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Joint Workshop of IMS and IMI on Mathematics for Industry: Biological and Climatic Prospects
(3 - 7 Sep 2012)
~ Abstracts ~
Accurate detection of SNPs using base-specific cleavage and mass spectrometry
Xin Chen, Nanyang Technological University
Single nucleotide polymorphisms (SNPs) are among the most important genetic factors that contribute to human evolution, disease and biological functions. One approach used to discover these sequence variations is based on base-specific cleavage and matrix assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. However, a question arises on how to integrate four complementary base-specific mass spectra in an efficient and effective way. To address this question, we formulate two new combinatorial optimization problems based on the maximum parsimony principle. They are designated as SNP-MS-p and SNP-MS-q, respectively. In this talk, I will first present an exact dynamic programming algorithm for solving the SNP-MS-p problem and then show that the SNP-MS-q problem is NP-hard. For practical use, an efficient heuristic algorithm was instead developed and implemented. Its SNP detection performance when tested on both simulated and real biological datasets will be discussed.
« Back... Level set methods for fluid-structure problems arising in biological flows
Georges-Henri Cottet, Université de Grenoble and CNRS, France
In the first part of my talk I will present some current research in our group concerning the design and application of immersed boundary techniques to deal with complex uid structure interactions. The models heavily rely on level setmethods to capture interfaces and compute elastic stresses or collisions in solid bodies. Applications to the simulation of various biological systems will be shown.
In the second part of the talk I will present a recent national initiative to promote collaborations between mathematicians and enterprises in France.
« Back... Computational topology and its application to protein structure analysis
Yasuaki Hiraoka, Kyushu University, Japan
In this talk, we review a recent progress of computational topology. Computational topology is one of the important developments which promotes a new research field called applied topology, and is used in a wide variety of scientific problems. After a brief introduction of this topics, we will present an application to protein structure analysis. The subjects we focus on are topological characterizations of protein compressibility [1] and phylogenetic trees.
References
[1] M. Gameiro, Y. Hiraoka, S. Izumi, M. Kramar, K. Mischaikow, and V. Nanda, Topological Measurement of Protein Compressibility via Persistence Diagrams, IMI Preprint, Kyushu University.
« Back... Mathematical methods for blind image deconvolution
Hui Ji, National University of Singapore
Despite all the advances in digital photography, people are still often plagued by the problem of blurry photos when using digital cameras and camera phones. In this talk, I will first give a brief introduction on several mathematical concepts and algorithms extensively studied in recent years, including wavelet, tight frame, sparse approximation and L1 norm related minimization. Built upon these mathematical tools, several mathematical approaches are then introduced to show how they can be used to characterize image blurring and be used to remove image blurring from a given photo. At last, I will demonstrate some preliminary results on improving signal-to-noise ratio of cryo-EM images using related techniques.
« Back... Statistical dynamics of tropical wind in radiosonde data
Tieh-Yong Koh, Nanyang Technological University
Weibull distributions were fitted to wind speed data from radiosonde stations in the global tropics. A statistical theory of independent wind contributions was proposed to partially explain the shape parameter k obtained over Malay Peninsula and the wider Equatorial Monsoon Zone. This statistical dynamical underpinning provides some justification for using empirical Weibull fits to derive wind speed thresholds for monitoring data quality. The regionally adapted thresholds retain more useful data than conventional ones defined from taking the regional mean plus three standard deviations. The new approach is shown to eliminate reports of atypically strong wind over Malay Peninsula which may have escaped detection in quality control of global datasets as the latter has assumed a larger spread of wind speed. New scientific questions are raised in the pursuit of statistical dynamical understanding of meteorological variables in the tropics.
accepted in April 2011, by Atmospheric Chemistry and Physics.
« Back... Protein complex prediction
Osamu Maruyama, Kyushu University, Japan
In this talk, we will consider the problem of protein complex prediction, which is a challenging problem in computational biology. After a brief introduction of this problem, we will present a few computational models used in prediction algorithms, some of which are based on random walks with restarts and MCMC (Markov chain Monte Carlo) sampling methods.
« Back... Mathematical modeling of jamming phenomena and its application to biological transportation
Katsuhiro Nishinari, University of Tokyo, Japan
Jamming phenomena are seen in various transportation system including cars, buses, pedestrians, ants and molecular motors, which are considered as "self-driven particles". There is universality of jam formation among various sorts of flows. Recently we call this interdisciplinary research on jamming of self-driven particles as "jamology". This is based on mathematics and theoretical physics, and includes engineering applications as well. In the talk, starting from the backgroud of this research, a simple mathematical model, called the asymmetric simple exclusion process, is introduced as basis of all kinds of traffic flow. Then it is extended in order to account various traffic phenomena, and the comparison between theory and experiment is given to show that the models are able to capture fundamental features of observations. Especially transportation in nerve cells, i.e, Kinesins on a microtubule is discussed quantitatively in detail.
« Back... Spectral techniques for fast interactive shape animation
Konrad Polthier, Freie Universität Berlin, Germany
We study spectral properties of surface energies with the aim to effectively encode and animate natural shapes. In this talk we design a new family of energies and operators and study their usefulness for applications including fast interactive surface modeling and animation, derivation of surface signatures and mesh filtering.
« Back... Global remeshing of surface and volume meshes
Konrad Polthier, Freie Universität Berlin, Germany
Meshes arising from 3D scans or other 3D imaging techniques are often not well adjusted to the geometry or topology of the underlying shapes. The generation of good meshes is still an active research area in various disciplines. We discuss novel techniques to generate highly structured surface and volume meshes that are consistent with many geometric and topological features of the underlying shapes. The presented algorithms have applications in scientific computing, computer aided design, architecture and computer graphics.
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