Exhaustive search of the configurational space of heat-shock protein 90 with its inhibitor by multicanonical molecular dynamics based dynamic docking

Multicanonical molecular dynamics based dynamic docking was used to exhaustively search the configurational space of an inhibitor binding to the N-terminal domain of heat-shock protein 90 (Hsp90). The obtained structures at 300 K cover a wide structural ensemble, with the top two clusters ranked by their free energy coinciding with the native binding site. The representative structure of the most stable cluster reproduced the experimental binding configuration, but an interesting conformational change in Hsp90 could be observed. The combined effects of solvation and ligand binding shift the equilibrium from a preferred loop-in conformation in the unbound state to an α-helical one in the bound state for the flexible lid region of Hsp90. Thus, our dynamic docking method is effective at predicting the native binding site while exhaustively sampling a wide configurational space, modulating the protein structure upon binding.     

Extension of the LP-Newton method to conic programming problems via semi-infinite representation

Numerical Algorithms - The LP-Newton method solves linear programming (LP) problems by repeatedly projecting a current point onto a certain relevant polytope. In this paper, we extend the...     

N=8 Armchair Graphene Nanoribbons: Solution Synthesis and High Charge Carrier Mobility**

Structurally defined graphene nanoribbons (GNRs) have emerged as promising candidates for nanoelectronic devices. Low band gap (<1 eV) GNRs are particularly important when considering the Schottky barrier in device performance. Here, we demonstrate the first solution synthesis of 8-AGNRs through a carefully designed arylated polynaphthalene precursor. The efficiency of the oxidative cyclodehydrogenation of the tailor-made polymer precursor into 8-AGNRs was validated by FT-IR, Raman, and UV/Vis-near-infrared (NIR) absorption spectroscopy, and further supported by the synthesis of naphtho[1,2,3,4-ghi]perylene derivatives ( 1 and 2 ) as subunits of 8-AGNR , with a width of 0.86 nm as suggested by the X-ray single crystal analysis. Low-temperature scanning tunneling microscopy (STM) and solid-state NMR analyses provided further structural support for 8-AGNR . The resulting 8-AGNR exhibited a remarkable NIR absorption extending up to ∼2400 nm, corresponding to an optical band gap as low as ∼0.52 eV. Moreover, optical-pump TeraHertz-probe spectroscopy revealed charge-carrier mobility in the dc limit of ∼270 cm² V⁻¹ s⁻¹ for the 8-AGNR .     

Force-field parametrization based on radial and energy distribution functions

We propose a novel force-field-parametrization procedure that fits the parameters of potential functions in a manner that the pair distribution function (DF) of molecules derived from candidate parameters can reproduce the given target DF. Conventionally, approaches to minimize the difference between the candidate and target DFs employ radial DFs (RDF). RDF itself has been reported to be insufficient for uniquely identifying the parameters of a molecule. To overcome the weakness, we introduce energy DF (EDF) as a target DF, which describes the distribution of the pairwise energy of molecules. We found that the EDF responds more sensitively to a small perturbation in the pairwise potential parameters and provides better fitting accuracy compared to that of RDF. These findings provide valuable insights into a wide range of coarse graining methods, which determine parameters using information obtained from a higher-level calculation than that of the developed force field. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.     

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.     

Development of Plasma Window for gas charge stripper at RIKEN RIBF

A differential pumping system with a Plasma Window (PW) has been developed for an application to a window-less He gas charge stripper. A PW with Southern Methodist University design was newly fabricated and tested off-line for evaluation of differential pumping efficiency. Switching gases for plasma seed from Ar to He was tested. It was found that the PW reduced the pressure at the first differential pumping section to 1/13 for Ar and to 1/17 for He, comparing with differential pumping without PW. At the second pumping section, the pressures were drastically reduced to 1/160 and to 1/4,520 for Ar and He, respectively. These pressure reduction factors indicate that one differentially pumped stage could be removed from a conventional differential pumping system.     

Pressure effect to chemical reaction,hydrogen isotope recombination reactions in liquid helium at cryogenic temperature — Part II

Behavior of the hydrogen isotope in recombination reactions, H+H→H₂ H+T→HT and T+T→T₂ under pressurized conditions at 1.6 K were investigated using liquid helium as cryogenic reaction media by radiochemical methods. Pressure effects were observed in changes of isotope ratio HT/T₂. It became clearer that the balance of changes in bubble energy effective mass associated with energy and chemical potential contributed to the recombination reactions through bubble states. It was suggested that bubble radius was decreased significantly at higher pressure.     

An efficient procedure for preparation of 2-monoalkyl or 2-monoaryl-3-ethoxycyclobutanones

Optimized reaction conditions for the preparation of various 2-monosubstituted 3-ethoxycyclobutanones are described. 2-Monoalkyl 3-ethoxycyclobutanones were efficiently prepared by the reaction of the corresponding carboxylic acid chlorides and an excess amount of ethyl vinyl ether in the presence of diisopropylethylamine at 90 °C in a sealed tube. 2-Monoaryl 3-ethoxycyclobutanones were prepared by using 2,6-lutidine as a base in the above-mentioned procedure.     

Ellagic Acid Suppresses ApoB Secretion and Enhances ApoA-1 Secretion from Human Hepatoma Cells,HepG2

The effect of ellagic acid (EA), a naturally occurring polyphenolic compound, on the secretion of apolipoproteins from human hepatocytes, HepG2, was investigated. The levels of apoB and apoA-1 secreted in the cell culture medium were determined by sandwich ELISA. EA did not affect cell viability at the tested concentrations (up to 50 µM). EA suppressed the secretion of apoB and enhanced that of apoA-1 from HepG2 cells. However, cellular apoB levels were increased, suggesting that EA inhibited the trafficking of apoB during the process of secretion. In contrast, the increase in the cellular levels of apoA-1 was consistent with its secreted levels. These results indicate that EA inhibits the secretion of apoB from hepatocytes and increases the secretion of apoA-1. Both of these effects are beneficial for lipoprotein metabolism in the prevention of lifestyle-related diseases. The detailed mechanism underlying these effects of EA on lipoprotein metabolism should be elucidated in the future, but this naturally occurring polyphenolic compound might be antihyperlipidemic. Based on these results, EA is suggested as a candidate food-derived compound for the prevention of hyperlipidemia.