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4D Monte Carlo dose calculations for particle therapy combined with the spring network model of lung motion

World Congress on Medical Physics and Biomedical engineering: Radiation Oncology

作者： Ishikawa, K.L. Takagi, S. Matthys, K. Wada, S. Integrated Simulation of Living Matter Group RIKEN Computational Science Research Program 2-1 Hirosawa Wako Saitama Japan School of Engineering and Design Brunel University Uxbridge Middlesex United Kingdom School of Engineering Science Osaka University Toyonaka Osaka Japan

ISBN: (纸本)9783642034725

To enable the evaluation of the impact of respiratory motion on charged particle therapy and to realize 4D treatment planning while keeping CT exposure as low as possible, we are developing a Monte Carlo dose calculation system combined with a computational biomechanical model of lung motion. The human lung is CT scanned for a single phase of a respiratory motion. The CT images are transformed into tetrahedral elements by automated segmentation. Then, the respiratory motion is simulated using a computational biomechanical model called the spring network model, and the calculated 3D shape of the lung for a given phase is transformed to a voxel data set. For each phase, assuming carbon-ion beam irradiation, biological dose distribution is calculated using the Monte Carlo particle and heavy ion transport code PHITS coupled with a microdosimetric kinetic model. The dose is mapped onto the reference data set to obtain the accumulated dose. The first version of the 4D dose calculation system we have developed so far can realistically reproduce the lung motion, successfully read the data set for each phase and calculate the accumulated dose. The number of the phases to be sampled and their weights can be set arbitrarily, without need of additional CT scanning. Our first simulations for a 70 MeV/u carbon ion beam with a diameter of 2 cm indicate that the dose distribution can significantly change with phase and that many data sets may be needed to accurately evaluate the dose to the surrounding normal tissue. The impact of the system we developed is two-fold: in the short term, it can be used to investigate different issues of 4D treatment planning;our goal is an entirely simulation-based 4D planning from a single CT scanning. The system is being developed further. © 2009 Springer-Verlag.

关键词： Monte Carlo methods

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STYLISTIC ANALYSIS OF PAINTINGS USING WAVELETS AND MACHINE LEARNING

STYLISTIC ANALYSIS OF PAINTINGS USING WAVELETS AND MACHINE L...

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European signal processing conference

作者： Sina Jafarpour Guengor Polatkan Eugene Brevdo Shannon Hughes Andrei Brasoveanu Ingrid Daubechies Departments of Electrical Engineering Computer Science and Mathematics and the Program in Applied and Computational Mathematics Princeton NJ 08544

ISBN: (纸本)9781617388767

Wavelet transforms and machine learning tools can be used to assist art experts in the stylistic analysis of paintings. A dual-tree complex wavelet transform, Hidden Markov Tree modeling and Random Forest classifiers are used here for a stylistic analysis of Vincent van Gogh's paintings with results on two stylometry challenges that concern "dating, resp. extracting distinguishing features".

关键词： Support vector machines Abstracts Image resolution Radio frequency

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Comparison of load path definitions in 2-D continuum structures

Comparison of load path definitions in 2-D continuum structu...

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作者： Marhadi, Kun S. Venkataraman., Satchi Computational Science Program San Diego State University San Diego CA 92182-1308 United States Department of Aerospace Engineering and Engineering Mechanics San Diego State University Mail Code 1308 5500 Campanile Drive San Diego CA 92182-1308 United States

ISBN: (纸本)9781563479731

The structural mechanics community has developed several methods to identify and visualize load paths in structures. There is no single accepted approach or method to characterize, quantify, visualize and tailor load paths. This paper compares various methods proposed to characterize and visualize load paths. The comparison is performed for a two-dimensional (2-D) rectangular plate under plane stress conditions arising from different loading and boundary conditions. The effectiveness and computational effort of each method are compared. The comparisons shows the methods provide different results and insights into the load transfer mechanisms. No single method appears to emerge as a clear choice for characterizing load paths. However, some methods provide more qualitative and quantitative information on the trajectory and efficiency of load transfer along load paths. Copyright © 2009 by the authors.

关键词： Rectangular plate

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Critical dynamics in multicomponent lipid membranes

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Physical Review E 2009年第2期80卷 020902(R)-020902(R)页

作者： Mikko Haataja Department of Mechanical and Aerospace Engineering Princeton Institute for the Science and Technology of Materials (PRISM) and Program in Applied and Computational Mathematics (PACM) Princeton University Princeton New Jersey 08544 USA

The formation and dynamics of spatially extended compositional domains in multicomponent lipid membranes both in vivo and in vitro lie at the heart of many important biological and biophysical phenomena. While the thermodynamic basis for domain formation has been explored extensively in the past, the roles of membrane and exterior fluid hydrodynamics on domain formation kinetics have received less attention. A case in point is the impact of hydrodynamics on the dynamics of compositional heterogeneities in lipid membranes in the vicinity of a critical point. In this Rapid Communication it is argued that the asymptotic dynamic behavior of a lipid membrane system in the vicinity of a critical point is strongly influenced by hydrodynamic interactions. More specifically, a mode-coupling argument is developed which predicts a scaling behavior of lipid transport coefficients near the critical point for both symmetric and asymmetric bilayers immersed in a bulk fluid.

