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16 pages, 2629 KiB

Open AccessArticle

Ligand Binding Path Sampling Based on Parallel Cascade Selection Molecular Dynamics: LB-PaCS-MD

by Hayato Aida, Yasuteru Shigeta and Ryuhei Harada

Materials 2022, 15(4), 1490; https://doi.org/10.3390/ma15041490 - 17 Feb 2022

Cited by 8 | Viewed by 3295

Abstract

Parallel cascade selection molecular dynamics (PaCS-MD) is a rare-event sampling method that generates transition pathways between a reactant and product. To sample the transition pathways, PaCS-MD repeats short-time MD simulations from important configurations as conformational resampling cycles. In this study, PaCS-MD was extended [...] Read more.

Parallel cascade selection molecular dynamics (PaCS-MD) is a rare-event sampling method that generates transition pathways between a reactant and product. To sample the transition pathways, PaCS-MD repeats short-time MD simulations from important configurations as conformational resampling cycles. In this study, PaCS-MD was extended to sample ligand binding pathways toward a target protein, which is referred to as LB-PaCS-MD. In a ligand-concentrated environment, where multiple ligand copies are randomly arranged around the target protein, LB-PaCS-MD allows for the frequent sampling of ligand binding pathways. To select the important configurations, we specified the center of mass (COM) distance between each ligand and the relevant binding site of the target protein, where snapshots generated by the short-time MD simulations were ranked by their COM distance values. From each cycle, snapshots with smaller COM distance values were selected as the important configurations to be resampled using the short-time MD simulations. By repeating conformational resampling cycles, the COM distance values gradually decreased and converged to constants, meaning that a set of ligand binding pathways toward the target protein was sampled by LB-PaCS-MD. To demonstrate relative efficiency, LB-PaCS-MD was applied to several proteins, and their ligand binding pathways were sampled more frequently than conventional MD simulations. Full article

(This article belongs to the Special Issue Self-Organization and Spontaneous Order for Functional Materials)

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16 pages, 3396 KiB

Open AccessArticle

Enhancement of Multi-Scale Self-Organization Processes during Inconel DA 718 Machining through the Optimization of TiAlCrSiN/TiAlCrN Bi-Nano-Multilayer Coating Characteristics

by Guerman Fox-Rabinovitch, Goulnara Dosbaeva, Anatoly Kovalev, Iosif Gershman, Kenji Yamamoto, Edinei Locks, Jose Paiva, Egor Konovalov and Stephen Veldhuis

Materials 2022, 15(4), 1329; https://doi.org/10.3390/ma15041329 - 11 Feb 2022

Cited by 6 | Viewed by 2174

Abstract

Optimization of the composition of a new generation of bi-nano-multilayered TiAlCrSiN/TiAlCrN-based coatings is outlined in this study for the machining of direct aged (DA) Inconel 718 alloy. Three types of TiAlCrSiN/TiAlCrN-based bi-nano-multi-layer coatings with varying chemical compositions were investigated: (1) a previous state-of-the-art [...] Read more.

Optimization of the composition of a new generation of bi-nano-multilayered TiAlCrSiN/TiAlCrN-based coatings is outlined in this study for the machining of direct aged (DA) Inconel 718 alloy. Three types of TiAlCrSiN/TiAlCrN-based bi-nano-multi-layer coatings with varying chemical compositions were investigated: (1) a previous state-of-the-art Ti_0.2Al_0.55Cr_0.2Si_0.03Y_0.02N/Ti_0.25Al_0.65Cr_0.1N (coating A); (2) Ti_0.2Al_0.52Cr_0.2Si_0.08N/Ti_0.25Al_0.65Cr_0.1N with increased amount of Si (up to 8 at.%; coating B); (3) a new Ti_0.18Al_0.55Cr_0.17Si_0.05Y_0.05N/Ti_0.25Al_0.65Cr_0.1N coating (coating C) with an increased amount of both Si and Y (up to 5 at.% each). The structure of each coating was evaluated by XRD analysis. Micro-mechanical characteristics were investigated using a MicroMaterials NanoTest system and an Anton Paar-RST3 tester. The wear performance of nano-multilayered TiAlCrSiN/TiAlCrN-based coatings was evaluated during the finish turning of direct aged (DA) Inconel 718 alloy. The wear patterns were assessed using optical microscopy imaging. The tribological performance was evaluated through (a) a detailed chip characteristic study and (b) XPS studies of the worn surface of the coated cutting tool. The difference in tribological performance was found to correspond with the type and amount of tribo-films formed on the friction surface under operation. Simultaneous formation of various thermal barrier tribo-films, such as sapphire, mullite, and garnet, was observed. The overall amount of beneficial tribo-films was found to be greater in the new Ti_0.18Al_0.55Cr_0.17Si _0.05Y_0.05N/Ti_0.25Al_0.65Cr_0.1N nano-bi-multilayer coating (coating C) than in the previous state-of-the-art coatings (A and B). This resulted in over two-fold improvement of this coating’s tool life compared with those of the commercial benchmark AlTiN coating and coating B, as well as a 40% improvement of the tool life of the previous state-of-the-art coating A. Multi-scale self-organization processes were observed: nano-scale tribo-film formation on the cutting tool surface combined with micro-scale generation of strain-induced martensite zones as a result of intensive metal flow during chip formation. Both of these processes are strongly enhanced in the newly developed coating C. Full article

