, wideband speech. The approach adds three novel developments to our previous LMS research. First, we address the problem of channel distortion as well as additive noise. Second, we present an improved method for modeling noise for speech estimation. Third, we present an iterative algorithm which updates the noise and channel estimates of the corpus data model. In experiments using speech recognition as a test with the Aurora 4 database, the use of our enhancement approach as a preprocessor for feature extraction significantly improved the performance of a baseline recognition system. In another comparison against conventional enhancement algorithms, both the PESQ and the segmental SNR ratings of the LMS algorithm were superior to the other methods for noisy speech enhancement.

Improving the robustness of the iterative solver in state-space modelling of guitar distortion circuitry

Iterative solvers are required for the discrete-time simulation of nonlinear behaviour in analogue distortion circuits. Unfortunately,these methods are often computationally too expensive for realtime simulation. Two methods are presented which attempt to reduce the expense of iterative solvers. This is achieved by applying information that is derived from the specific form of the non linearity.The approach is first explained through the modelling of an asymmetrical diode clipper, and further exemplified by application to the Dallas Rangemaster Treble Booster guitar pedal, which provides an initial perspective of the performance on systems with multiple nonlinearities.

Applications of Statistical Modeling in Iterative CT Image Reconstruction

Thesis (Master's)--University of Washington, 2015

Stereo-Based Head Pose Tracking Using Iterative Closest Point and Normal Flow Constraint

In this text, we present two stereo-based head tracking techniques along with a fast 3D model acquisition system. The first tracking technique is a robust implementation of stereo-based head tracking designed for interactive environments with uncontrolled lighting. We integrate fast face detection and drift reduction algorithms with a gradient-based stereo rigid motion tracking technique. Our system can automatically segment and track a user's head under large rotation and illumination variations. Precision and usability of this approach are compared with previous tracking methods for cursor control and target selection in both desktop and interactive room environments. The second tracking technique is designed to improve the robustness of head pose tracking for fast movements. Our iterative hybrid tracker combines constraints from the ICP (Iterative Closest Point) algorithm and normal flow constraint. This new technique is more precise for small movements and noisy depth than ICP alone, and more robust for large movements than the normal flow constraint alone. We present experiments which test the accuracy of our approach on sequences of real and synthetic stereo images. The 3D model acquisition system we present quickly aligns intensity and depth images, and reconstructs a textured 3D mesh. 3D views are registered with shape alignment based on our iterative hybrid tracker. We reconstruct the 3D model using a new Cubic Ray Projection merging algorithm which takes advantage of a novel data structure: the linked voxel space. We present experiments to test the accuracy of our approach on 3D face modelling using real-time stereo images.

Approximate Gauss-Newton methods for nonlinear least squares problems

The Gauss–Newton algorithm is an iterative method regularly used for solving nonlinear least squares problems. It is particularly well suited to the treatment of very large scale variational data assimilation problems that arise in atmosphere and ocean forecasting. The procedure consists of a sequence of linear least squares approximations to the nonlinear problem, each of which is solved by an “inner” direct or iterative process. In comparison with Newton’s method and its variants, the algorithm is attractive because it does not require the evaluation of second-order derivatives in the Hessian of the objective function. In practice the exact Gauss–Newton method is too expensive to apply operationally in meteorological forecasting, and various approximations are made in order to reduce computational costs and to solve the problems in real time. Here we investigate the effects on the convergence of the Gauss–Newton method of two types of approximation used commonly in data assimilation. First, we examine “truncated” Gauss–Newton methods where the inner linear least squares problem is not solved exactly, and second, we examine “perturbed” Gauss–Newton methods where the true linearized inner problem is approximated by a simplified, or perturbed, linear least squares problem. We give conditions ensuring that the truncated and perturbed Gauss–Newton methods converge and also derive rates of convergence for the iterations. The results are illustrated by a simple numerical example. A practical application to the problem of data assimilation in a typical meteorological system is presented.

Integrating methods for developing sustainability indicators that can facilitate learning and action

Bossel's (2001) systems-based approach for deriving comprehensive indicator sets provides one of the most holistic frameworks for developing sustainability indicators. It ensures that indicators cover all important aspects of system viability, performance, and sustainability, and recognizes that a system cannot be assessed in isolation from the systems upon which it depends and which in turn depend upon it. In this reply, we show how Bossel's approach is part of a wider convergence toward integrating participatory and reductionist approaches to measure progress toward sustainable development. However, we also show that further integration of these approaches may be able to improve the accuracy and reliability of indicators to better stimulate community learning and action. Only through active community involvement can indicators facilitate progress toward sustainable development goals. To engage communities effectively in the application of indicators, these communities must be actively involved in developing, and even in proposing, indicators. The accuracy, reliability, and sensitivity of the indicators derived from local communities can be ensured through an iterative process of empirical and community evaluation. Communities are unlikely to invest in measuring sustainability indicators unless monitoring provides immediate and clear benefits. However, in the context of goals, targets, and/or baselines, sustainability indicators can more effectively contribute to a process of development that matches local priorities and engages the interests of local people.

Implicit-factorization preconditioning and iterative solvers for regularized saddle-point systems

We consider conjugate-gradient like methods for solving block symmetric indefinite linear systems that arise from saddle-point problems or, in particular, regularizations thereof. Such methods require preconditioners that preserve certain sub-blocks from the original systems but allow considerable flexibility for the remaining blocks. We construct a number of families of implicit factorizations that are capable of reproducing the required sub-blocks and (some) of the remainder. These generalize known implicit factorizations for the unregularized case. Improved eigenvalue clustering is possible if additionally some of the noncrucial blocks are reproduced. Numerical experiments confirm that these implicit-factorization preconditioners can be very effective in practice.