Shigeho Noda

Binding Free-Energy Calculation Is a Powerful Tool for Drug Optimization: Calculation and Measurement of Binding Free Energy for 7-Azaindole Derivatives to Glycogen Synthase Kinase-3β

Present computational lead (drug)-optimization is lacking in thermodynamic tactics. To examine whether calculation of binding free-energy change (ΔG) is effective for the lead-optimization process, binding ΔGs of 7-azaindole derivatives to the ATP binding site of glycogen synthase kinase-3β (GSK-3β) were calculated. The result was a significant correlation coefficient of r = 0.895 between calculated and observed ΔGs. This indicates that calculated ΔG reflects the inhibitory activities of 7-azaindole derivatives. In addition to quantitative estimation of activity, ΔG calculation characterizes the thermodynamic behavior of 7-azaindole derivatives, providing also useful information for inhibitor optimization on affinity to water molecules.

Simulations of Needle Insertion by Using a Eulerian Hydrocode FEM and the Experimental Validations

In this paper, simulations for needle insertion were performed by using a novel Eulerian hydrocode FEM, which was adaptive for large deformation and tissue fracture. We also performed experiments for the same needle insertion with silicon rubbers and needles, which had conical tips of different angles in order to investigate the accuracy of the simulations. The resistance forces in the simulations accurately followed those in the experiments until the conical portion of the needle was inside the rubbers, and the validation of the Eulerian hydrocode was revealed. However, the present simulation showed that after the conical portion was inside the tissue, the simulated resistance forces became lower than the experimental ones. The proportional increase of the friction forces and the roughly flatness of the tip force along the time were simulated. It was predicted that the tightening force along the needle side was underestimated.

Cardiovascular disease-induced thermal responses during passive heat stress: an integrated computational study.

The cardiovascular system plays a crucial role in human thermoregulation; cardiovascular diseases may lead to significantly degrading the thermoregulation ability for patients during exposure to heat stress. To evaluate the thermal responses of patients with common chronic cardiovascular diseases, we here propose an integrated computational model by coupling a two-node thermoregulation model with a closed-loop, multi-compartment, lumped-parameter cardiovascular model. This bioheat transfer model is validated, capable to predict cardiovascular functions and thermal responses under varying environmental conditions. Our results demonstrate that the cardiovascular disease-induced reduction in cardiac output and skin blood flow causes extra elevation in core temperature during hyperthermic challenges. In addition, a combination of aging, obesity, and cardiovascular diseases shows a pronounced increase in core temperature during heat exposure, which implies that such combined effect may increase the risk of heat-related morbidity and mortality. Copyright

Automatic Resource Scheduling with Latency Hiding for Parallel Stencil Applications on GPGPU Clusters

Overlapping computations and communication is a key to accelerating stencil applications on parallel computers, especially for GPU clusters. However, such programming is a time-consuming part of the stencil application development. To address this problem, we developed an automatic code generation tool to produce a parallel stencil application with latency hiding automatically from its dataflow model. With this tool, users visually construct the workflows of stencil applications in a dataflow programming model. Our dataflow compiler determines a data decomposition policy for each application, and generates source code that overlaps the stencil computations and communication (MPI and PCIe). We demonstrate two types of overlapping models, a CPU-GPU hybrid execution model and a GPU-only model. We use a CFD benchmark computing 19-point 3D stencils to evaluate our scheduling performance, which results in 1.45 TFLOPS in single precision on a cluster with 64 Tesla C1060 GPUs.

A parallel programming framework orchestrating multiple languages and architectures

This paper presents a novel parallel programming framework that orchestrates multiple languages such as C, C++, and Fortran and multiple computational architectures such as x86, POWER, and NVIDIAs Fermi to enhance productivity of parallel stencil applications while supporting high performance. Unlike traditional parallel programming frameworks, our framework provides three unique features: (1) simple meta-level, visual programming to construct workflows of components written in traditional programming languages, (2) optimal component parallelization and resource scheduling with the stencil communication pattern resolution, and (3) automatic network code generation including MPI, sockets, memory copies, and pointer passing. We prototyped incompressible computational fluid dynamics applications and demonstrate the effectiveness of our approach by evaluating our framework.

Solvable model for chemical oscillations

The Lotka–Volterra equation, proposed first with two variables by A. J. Lotka, underpins the well-known classic model for chemical oscillations. The general solutions of the Lotka–Volterra equation, with

A Full Eulerian Method for Fluid-structure Interaction Problems☆

n

GEL DOSIMETER FOR MEASURING RADIATION DOSAGE AND MANUFACTURING METHOD THEREFOR

n variables, however, remain unknown. We describe a solvable nonlinear model and general solution, previously unstudied for chemical oscillations, that is analogous to the Lotka–Volterra equations with