(This article belongs to the Special Issue Self-Organization and Spontaneous Order for Functional Materials)

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13 pages, 4098 KiB

Open AccessArticle

Nucleation of Surfactant–Alkane Mixed Solid Monolayer and Bilayer Domains at the Air–Water Interface

by Hiroki Matsubara, Rikako Mori and Eisuke Ohtomi

Materials 2022, 15(2), 485; https://doi.org/10.3390/ma15020485 - 9 Jan 2022

Cited by 1 | Viewed by 1383

Abstract

We investigated the wetting transitions of tetradecane and hexadecane droplets in dodecyltrimethylammonium bromide (C12TAB), tetradecyltrimethylammonium bromide (C14TAB), and hexadecyltrimethylammonium bromide (C16TAB) aqueous solutions. By varying the surfactant concentration, the formation of mixed monolayers of a surfactant and an alkane was observed at the [...] Read more.

We investigated the wetting transitions of tetradecane and hexadecane droplets in dodecyltrimethylammonium bromide (C12TAB), tetradecyltrimethylammonium bromide (C14TAB), and hexadecyltrimethylammonium bromide (C16TAB) aqueous solutions. By varying the surfactant concentration, the formation of mixed monolayers of a surfactant and an alkane was observed at the air–water interface. Depending on the combination of surfactant and alkane, these wetting monolayers underwent another thermal phase transition upon cooling either to a frozen mixed monolayer (S1) or a bilayer structure composed of a solid monolayer of a pure alkane rested on a liquid-like mixed monolayer (S2). Based on the phase diagrams determined by phase modulation ellipsometry, the difference in the morphology of the nucleated S1 and S2 phase domains was also investigated using Brewster angle microscopy. Domains of the S1 phase were relatively small and highly branched, whereas those of the S2 phase were large and circular. The difference in domain morphology was explained by the competition of the domain line tension and electrostatic dipole interactions between surfactant molecules in the domains. Full article

(This article belongs to the Special Issue Self-Organization and Spontaneous Order for Functional Materials)

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8 pages, 2002 KiB

Open AccessArticle

Periodic Expansion and Contraction Phenomena in a Pendant Droplet Associated with Marangoni Effect

by Koutaro Onoda and Ben Nanzai

Materials 2022, 15(1), 239; https://doi.org/10.3390/ma15010239 - 29 Dec 2021

Cited by 1 | Viewed by 1603

Abstract

A spontaneous oscillation between the expansion and contraction of a nitrobenzene pendant droplet containing di-(2-ethylhexyl)phosphoric acid (DEHPA) was observed in an aqueous phase under alkaline conditions. We described this phenomenon as the spontaneous oscillation of the oil–water interfacial tension. The oscillation characteristics such [...] Read more.