关键词： Hydrodynamics

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On-line Transient Stability Assessment using Matlab parallel programming environment

On-line Transient Stability Assessment using Matlab parallel...

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International Conference on Soft Computing, Computing with Words and Perceptions in System Analysis, Decision and Control, ICSCCW

作者： Gürkan Soykan Hasan Dağ Computational Science and Engineering Program Istanbul Technical University Istanbul Turkey Information Technologies Department Kadir Has University Istanbul Turkey

Transient Stability Assessment (TSA) is the major part of Dynamic Security Assessment (DSA) in an electric power system. On-line TSA has gained more importance for power system security in last two decades. The decreasing costs of hardware and advanced package programs and techniques encourage researchers to apply parallel programming to the problems that are either too much time consuming or impossible to solve using serial computers. The real-time evaluation of TSA is now almost possible thanks to such tools and techniques. We demonstrate the use of the parallel computing toolbox of Matlab for TSA. In this regard, IEEE 57 and 118 bus systems are tested with 57 and 56 contingencies respectively. Each contingency requires solution of a transient stability problem. The parallel performance of this implementation is expected to spur researchers to use parallel programming in Matlab environment. It requires minimal knowledge regarding parallel programming.

关键词： Parallel programming Power system transients Power system stability Power system security Power system dynamics Costs Hardware Packaging Concurrent computing Parallel processing

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Coarse-grained modeling and simulation of actin filament behavior based on Brownian dynamics method

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MCB Molecular and Cellular Biomechanics 2009年第3期6卷 161-173页

作者： Shimada, Yoshitaka Adachi, Taiji Inoue, Yasuhiro Hojo, Masaki Department of Mechanical Engineering and Science Kyoto University Yoshida-Honmachi Sakyo Kyoto 606-8501 Japan Computational Cell Biomechanics Team VCAD System Research Program RIKEN Japan

The actin filament, which is the most abundant component of the cytoskeleton, plays important roles in fundamental cellular activities such as shape determination, cell motility, and mechanosensing. In each activity, the actin filament dynamically changes its structure by polymerization, depolymerization, and severing. These phenomena occur on the scales ranging from the dynamics of actin molecules to filament structural changes with its deformation due to the various forces, for example, by the membrane and solvent. To better understand the actin filament dynamics, it is important to focus on these scales and develop its mathematical model. Thus, the objectives of this study were to model and simulate actin filament polymerization, depolymerization, and severing based on the Brownian dynamics method. In the model, the actin monomers and the solvent were considered as globular particles and a continuum, respectively. The motion of the actin molecules was assumed to follow the Langevin equation. The polymerization, which increases the filament length, was determined by the distance between the center of the actin particle at the barbed end and actin particles in the solvent. The depolymerization, which decreases the filament length, was modeled such that the number of dissociation particles from the filament end per unit time was constant. In addition, the filament severing, in which one filament divides into two, was modeled to occur at an equal rate along the filament. Then, we simulated the actin filament dynamics using the developed model, and analyzed the filament elongation rate, its turnover, and the effects of filament severing on the polymerization and depolymerization. Results indicated that the model reproduced the linear dependence of the filament elongation on time, filament turnover process by polymerization and depolymerization, and acceleration of the polymerization and depolymerization by severing, which qualitatively agreed with those observed in ex

关键词： Coarse-grained modeling

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Multiscale modeling in rodent ventricular myocytes

Multiscale modeling in rodent ventricular myocytes

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作者： Lu, Shaoying Michailova, Anushka Saucerman, Jeffrey Cheng, Yuhui Yu, Zeyun Kaiser, Timothy Li, Wilfred Bank, Randolph Holst, Michael McCammon, J. Hayashi, Takeharu Hoshijima, Masahiko Arzberger, Peter McCulloch, Andrew Bioengineering Department University of Illinois United States Bioengineering Department UCSD United States Department of Biomedical Engineering University of Virginia United States Department of Mathematics UCSD United States UCSD United States College of Computer Science and Technology Jilin University China Department of Mathematics Center for Computational Mathematics and the Computational Science Mathematics and Engineering Doctoral Program at UCSD Department of Pharmacology UCSD United States Center for Research in Biological Systems UCSD United States Department of Bioengineering UCSD United States Department of Bioengineering PFBH 241 University of California San Diego 9500 Gilman Drive San Diego CA 92093-0412 United States

There is a growing body of experimental evidence suggesting that the Ca2+ signaling in ventricular myocytes is characterized by a high gradient near the cell membrane and a more uniform Ca2+ distribution in the cell interior [1]--[7]. An important reason for this phenomenon might be that in these cells the t-tubular system forms a network of extracellular space, extending deep into the cell interior. This allows the electrical signal, that propagates rapidly along the cell membrane, to reach the vicinity of the sarcoplasmic reticulum (SR), where intracellular Ca2+ required for myofilament activation is stored [1], [8]--[11]. Early studies of cardiac muscle showed that the t-tubules are found at intervals of about 2 lm along the longitudinal cell axis in close proximity to the Z-disks of the sarcomeres [12]. Subsequent studies have demonstrated that the t-tubular system has also longitudinal extensions [9]--[11], [13].

