Tsutomu Ikegami

Fragment molecular orbital study of the electronic excitations in the photosynthetic reaction center of Blastochloris viridis

All electron calculations were performed on the photosynthetic reaction center of Blastochloris viridis, using the fragment molecular orbital (FMO) method. The protein complex of 20,581 atoms and 77,754 electrons was divided into 1398 fragments, and the two‐body expansion of FMO/6‐31G* was applied to calculate the ground state. The excited electronic states of the embedded electron transfer system were separately calculated by the configuration interaction singles approach with the multilayer FMO method. Despite the structural symmetry of the system, asymmetric excitation energies were observed, especially on the bacteriopheophytin molecules. The asymmetry was attributed to electrostatic interaction with the surrounding proteins, in which the cytoplasmic side plays a major role.

Fine De Novo Sequencing of a Fungal Genome Using only SOLiD Short Read Data: Verification on Aspergillus oryzae RIB40

The development of next-generation sequencing (NGS) technologies has dramatically increased the throughput, speed, and efficiency of genome sequencing. The short read data generated from NGS platforms, such as SOLiD and Illumina, are quite useful for mapping analysis. However, the SOLiD read data with lengths of <60 bp have been considered to be too short for de novo genome sequencing. Here, to investigate whether de novo sequencing of fungal genomes is possible using only SOLiD short read sequence data, we performed de novo assembly of the Aspergillus oryzae RIB40 genome using only SOLiD read data of 50 bp generated from mate-paired libraries with 2.8- or 1.9-kb insert sizes. The assembled scaffolds showed an N50 value of 1.6 Mb, a 22-fold increase than those obtained using only SOLiD short read in other published reports. In addition, almost 99% of the reference genome was accurately aligned by the assembled scaffold fragments in long lengths. The sequences of secondary metabolite biosynthetic genes and clusters, whose products are of considerable interest in fungal studies due to their potential medicinal, agricultural, and cosmetic properties, were also highly reconstructed in the assembled scaffolds. Based on these findings, we concluded that de novo genome sequencing using only SOLiD short reads is feasible and practical for molecular biological study of fungi. We also investigated the effect of filtering low quality data, library insert size, and k-mer size on the assembly performance, and recommend for the assembly use of mild filtered read data where the N50 was not so degraded and the library has an insert size of ∼2.0 kb, and k-mer size 33.

Parallel Fock matrix construction with distributed shared memory model for the FMO‐MO method

A parallel Fock matrix construction program for FMO‐MO method has been developed with the distributed shared memory model. To construct a large‐sized Fock matrix during FMO‐MO calculations, a distributed parallel algorithm was designed to make full use of local memory to reduce communication, and was implemented on the Global Array toolkit. A benchmark calculation for a small system indicates that the parallelization efficiency of the matrix construction portion is as high as 93% at 1,024 processors. A large FMO‐MO application on the epidermal growth factor receptor (EGFR) protein (17,246 atoms and 96,234 basis functions) was also carried out at the HF/6‐31G level of theory, with the frontier orbitals being extracted by a Sakurai‐Sugiura eigensolver. It takes 11.3 h for the FMO calculation, 49.1 h for the Fock matrix construction, and 10 min to extract 94 eigen‐components on a PC cluster system using 256 processors.

Performance comparison of parallel eigensolvers based on a contour integral method and a Lanczos method

Abstract We study the performance of a parallel nonlinear eigensolver SSEig which is based on a contour integral method. We focus on symmetric generalized eigenvalue problems (GEPs) of computing interior eigenvalues. We chose to focus on GEPs because we can then compare the performance of SSEig with that of a publicly-available software package TRLan, which is based on a thick restart Lanczos method. To solve this type of problems, SSEig requires the solution of independent linear systems with different shifts, while TRLan solves a sequence of linear systems with a single shift. Therefore, while SSEig typically has a computational cost greater than that of TRLan, it also has greater parallel scalability. To compare the performance of these two solvers, in this paper, we develop performance models and present numerical results of solving large-scale eigenvalue problems arising from simulations of modeling accelerator cavities. In particular, we identify the crossover point, where SSEig becomes faster than TRLan. The parallel performance of SSEig solving nonlinear eigenvalue problems is also studied.

