Previous studies on elastomers have revealed that the physical property of elastomers can be affected by the topological feature of their network structure. In the paper, for the simulation data of construction and elongation of elastomers, we analyzed the weighted network structure of each elastomer, where each node is a crosslinking point and the distance between crosslinking points is incorporated into the weight of a link. We derived centrality of each link based on the idea of closeness centrality in complex networks. We found that how the centrality of each node changes during elongation was significantly affected by the concentration under which crosslinking reaction was carried out, implicating that the weighted network structure of elastomer changed differently according to the reaction concentration.

The aim of this study is to improve the accuracy of crystal structure prediction for Target XXIII, which was the target of the 6th Crystal Structure Prediction Blind Test (CSP6), by using the fragment molecular orbital (FMO) method. The intermolecular interaction analysis revealed that the dispersion interaction is stronger than the electrostatic interaction in all crystal polymorphs. In our method, the three correct structures included in the predicted structures were located within the top five. Furthermore, it was possible to evaluate the stability of polymorphs by the difference of intramolecular hydrogen bonds.

Heat Shock Protein 90 (HSP90) has been known as one of the molecular chaperone proteins, and it supports the correct folding of client proteins. It has been getting attention as the target protein for an anti-cancer drug because the client proteins sometimes include the critical proteins of progressing cancer. In the HSP90 chaperon cycle, several co-chaperones and substrates interact with HSP90 in turn. In this study, we focused on the interaction between HSP90 and p23, which is one of the co-chaperones. After the HSP90 dimer forms the closed conformation, the p23 and ATP bind to the HSP90. However, the detailed interaction among them has not been clear yet. To clear the mechanism of the interaction among HSP90, ATP, and p23, we performed the all-atom molecular dynamics simulations of ATP bound/unbound HSP90 with/without p23. We found that the domain swapping in HSP90 closed conformation is essential for the stable binding between HSP90 and p23, and the ATP binding supports the stability of the HSP90 and p23 complex.

In this letter, we investigated the contribution of bridging hydrogen bonds (BHB) via Cl⁻ on the T-R transition of human adult hemoglobin (HbA). We applied the time-series clustering method to time-series data of the αβ dimer rotation angle φ and the total number of the BHBs. Compared with the above two results, we have concluded that Cl⁻-BHBs do not significantly contribute to the structural regulation of HbA.

The simulation to obtain stress-strain curves of block copolymers requires large computational resources. As an alternative to simulation, a method for high-throughput prediction of stress-strain curves using a three-dimensional convolutional neural network has been reported. In this study, we incorporated shortcut coupling into the neural network and performed pre-training and transfer learning in a step-by-step manner to successfully predict the stress-strain curve with high accuracy while reducing the training cost.

Crystalline polymers have a hierarchical structure in which polymer chains are folded. Although each hierarchical structure strongly affects the physical properties of crystalline polymers, it is hard to describe the relationship between the formation conditions, crystal structure and physical properties. We used Random Forest regression to comprehensively investigate the relationship between these features of polylactic acid (PLA), a biodegradable crystalline polymer. It was suggested that important features for mechanical property and biodegradability, where the trade-off relationship between them is a significant issue of PLA, are related to the different level crystal structures. This shows that it is possible to use Random Forest for complex prediction of crystalline polymer properties to search for important forming conditions and crystal structures.

In the present report, we introduce our new three approaches based on the mathematics / mathematical sciences to the classical molecular dynamics calculations; 1) the approach by the analytical mechanics instead of the classical mechanics; 2) the approach to the periodic boundary condition by the torus model; 3) the approach by the mathematics-based programming substituting for the procedural (imperative) programming. Then, we found that these approaches are very effective to make calculations simpler, more compact, steadier, and firmer. Thus, it was concluded that the mathematical / mathematical scientific approaches are the promising ones to overcome various problems that we confront in the computational chemistry.

Cyclization generally stabilizes the bioactive conformation of the peptide and increases its affinity for the target. However, since cyclic peptides frequently adopt multiple conformations in solution, the structural information is not fully understood in experiments, and the relationship between structure and function is not well understood. We demonstrate the practical possibilities of using a combination of a special purpose computing engine (Digital Annealer) and REST2 (replica exchange with solute tempering) simulation in "ab initio" structure prediction of macrocyclic peptides.

It has been reported that the introduction of a 2, 1, 3-benzothiadiazole (BTD) into an organic dye used in dye sensitized solar cells (DSSC) makes its conversion efficiency improve. In this study, we examine the effects of BTD's from viewpoints of its number and position, for DSSC with triphenylamine (TPA) as a donor moiety and cyanoacrylic acid (CA) as an acceptor one. And it is found that the best optical response was obtained when only one BTD was introduced on the side of the acceptor moiety.

Molecular dynamics calculations were performed to consider the peculiarities of microwave chemistry. The temperature rise curve obtained without using the parameters of permittivity and conductivity showed the rise due to the traveling energy in addition to the accumulation of thermal energy in the periodic application of the electric field. We showed that the non-thermal effects of microwave chemistry might be caused by this traveling energy.

We have been studying the time-evolution technique in imaginary time. The electronic structure calculated in this technique is valid for the ground state, which is easily confirmed from the completeness of the wavefunction. However, the excited states can be also obtained by Gram-Schmidt orthogonalization technique. As a practical 3D calculation, we applied this technique to hydrogen atom and molecule systems. The results are in good agreement with their analytical solutions, including the excited states. The purpose of this study is to present the effectiveness of this technique for practical electronic structure calculations. To realize it, we will start to apply this to hydrogen and practical small molecule systems.