Simulation of collisions of two droplets containing two different liquids using incompressible smoothed particle hydrodynamics method

Theoretical and Computational Fluid Dynamics - The present study aims to simulate a collision of two droplets containing immiscible liquids by employing a three- dimensional incompressible smoothed...     

Adsorption of fission products onto soils using a fission multitracer

The adsorption behavior of fission products to various soils was studied using a multitracer. The multitracer was prepared by neutron irradiation of ²³⁵U. Distribution coefficients of fission products were obtained for seventeen kinds of Japanese soils. It was found that zirconium, niobium, and rare earth elements show high distribution coefficients for all soil samples, however, elements like alkali metals show varied values.     

Positive muons in [Co(NH3)6]Cl3 and [Co(ND3)6]Cl3

We have carried out SR experiments on [Co(NH₃)₆]Cl₃ and [Co(ND₃)₆]Cl₃. At 293 K, all the muons implanted into the complexes were in the diamagnetic state. The observed Gaussian-type muon spin relaxation function proved that the internal magnetic field was caused by nuclear dipole moments of the atoms in the complexes. In addition, another exponential-type muon spin relaxation function was observed in [Co(ND₃)₆]Cl₃ below 50 K.     

Charge strippers for Radioisotope Beam Factory at RIKEN

The accelerator complex at the RIKEN Radioisotope Beam Factory accelerates heavy ions ranging from oxygen to uranium using triple stripping system to provide the beams at required charge. In many cases, the charge strippers cause problems during high-intensity beams accelerator operation. The charge stripper problem has been most significant during uranium beam acceleration because the lifetimes of the conventional carbon foils are extremely short. We conducted extensive R&D on the first stripper and found a solution using a low-Z gas stripper. We also plan to modify a second stripper operating recently with short-lifetime carbon foils. The stripper with better parameters will be needed when the beam intensity is increased by a new injector system for acceleration of uranium beam with higher charge.     

Supervised scoring models with docked ligand conformations for structure-based virtual screening

Protein-ligand docking programs have been used to efficiently discover novel ligands for target proteins from large-scale compound databases. However, better scoring methods are needed. Generally, scoring functions are optimized by means of various techniques that affect their fitness for reproducing X-ray structures and protein-ligand binding affinities. However, these scoring functions do not always work well for all target proteins. A scoring function should be optimized for a target protein to enhance enrichment for structure-based virtual screening. To address this problem, we propose the supervised scoring model (SSM), which takes into account the protein-ligand binding process using docked ligand conformations with supervised learning for optimizing scoring functions against a target protein. SSM employs a rough linear correlation between binding free energy and the root mean square deviation of a native ligand for predicting binding energy. We applied SSM to the FlexX scoring function, that is, F-Score, with five different target proteins: thymidine kinase (TK), estrogen receptor (ER), acetylcholine esterase (AChE), phosphodiesterase 5 (PDE5), and peroxisome proliferator-activated receptor gamma (PPARgamma). For these five proteins, SSM always enhanced enrichment better than F-Score, exhibiting superior performance that was particularly remarkable for TK, AChE, and PPARgamma. We also demonstrated that SSM is especially good at enhancing enrichments of the top ranks of screened compounds, which is useful in practical drug screening.     

An intelligent data acquisition system for fluid mechanics research

Conclusions A new approach to experimental data acquisition has been demonstrated. The results of the proof-of-concept experiment show that by incorporating a degree of specific fluid dynamics knowledge to the data acquisition process, it is possible to increase the resolution of the experiment, or alternately, reduce the total number of data points required to achieve parity with the results of most conventional data acquisition approaches.     

Dynamical origin of enhanced conformational searches of Tsallis statistics sampling

The characteristic sampling dynamics of importance samplings driven by the Tsallis weight [C. Tsallis, J. Stat. Phys. 52, 479 (1988)] has been analyzed in terms of recently developed Langevin stochastic model by considering the effects of the density of states and the potential smoothing of the Tsallis transformation. Our study reveals that the fixed points, which are determined by the crossing points of the statistical temperature and the Tsallis effective temperature, play a critical role in overall dynamics of the Tsallis statistics sampling. The dynamical origin of enhanced conformational searches of the Tsallis weight has been investigated by unveiling the intimate relationship between the sampling dynamics and the stability change of corresponding fixed points. Based on this stochastic analysis, we propose one effective method to realize a broad energy distribution in the Tsallis statistics sampling by determining optimal Tsallis parameters systematically based on preliminary canonical samplings. The effectiveness of our method has been validated in the folding simulation of Met-Enkephalin and liquid-solid transition simulation of Lennard-Jones cluster systems.     

An efficient in silico screening method based on the protein-compound affinity matrix and its application to the design of a focused library for cytochrome P450 (CYP) ligands

A new method has been developed to design a focused library based on available active compounds using protein-compound docking simulations. This method was applied to the design of a focused library for cytochrome P450 (CYP) ligands, not only to distinguish CYP ligands from other compounds but also to identify the putative ligands for a particular CYP. Principal component analysis (PCA) was applied to the protein-compound affinity matrix, which was obtained by thorough docking calculations between a large set of protein pockets and chemical compounds. Each compound was depicted as a point in the PCA space. Compounds that were close to the known active compounds were selected as candidate hit compounds. A machine-learning technique optimized the docking scores of the protein-compound affinity matrix to maximize the database enrichment of the known active compounds, providing an optimized focused library.     

Syntheses of 2,3‐dicyano‐5a,8a‐dihydro‐5a‐hydroxycyclopentano[1′,2′:4,5]pyrrolo[2,3‐b]pyrazines and 2,3‐dicyanocyclohexano[1′,2′:4,5]pyrrolo‐[2,3‐b]pyrazines

Previously synthesized 2‐(3′‐chloro‐5′,6′‐dicyanopyrazin‐2′‐yl)cyclopentan‐1‐one 1 , obtained from the reaction of 2,3‐dichloro‐5,6‐dicyanopyrazine with 1‐pyrrolidino‐1‐cyclopentene, was further reacted with primary alkylamines to give mixtures of diastereomer of 5‐alkyl‐2,3‐dicyano‐5a,8a‐dihy‐dro‐5a‐hydroxycyclopentano[1′,2′:4,5]pyrrolo[2,3‐b]pyrazines 3a‐h in high yield. The reaction of 2‐alkylamino‐3‐chloro‐5,6‐dicyanopyrazine with 1‐pyrrolidino‐1‐cyclohexene gave 5‐alkyl‐2,3‐dicyanocyclopentano[1′,2′:4,5]pyrrolo[2,3‐b]pyrazines 5a‐b together with 5‐alkylamino‐2,3‐dicyano‐6‐pyrrolidinopyrazines 6a‐b . The products prepared are all of interest as potential pesticides and new fluorescent chromophores.     

Development of a new foil compounded from carbon nanotubes and sputter-deposition carbon

New carbon-nanotube–sputter-deposition-carbon (CNT–SDC) foils were developed and used in the U beam time at the RIKEN RI Beam Factory (RIBF) from October to December 2011. The lifetimes of these new foils were drastically extended, and stable, high-intensity U beams were successfully provided to users. The lifetime of the CNT–SDC foils was 2–5 C, which was 100 times longer than those of static C-foils previously used. The qualitative analysis of the CNT–SDC foils clearly showed that the CNT structure and bundles were broken by beam irradiation. In addition, it was found that CNT bundles in the CNT–SDC foil were grown after the carbon deposition procedure. This structure was considered to be the reason that the CNT–SDC foils maintain advantages of both CNT and SDC foils.