A spontaneous oscillation between the expansion and contraction of a nitrobenzene pendant droplet containing di-(2-ethylhexyl)phosphoric acid (DEHPA) was observed in an aqueous phase under alkaline conditions. We described this phenomenon as the spontaneous oscillation of the oil–water interfacial tension. The oscillation characteristics such as the induction period and the interfacial-tension oscillation frequency were investigated under different temperatures and aqueous phase polarities. The effects of the interfacial tension of the biphasic pendant-droplet, the surface excess of the surfactant molecules, and the amount of nitrobenzene elution from the droplet to the aqueous phase on the oscillation characteristics were investigated. Consequently, the periodic expansion–contraction oscillation mechanism was explained through the adsorption–desorption cycle of DEHPA with respect to the aggregate formation of the inverted micelle of DEHPA. This study was based on a simple vibration phenomenon of interfacial tension, and is extremely important for clarifying the predominant factors that cause fluctuations in the free interface energy, which has been ambiguous. Full article

(This article belongs to the Special Issue Self-Organization and Spontaneous Order for Functional Materials)

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10 pages, 2876 KiB

Open AccessArticle

Instability of the Homogeneous Distribution of Chemical Waves in the Belousov–Zhabotinsky Reaction

by Nobuhiko J. Suematsu and Satoshi Nakata

Materials 2021, 14(20), 6177; https://doi.org/10.3390/ma14206177 - 18 Oct 2021

Cited by 2 | Viewed by 1933

Abstract

Chemical traveling waves play an important role in biological functions, such as the propagation of action potential and signal transduction in the nervous system. Such chemical waves are also observed in inanimate systems and are used to clarify their fundamental properties. In this [...] Read more.

Chemical traveling waves play an important role in biological functions, such as the propagation of action potential and signal transduction in the nervous system. Such chemical waves are also observed in inanimate systems and are used to clarify their fundamental properties. In this study, chemical waves were generated with equivalent spacing on an excitable medium of the Belousov–Zhabotinsky reaction. The homogeneous distribution of the waves was unstable and low- and high-density regions were observed. In order to understand the fundamental mechanism of the observations, numerical calculations were performed using a mathematical model, the modified Oregonator model, including photosensitive terms. However, the homogeneous distribution of the traveling waves was stable over time in the numerical results. These results indicate that further modification of the model is required to reproduce our experimental observations and to discover the fundamental mechanism for the destabilization of the homogeneous-distributed chemical traveling waves. Full article

(This article belongs to the Special Issue Self-Organization and Spontaneous Order for Functional Materials)

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10 pages, 3758 KiB

Open AccessArticle

Growing Interface with Phase Separation and Spontaneous Convection during Hydrodynamically Stable Displacement

by Takahiko Ban, Ryohei Tanaka, Ryuta X. Suzuki and Yuichiro Nagatsu

Materials 2021, 14(20), 6089; https://doi.org/10.3390/ma14206089 - 14 Oct 2021

Viewed by 2379

Abstract

The displacement of one fluid by another is an important process, not only in industrial and environmental fields, such as chromatography, enhanced oil recovery, and CO₂ sequestration, but also material processing, such as Lost Foam Casting. Even during hydrodynamically stable fluid displacement [...] Read more.

The displacement of one fluid by another is an important process, not only in industrial and environmental fields, such as chromatography, enhanced oil recovery, and CO₂ sequestration, but also material processing, such as Lost Foam Casting. Even during hydrodynamically stable fluid displacement where a more viscous fluid displaces a less viscous fluid in porous media or in Hele-Shaw cells, the growing interface fluctuates slightly. This fluctuation is attributed to thermodynamic conditions, which can be categorized as the following systems: fully miscible, partially miscible, and immiscible. The dynamics of these three systems differ significantly. Here, we analyze interfacial fluctuations under the three systems using Family–Vicsek scaling and calculate the scaling indexes. We discovered that the roughness exponent,

α

, and growth exponent,

β

, of the partially miscible case are larger than those of the immiscible and fully miscible cases due to the effects of the Korteweg convection as induced during phase separation. Moreover, it is confirmed that fluctuations in all systems with steady values of

α

and

β

are represented as a single curve, which implies that accurate predictions for the growing interface with fluctuations in Hele-Shaw flows can be accomplished at any scale and time, regardless of the miscibility conditions. Full article

(This article belongs to the Special Issue Self-Organization and Spontaneous Order for Functional Materials)

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13 pages, 4531 KiB

Open AccessArticle

Analysis of Molecular Disordering Processes in the Phase Transition of Liquid Crystals Observed by Patterned-Illumination Time-Resolved Phase Microscopy

by Nozomi Sato and Kenji Katayama

Materials 2021, 14(19), 5491; https://doi.org/10.3390/ma14195491 - 23 Sep 2021

Viewed by 2240

Abstract

The initial processes of the phase transition dynamics of liquid crystals (LCs) subject to UV pulse irradiation were clarified using a nanosecond time-resolved imaging technique called pattern-illumination time-resolved phase microscopy (PI-PM). Two types of LCs were studied: a photo-responsive LC and dye-doped LCs. [...] Read more.

