Minimal model for the secondary structures and conformational conversions in proteins

Better understanding of protein folding process can provide physical insights on the function of proteins and makes it possible to benefit from genetic information accumulated so far. Protein folding process normally takes place in less than seconds but even seconds are beyond reach of current computational power for simulations on a system of all-atom detail. Hence, to model and explore protein folding process it is crucial to construct a proper model that can adequately describe the physical process and mechanism for the relevant time scale. We discuss the reduced off-lattice model that can express α-helix and β-hairpin conformations defined solely by a given sequence in order to investigate a protein folding mechanism of conformations such as a β-hairpin and also to investigate conformational conversions in proteins. The first two chapters introduce and review essential concepts in protein folding modelling physical interaction in proteins, various simple models, and also review computational methods, in particular, the Metropolis Monte Carlo method, its dynamic interpretation and thermodynamic Monte Carlo algorithms. Chapter 3 describes the minimalist model that represents both α-helix and β-sheet conformations using simple potentials. The native conformation can be specified by the sequence without particular conformational biases to a reference state. In Chapter 4, the model is used to investigate the folding mechanism of β-hairpins exhaustively using the dynamic Monte Carlo and a thermodynamic Monte Carlo method an effcient combination of the multicanonical Monte Carlo and the weighted histogram analysis method. We show that the major folding pathways and folding rate depend on the location of a hydrophobic. The conformational conversions between α-helix and β-sheet conformations are examined in Chapter 5 and 6. First, the conformational conversion due to mutation in a non-hydrophobic system and then the conformational conversion due to mutation with a hydrophobic pair at a different position at various temperatures are examined

Symmetry of `molecular' configurations of interacting electrons in a quantum dot in strong magnetic fields

A molecular description for magic-number configurations of interacting electrons in a quantum dot in high magnetic fields developed by one of the authors has been elaborated for four, five and six electron dots. For four electrons, the magic spin-singlet states are found to alternate between two different resonating valence bond (RVB)-like states. For the five-electron spin-polarized case, the molecular description is shown to work for the known phenomenon of magic-number sequences that correspond to both the N-fold symmetric ring configuration and a $(N-1)$-fold symmetric one with a center electron. A six-electron dot is shown here to have an additional feature in which inclusion of quantum mechanical mixing between classical configurations, which are deformed and degenerate, restores the N-fold symmetry and reproduces the ground-state energy accurately.Comment: 4 pages, to be published in Physisca

Willingness to pay for health care services in common cold, retinal detachment, and myocardiac infarction: an internet survey in Japan

BACKGROUND: The application of Willingness To Pay (WTP) measurement with Contingent Valuation Method (CVM) to medical services is gradually increasing. Knowing what influences WTP is an important matter because validity of CVM in medical services remains controversial. The objective of this survey is to measure WTP for the treatment of typical acute illnesses and to analyze the factors affecting WTP. METHODS: A questionnaire survey was conducted over the Internet, in which 795 men and women between 40 and 59 years old responded to questions about WTP for medical expenses in three hypothetical scenarios: common cold (CC), retinal detachment (RD) and myocardiac infarction (MI). RESULTS: Mean WTP was $29.9 for CC,$2,233 for RD, and $8,976 for MI. WTP for RD and MI was lower in the low-income group. While WTP for CC did not vary with income, WTP was higher in groups whose current subjective fitness levels were low. CONCLUSION: Although WTP measurements are criticized frequently for their validity and reliability, they are still useful for determining the economic value of medical services. Based on the results of this study, it is deemed necessary to enhance safety nets for low-income earners in regards to serious illnesses that incur high medical expenses. Further, it is recommended that the rate of co-payments be set relatively high with respect to mild illnesses for which alternative services are available

