Design and implementation of a hybrid cloud system for large-scale human genomic research.

In the field of genomic medical research, the amount of large-scale information continues to increase due to advances in measurement technologies, such as high-performance sequencing and spatial omics, as well as the progress made in genomic cohort studies involving more than one million individuals. Therefore, researchers require more computational resources to analyze this information. Here, we introduce a hybrid cloud system consisting of an on-premise supercomputer, science cloud, and public cloud at the Kyoto University Center for Genomic Medicine in Japan as a solution.

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.

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.

Parallel Fock matrix construction program for molecular orbital calculation--specific computer with a hierarchical network.

A parallel Fock matrix construction program for a hierarchical network has been developed on the molecular orbital calculation-specific EHPC system. To obtain high parallelization efficiency on the hierarchical network system, a multilevel dynamic load-balancing scheme was adopted, which provides equal load balance and localization of communications on a tree-structured hierarchical network. The parallelized Fock matrix construction routine was implemented into a GAMESS program on the EHPC system, which has a tree-structured hierarchical network.

DNA and estrogen receptor interaction revealed by fragment molecular orbital calculations.

Molecular orbital calculations of the complex between DNA-ERE (estrogen response element) and ER (estrogen receptor)-DBD (DNA-binding domain) were performed using the fragment molecular orbital (FMO) method, which enables large-scale MO (molecular orbital) calculations by reducing the computational cost and by significantly increasing efficiency for parallel computation. Such a large system, which contains 3354 atoms, is impractical via conventional MO methods due to the immense computational cost. Details of the interaction between DNA-ERE and ER-DBD were revealed in this study as follows by using the FMO calculations to analyze the interfragment interaction energies (IFIEs) and the electrostatic potentials (ESPs).

PEACH 4 with ABINIT-MP: a general platform for classical and quantum simulations of biological molecules.

A program package for molecular simulations of biological molecules was developed. The package, "PEACH version 4 with ABINIT-MP version 20021029," was constructed by incorporating ABINIT-MP, a program for the fragment molecular orbital (FMO) method [Chem.Phys.