关键词： Cells

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Novel Low-Temperature Behavior in Classical Many-Particle Systems

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Physical Review Letters 2009年第5期103卷 050602-050602页

作者： Robert D. Batten Frank H. Stillinger Salvatore Torquato Department of Chemical Engineering Princeton University Princeton New Jersey 08544 USA Department of Chemistry Princeton University Princeton New Jersey 08544 USA Princeton Materials Institute Program in Applied and Computational Mathematics Princeton Center for Theoretical Science Princeton University Princeton New Jersey 08544 USA School of Natural Sciences Institute for Advanced Study Princeton New Jersey 08544 USA

We show that classical many-particle systems interacting with certain soft pair interactions in two dimensions exhibit novel low-temperature behaviors. Ground states span from disordered to crystalline. At some densities, a large fraction of normal-mode frequencies vanish. Lattice ground-state configurations have more vanishing frequencies than disordered ground states at the same density and exhibit vanishing shear moduli. For the melting transition from a crystal, the thermal expansion coefficient is negative. These unusual results are attributed to the topography of the energy landscape.

关键词： Ground state

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Optimal packings of superballs

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Physical Review E 2009年第4期79卷 041309-041309页

作者： Y. Jiao F. H. Stillinger S. Torquato Department of Mechanical and Aerospace Engineering Princeton University Princeton New Jersey 08544 USA Department of Chemistry Princeton University Princeton New Jersey 08544 USA Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA Princeton Center for Theoretical Science Princeton University Princeton New Jersey 08544 USA School of Natural Sciences Institute for Advanced Study Princeton New Jersey 08540 USA

Dense hard-particle packings are intimately related to the structure of low-temperature phases of matter and are useful models of heterogeneous materials and granular media. Most studies of the densest packings in three dimensions have considered spherical shapes, and it is only more recently that nonspherical shapes (e.g., ellipsoids) have been investigated. Superballs (whose shapes are defined by |x1|2p+|x2|2p+|x3|2p≤1) provide a versatile family of convex particles (p≥0.5) with both cubic-like and octahedral-like shapes as well as concave particles (0

关键词： Temperature

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Dense packings of polyhedra: Platonic and Archimedean solids

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Physical Review E 2009年第4期80卷 041104-041104页

作者： S. Torquato Y. Jiao Department of Chemistry Princeton University Princeton New Jersey 08544 USA Princeton Center for Theoretical Science Princeton University Princeton New Jersey 08544 USA Princeton Institute for the Science and Technology of Materials Princeton University Princeton New Jersey 08544 USA Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA School of Natural Sciences Institute for Advanced Study Princeton New Jersey 08540 USA Department of Mechanical and Aerospace Engineering Princeton University Princeton New Jersey 08544 USA

Understanding the nature of dense particle packings is a subject of intense research in the physical, mathematical, and biological sciences. The preponderance of previous work has focused on spherical particles and very little is known about dense polyhedral packings. We formulate the problem of generating dense packings of nonoverlapping, nontiling polyhedra within an adaptive fundamental cell subject to periodic boundary conditions as an optimization problem, which we call the adaptive shrinking cell (ASC) scheme. This optimization problem is solved here (using a variety of multiparticle initial configurations) to find the dense packings of each of the Platonic solids in three-dimensional Euclidean space R3, except for the cube, which is the only Platonic solid that tiles space. We find the densest known packings of tetrahedra, icosahedra, dodecahedra, and octahedra with densities 0.823…, 0.836…, 0.904…, and 0.947…, respectively. It is noteworthy that the densest tetrahedral packing possesses no long-range order. Unlike the densest tetrahedral packing, which must not be a Bravais lattice packing, the densest packings of the other nontiling Platonic solids that we obtain are their previously known optimal (Bravais) lattice packings. We also derive a simple upper bound on the maximal density of packings of congruent nonspherical particles and apply it to Platonic solids, Archimedean solids, superballs, and ellipsoids. Provided that what we term the “asphericity” (ratio of the circumradius to inradius) is sufficiently small, the upper bounds are relatively tight and thus close to the corresponding densities of the optimal lattice packings of the centrally symmetric Platonic and Archimedean solids. Our simulation results, rigorous upper bounds, and other theoretical arguments lead us to the conjecture that the densest packings of Platonic and Archimedean solids with central symmetry are given by their corresponding densest lattice packings. This can be regarded to be

关键词： Optimization

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