CCS Report: PART II, Research Activities, Results Collaborations and Plan 2008-2013 CCS Report: PART II Research Activities, Results, Collaborations and Plan 2008 – 2013 February 2014 Center for Computational Sciences University of Tsukuba 1 CCS Report: PART II, Research Activities, Results Collaborations and Plan 2008-2013 1 DIVISION OF PARTICLE PHYSICS: PARTICLE PHYSICS GROUP ................................................................................ 5 1.1 RESEARCH ACTIVITY ............................................................................................ 5 1.2 RESEARCH RESULTS ............................................................................................ 6 1.3 COLLABORATION ................................................................................................ 11 1.4 FUTURE PLAN .................................................................................................... 11 1.5 PUBLICATIONS ................................................................................................... 12 1.5.1 Journal Papers ........................................................................................... 12 1.5.2 Proceedings ................................................................................................ 18 2 DIVISION OF ASTROPHYSICS AND NUCLEAR PHYSICS: ASTROPHYSICS GROUP ..................................................................................... 26 2.1 RESEARCH ACTIVITY .......................................................................................... 26 2.2 RESEARCH RESULTS .......................................................................................... 26 2.2.1 Numerical Methods .................................................................................... 26 2.2.2 Numerical Simulations .............................................................................. 29 2.3 COLLABORATION ................................................................................................ 33 2.4 FUTURE PLAN .................................................................................................... 35 2.5 PUBLICATIONS .............................................................................................. 35 2.5.1 Journal Papers ........................................................................................... 35 2.5.2 Proceedings ................................................................................................ 39 2.6 GRANTS ........................................................................................................... 41 3 DIVISION OF ASTROPHYSICS AND NUCLEAR PHYSICS: NUCLEAR PHYSICS GROUP .............................................................................. 42 3.1 RESEARCH ACTIVITY .......................................................................................... 42 3.2 RESEARCH RESULTS .......................................................................................... 43 3.3 COLLABORATION ................................................................................................ 47 3.4 FUTURE PLAN .................................................................................................... 47 3.5 PUBLICATIONS ................................................................................................... 48 3.5.1 Journal Papers ........................................................................................... 48 3.5.2 Proceedings ................................................................................................ 49 4 DIVISION OF QUANTUM CONDENSED MATTER PHYSICS ..................... 51 4.1 RESEARCH ACTIVITY .......................................................................................... 51 4.2 RESEARCH RESULTS .......................................................................................... 52 4.3 COLLABORATION ................................................................................................ 57 4.4 FUTURE PLAN .................................................................................................... 58 4.5 PUBLICATIONS ................................................................................................... 59 4.5.1 Journal Papers ........................................................................................... 59 4.5.2 Proceedings ................................................................................................ 71 5 DIVISION OF LIFE SCIENCES: BIOLOGICAL FUNCTION AND INFORMATION GROUP .................................. 76 5.1 RESEARCH ACTIVITY .......................................................................................... 76 5.2 RESEARCH RESULTS .......................................................................................... 76 2 CCS Report: PART II, Research Activities, Results Collaborations and Plan 2008-2013 5.3 COLLABORATION ................................................................................................ 80 5.4 FUTURE PLAN .................................................................................................... 80 5.5 PUBLICATIONS ................................................................................................... 81 5.5.1 Journal Papers ........................................................................................... 81 5.5.2 Proceedings ................................................................................................ 86 6 DIVISION OF LIFE SCIENCES: MOLECULAR EVOLUTION GROUP ................................................................... 87 6.1 RESEARCH ACTIVITY .......................................................................................... 87 6.2 RESEARCH RESULTS .......................................................................................... 89 6.2.1 Palpitomonas bilix...................................................................................... 89 6.2.2 Tsukubamonas globosa .............................................................................. 90 6.2.3 Carpediemonas-like organisms (CLOs) ..................................................... 92 6.2.4 Methodologial studies for phylogenetic analyses of nucleotide sequence data which bear across-tree base composition variation ................................... 94 6.2.5 Potential bias in bootstrap support values in the maximum-likelihood methods ............................................................................................................... 95 6.3 COLLABORATION ................................................................................................ 95 6.3.1 Collaboration within Division of Life Sciences .......................................... 95 6.3.2 Collaboration with Division of High Performance Computing System .... 96 6.3.3 Collaboration with Division of Computational Informatics ...................... 96 6.4 FUTURE PLAN .................................................................................................... 96 6.4.1 Phylogenomic analyses of novel microbial eukayrotes ............................. 96 6.4.2 Methodology for large-scale phylogenetic analyses ................................... 97 6.5 PUBLICATIONS ................................................................................................... 97 6.5.1 Journal Papers ........................................................................................... 97 6.5.2 Proceedings .............................................................................................. 101 7 DIVISION OF GLOBAL ENVIRONMENTAL SCIENCE: ATMOSPHERIC SCIENCE GROUP ................................................................... 102 7.1 RESEARCH ACTIVITY ........................................................................................ 102 7.2 RESEARCH RESULTS ........................................................................................ 103 7.3 COLLABORATION .............................................................................................. 107 1.COLLABORATIVE RESEARCH WITH JAPAN WEATHER ASSOCIATION (JWA) ......... 107 7.4 OUTSIDE FUND ................................................................................................ 108 7.5 FUTURE PLAN .................................................................................................. 109 7.6 PUBLICATIONS ................................................................................................. 110 7.6.1 Journal Papers ......................................................................................... 110 7.6.2 Proceedings .............................................................................................. 117 7.6.3 Books ........................................................................................................ 124 7.6.4 Press Release ............................................................................................ 125 7.6.5 Awards ...................................................................................................... 130 8 DIVISION OF HIGH PERFORMANCE COMPUTING SYSTEMS: HIGH PERFORMANCE COMPUTING SYSTEMS GROUP ............................... 131 8.1 RESEARCH ACTIVITY ........................................................................................ 131 8.1.1 Accelerated Computing System ............................................................... 131 8.1.2 Dependable System Design for Embedded Systems ............................... 133 3 CCS Report: PART II, Research Activities, Results Collaborations and