Weak preservation of local neutral substitution rates across mammalian genomes

<p>Abstract</p> <p>Background</p> <p>The rate at which neutral (non-functional) bases undergo substitution is highly dependent on their location within a genome. However, it is not clear how fast these location-dependent rates change, or to what extent the substitution rate <it>patterns </it>are conserved between lineages. To address this question, which is critical not only for understanding the substitution process but also for evaluating phylogenetic footprinting algorithms, we examine ancestral repeats: a predominantly neutral dataset with a significantly higher genomic density than other datasets commonly used to study substitution rate variation. Using this repeat data, we measure the extent to which orthologous ancestral repeat sequences exhibit similar substitution patterns in separate mammalian lineages, allowing us to ascertain how well local substitution rates have been preserved across species.</p> <p>Results</p> <p>We calculated substitution rates for each ancestral repeat in each of three independent mammalian lineages (primate – from human/macaque alignments, rodent – from mouse/rat alignments, and laurasiatheria – from dog/cow alignments). We then measured the correlation of local substitution rates among these lineages. Overall we found the correlations between lineages to be statistically significant, but too weak to have much predictive power (<it>r</it>²<<it>5%</it>). These correlations were found to be primarily driven by regional effects at the scale of several hundred kb or larger. A few repeat classes (e.g. 7SK, Charlie8, and MER121) also exhibited stronger conservation of rate patterns, likely due to the effect of repeat-specific purifying selection. These classes should be excluded when estimating local neutral substitution rates.</p> <p>Conclusion</p> <p>Although local neutral substitution rates have some correlations among mammalian species, these correlations have little predictive power on the scale of individual repeats. This indicates that local substitution rates have changed significantly among the lineages we have studied, and are likely to have changed even more for more diverged lineages. The correlations that do persist are too weak to be responsible for many of the highly conserved elements found by phylogenetic footprinting algorithms, leading us to conclude that such elements must be conserved due to selective forces.</p

Coherent transfer of light polarization to electron spins in a semiconductor

We demonstrate that the superposition of light polarization states is coherently transferred to electron spins in a semiconductor quantum well. By using time-resolved Kerr rotation we observe the initial phase of Larmor precession of electron spins whose coherence is transferred from light. To break the electron-hole spin entanglement, we utilized the big discrepancy between the transverse g-factors of electrons and light holes. The result encourages us to make a quantum media converter between flying photon qubits and stationary electron spin qubits in semiconductors.Comment: 4 pages. Submitted to Physical Review Letter

An adaptive speed function of level set method for moving object extraction

金沢大学理工研究域電子情報学系The convergence and stability of the level set method depend on the speed function. Therefore, it is important to define the speed function in a manner that is suitable for the individual application. In the present paper, we propose a novel speed function of the level set method for moving object extraction from a video sequence with a stationary background. The speed function focuses on the precision of moving object extraction. In the proposed extraction method, the outline between moving object regions and the background is estimated in advance based on the Gaussian noise distribution in the frame. The speed function is changed adaptively using the obtained outline in order to improve the convergence and precision of extraction. In addition, a new energy term in the direction of the contour of an object is incorporated into the speed function. The precision of the moving object extraction method using the proposed speed function is evaluated through computer simulations. ©2010 IEEE

Improvement of convergence and stability in moving object extraction by the level set method

金沢大学理工研究域電子情報学系Semantic object extraction from a video sequence is an indispensable technique in new content-based applications, such as in the international standards MPEG-4 and MPEG- 7. In the present paper, we propose a technique that extracts the shape of moving objects from a video sequence with a stationary background by the level set method. In the proposed method, two concepts are incorporated into a novel speed function of the level set method in order to improve convergence and stability. The first concept is the object map, which represents the outline of object regions and the background. The speed function is changed using the object map in order to improve convergence. The second concept is the contour potential energy, which represents the energy in the direction of an object\u27s contour. The efficiency of the proposed method for moving object extraction is demonstrated through computer simulations

Watershed algorithm for moving object extraction considering energy minimization by snakes

金沢大学理工研究域電子情報学系MPEG-4, which is a video coding standard, supports object-based functionalities for high efficiency coding. MPEG-7, a multimedia content description interface, handles the object data in, for example, retrieval and/or editing systems. Therefore, extraction of semantic video objects is an indispensable tool that benefits these newly developed schemes. In the present paper, we propose a technique that extracts the shape of moving objects by combining snakes and watershed algorithm. The proposed method comprises two steps. In the first step, snakes extract contours of moving objects as a result of the minimization of an energy function. In the second step, the conditional watershed algorithm extracts contours from a topographical surface including a new function term. This function term is introduced to improve the estimated contours considering boundaries of moving objects obtained by snakes. The efficiency of the proposed approach in moving object extraction is demonstrated through computer simulations. © 2007 IEEE