The initial processes of the phase transition dynamics of liquid crystals (LCs) subject to UV pulse irradiation were clarified using a nanosecond time-resolved imaging technique called pattern-illumination time-resolved phase microscopy (PI-PM). Two types of LCs were studied: a photo-responsive LC and dye-doped LCs. We found two steps of molecular disordering processes in the phase transition, namely local disordering proceeding anisotropically, followed by the spreading of the isotropic phase. These two processes were separated for a photo-responsive LC while being simultaneously observed for the dye-doped LCs. It was found that the photomechanical dyes induced the phase transition process faster than the photothermal dyes. Full article

(This article belongs to the Special Issue Self-Organization and Spontaneous Order for Functional Materials)

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8 pages, 1157 KiB

Open AccessArticle

Regular-Type Liesegang Pattern of AgCl in a One-Dimensional System

by Shun Sakamoto, Masaki Itatani, Kanta Tsukada and Hideki Nabika

Materials 2021, 14(6), 1526; https://doi.org/10.3390/ma14061526 - 20 Mar 2021

Cited by 3 | Viewed by 2343

Abstract

The Liesegang phenomenon can be used for micro- and nanofabrication processes to yield materials with periodic precipitation of diverse types of materials. Although there have been several attempts to control the periodicity of the Liesegang patterns, it remains unclear whether the periodic precipitation [...] Read more.

The Liesegang phenomenon can be used for micro- and nanofabrication processes to yield materials with periodic precipitation of diverse types of materials. Although there have been several attempts to control the periodicity of the Liesegang patterns, it remains unclear whether the periodic precipitation of AgCl in gel medium causes regular- or revert-type patterns. To confirm the periodicity of the AgCl pattern, we conduct one-dimensional experiments under various ion concentration conditions. From microscopic observations, three different precipitation modes were observed, i.e., continuous precipitation with a sharp front, periodic precipitation and continuous precipitation with a gradual front. For these three modes, numerical analyses of the pattern geometry are performed for the periodic precipitation. It was confirmed that the regular-type pattern appeared for all concentration conditions conducted in the present experiments. Furthermore, the pattern was found to obey the spacing law and the Matalon–Packter law. From our experiments, we concluded that AgCl forms regular-type Liesegang patterns, regardless of the dimension of diffusion. Full article

(This article belongs to the Special Issue Self-Organization and Spontaneous Order for Functional Materials)

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Review

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17 pages, 2741 KiB

Open AccessReview

Construction of Supramolecular Systems That Achieve Lifelike Functions

by Taisuke Banno, Daichi Sawada and Taro Toyota

Materials 2022, 15(7), 2391; https://doi.org/10.3390/ma15072391 - 24 Mar 2022

Cited by 7 | Viewed by 2888

Abstract

The Nobel Prize in Chemistry was awarded in 1987 and 2016 for research in supramolecular chemistry on the “development and use of molecules with structure-specific interactions of high selectivity” and the “design and production of molecular machines”, respectively. This confirmed the explosive development [...] Read more.

The Nobel Prize in Chemistry was awarded in 1987 and 2016 for research in supramolecular chemistry on the “development and use of molecules with structure-specific interactions of high selectivity” and the “design and production of molecular machines”, respectively. This confirmed the explosive development of supramolecular chemistry. In addition, attempts have been made in systems chemistry to embody the complex functions of living organisms as artificial non-equilibrium chemical systems, which have not received much attention in supramolecular chemistry. In this review, we explain recent developments in supramolecular chemistry through four categories: stimuli-responsiveness, time evolution, dissipative self-assembly, and hierarchical expression of functions. We discuss the development of non-equilibrium supramolecular systems, including the use of molecules with precisely designed properties, to achieve functions found in life as a hierarchical chemical system. Full article

(This article belongs to the Special Issue Self-Organization and Spontaneous Order for Functional Materials)

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