Fully coupled 3-D device simulation of negative capacitance FinFETs for sub 10 nm integration

Performances of negative capacitance FinFETs (NC-FinFETs) at sub 10 nm gate length are analyzed with a newly developed technology computer-aided design (TCAD) simulation. This simulation fully couples the Landau-Khalatnikov (L-K) equation with the physical equations for FinFETs in 3-D. It reveals an excellent immunity against short-channel effects in NC-FinFETs owing to NC-enhancement by the gate-to-drain coupling, for the first time. NC-FinFETs with a gate length of 10 nm are projected to operate with more than 26 times energy-efficiency of conventional FinFETs.

Implementation of Fault-Tolerant GridRPC Applications

A task parallel application is implemented with Ninf-G, a GridRPC system. A series of experiments are conducted on the Grid testbed in Asia Pacific for three months. Through tens of long executions, typical fault patterns were collected, and instability of the network throughput was determined to be a major reason of the faults. Several important points are stressed to avoid task throughput decline due to the fault-recovery operations: Timeout minimization for fault detection, background recovery, redundant task assignments, and so on. This study also issues a steer for design of the automated fault-tolerant mechanism in an upper layer of the GridRPC framework.

Full Electron Calculation Beyond 20,000 Atoms: Ground Electronic State of Photosynthetic Proteins

A full electron calculation for the photosynthetic reaction center of Rhodopseudomonas viridis was performed by using the fragment molecular orbital (FMO) method on a massive cluster computer. The target system contains 20,581 atoms and 77,754 electrons, which was divided into 1,398 fragments. According to the FMO prescription, the calculations of the fragments and pairs of the fragments were conducted to obtain the electronic state of the system. The calculation at RHF/6-31G* level of theory took 72.5 hours with 600 CPUs. The CPUs were grouped into several workers, to which the calculations of the fragments were dispatched. An uneven CPU grouping, where two types of workers are generated, was shown to be efficient.

GridFMO — Quantum chemistry of proteins on the grid

A GridFMO application was developed by recoining the fragment molecular orbital (FMO) method of GAMESS with grid technology. With the GridFMO, quantum calculations of macro molecules become possible by using large amount of computational resources collected from many moderate-sized cluster computers. A new middleware suite was developed based on Ninf-G, whose fault tolerance and flexible resource management were found to be indispensable for long-term calculations. The GridFMO was used to draw ab initio potential energy curves of a protein motor system with 16,664 atoms. For the calculations, 10 cluster computers over the pacific rim were used, sharing the resources with other users via butch queue systems on each machine. A series of 14 GridFMO calculations were conducted for 70 days, coping with more than 100 problems cropping up. The FMO curves were compared against the molecular mechanics (MM), and it was confirmed that (1) the FMO method is capable of drawing smooth curves despite several cut-off approximations, and that (2) the MM method is reliable enough for molecular modeling.

Hybrid De Novo Genome Assembly Using MiSeq and SOLiD Short Read Data.

A hybrid de novo assembly pipeline was constructed to utilize both MiSeq and SOLiD short read data in combination in the assembly. The short read data were converted to a standard format of the pipeline, and were supplied to the pipeline components such as ABySS and SOAPdenovo. The assembly pipeline proceeded through several stages, and either MiSeq paired-end data, SOLiD mate-paired data, or both of them could be specified as input data at each stage separately. The pipeline was examined on the filamentous fungus Aspergillus oryzae RIB40, by aligning the assembly results against the reference sequences. Using both the MiSeq and the SOLiD data in the hybrid assembly, the alignment length was improved by a factor of 3 to 8, compared with the assemblies using either one of the data types. The number of the reproduced gene cluster regions encoding secondary metabolite biosyntheses (SMB) was also improved by the hybrid assemblies. These results imply that the MiSeq data with long read length are essential to construct accurate nucleotide sequences, while the SOLiD mate-paired reads with long insertion length enhance long-range arrangements of the sequences. The pipeline was also tested on the actinomycete Streptomyces avermitilis MA-4680, whose gene is known to have high-GC content. Although the quality of the SOLiD reads was too low to perform any meaningful assemblies by themselves, the alignment length to the reference was improved by a factor of 2, compared with the assembly using only the MiSeq data.

A method for finding zeros of polynomial equations using a contour integral based eigensolver

In this paper, we present a method for finding zeros of polynomial equations in a given domain. We apply a numerical eigensolver using contour integral for a polynomial eigenvalue problem that is derived from polynomial equations. The Dixon resultant is used to derive the matrix polynomial of which eigenvalues involve roots of the polynomial equations with respect to one variable. The matrix polynomial obtained by the Dixon resultant is sometimes singular. By applying the singular value decomposition for a matrix which appears in the eigensolver, we can obtain the roots of given polynomial systems. Experimental results demonstrate the efficiency of the proposed method.