Redox-active chemical chaperones exhibiting promiscuous binding promote oxidative protein folding under condensed sub-millimolar conditions.

Proteins form native structures through folding processes, many of which proceed through intramolecular hydrophobic effect, hydrogen bond and disulfide-bond formation. , protein aggregation is prevented even in the highly condensed milieu of a cell through folding mediated by molecular chaperones and oxidative enzymes. Chemical approaches to date have not replicated such exquisite mediation.

Photothermally Heated Asymmetric Thin Nanopores Suggest the Influence of Temperature on the Intermediate Conformational State of Cytochrome in an Electric Field.

Nanopore sensing is a label-free single-molecule technique that enables the study of the dynamical structural properties of proteins. Here, we detect the translocation of cytochrome (Cyt ) through an asymmetric thin nanopore with photothermal heating to evaluate the influence of temperature on Cyt conformation during its translocation in an electric field. Before Cyt translocates through an asymmetric thin SiN nanopore, ∼1 ms trapping events occur due to electric field-induced denaturation.

Molecular Dynamics Study on the Effect of Cyclic Conducting Moieties on Poly(2,6-dimethyl-1,4-phenylene oxide) Anion Exchange Membranes.

We investigate PPO quaternized with different azoles (five-membered heterocyclic compounds) with a different odd number of Nitrogen atoms (1-pyrrole, 3-1,2,3-triazole, and 5-pentazole) to form pyrrolium-PPO(py-PPO), 1,2,3,-triazolium-PPO(tri-PPO) and pentazolium-PPO(pen-PPO) AEMs, using molecular dynamics (MD) simulations to compare and evaluate their OH transport via the vehicular mechanism. OH diffusivity at the hydration level λ = 12 is 3.10 × 10 m/s, 1.

Synthesis and Characterization of Ionic Li @C Endohedral Fullerene.

Ion-endohedral-fullerene has attracted growing interest due to the unique electronic and structural characteristics arising from its distinctive ionic nature. Although there has been only one reported ion-encapsulated fullerene, Li @C , a significant number of fundamental and applied studies have been conducted, making a substantial impact not only in chemistry and physics but also across various interdisciplinary research fields. Nevertheless, studies on ion-endohedral fullerenes are still in their infancy due to the limitations in variety, and hence, it remains an open question how the size and symmetry of fullerene, as well as the motion and position of the encapsulated ion, affect their physical/chemical properties.

Prediction of water transport properties on an anisotropic wetting surface deep learning.

Understanding the water flow behavior on an anisotropic wetting surface is of practical significance in nanofluidic devices for their performance improvement. However, current methods of experiments and simulations face challenges in measuring water transportation in real time and visually displaying it. Here, molecular dynamics simulation was integrated with our developed multi-attribute point cloud dataset and a customized network of deep learning to achieve mapping from an anisotropic wetting surface to the static and dynamic behaviors of water molecules and realize the high-performance prediction of water transport behavior.

DNA Nanopore-Tethered Gold Needle Electrodes for Channel Current Recording.

Synthetic DNA nanopores are attracting attention as alternatives to conventional biological nanopores in nanopore sensors because of the high designability of their pore structures and functionability. However, the efficient insertion of DNA nanopores into a planar bilayer lipid membrane (pBLM) remains challenging. Although hydrophobic modifications such as the use of cholesterol are required to insert DNA nanopores into pBLMs, these modifications also induce negative effects, including the undesired aggregation of DNA structures.

Deep Learning to Reveal the Distribution and Diffusion of Water Molecules in Fuel Cell Catalyst Layers.

Water management in the catalyst layers (CLs) of proton-exchange membrane fuel cells is crucial for its commercialization and popularization. However, the high experimental or computational cost in obtaining water distribution and diffusion remains a bottleneck in the existing experimental methods and simulation algorithms, and further mechanistic exploration at the nanoscale is necessary. Herein, we integrate, for the first time, molecular dynamics simulation with our customized analysis framework based on a multiattribute point cloud dataset and an advanced deep learning network.

Heat-Induced Conformational Transition Mechanism of Heat Shock Factor 1 Investigated by Tryptophan Probe.

A transcriptional regulatory system called heat shock response (HSR) has been developed in eukaryotic cells to maintain proteome homeostasis under various stresses. Heat shock factor-1 (Hsf1) plays a central role in HSR, mainly by upregulating molecular chaperones as a transcription factor. Hsf1 forms a complex with chaperones and exists as a monomer in the resting state under normal conditions.

Revealing the Anticorrelation Behavior Mechanism between the Grotthuss and Vehicular Diffusions for Proton Transport in Concentrated Acid Solutions.

In this study, we performed reactive molecular dynamics simulations to characterize proton solvation and transport in concentrated hydrochloric acid solutions. The correlation contribution to the total proton mean square displacement is found to be negative for all acid concentrations, indicating the anticorrelation between the Grotthuss and vehicular diffusions. For the vehicular diffusion, the hydronium ions tend to move freely toward the lone pair side independent of acid concentrations, whereas for the Grotthuss diffusion, the proton hopping direction is limited to one of the hydrogen-bonded water molecules on the opposite side of the lone pair region, which are specifically oriented with respect to the neighboring hydronium ion at higher acid concentrations.

Prediction of nanoscale thermal transport and adsorption of liquid containing surfactant at solid-liquid interface via deep learning.

Hypothesis: Recent advances in deep learning (DL) have enabled high level of real-time prediction of thermophysical properties of materials. On the other hand, molecular dynamics (MD) have been long used as a numerical microscope to observe detailed interfacial conditions but require separate simulations that are computationally costly. Hence, it should be possible to combine MD and DL to obtain high resolution interfacial details at a low computational cost.

Molecular Dynamics Study of Ion Transport in Polymer Electrolytes of All-Solid-State Li-Ion Batteries.

Atomistic analysis of the ion transport in polymer electrolytes for all-solid-state Li-ion batteries was performed using molecular dynamics simulations to investigate the relationship between Li-ion transport and polymer morphology. Polyethylene oxide (PEO) and poly(diethylene oxide-alt-oxymethylene), P(2EO-MO), were used as the electrolyte materials, and the effects of salt concentrations and polymer types on the ion transport properties were explored. The size and number of LiTFSI clusters were found to increase with increasing salt concentrations, leading to a decrease in ion diffusivity at high salt concentrations.

Relationship between Proton Transport and Morphology of Perfluorosulfonic Acid Membranes: A Reactive Molecular Dynamics Approach.

A reactive molecular dynamics simulation has been performed for the characterization of the relationship between proton transport and water clustering in polymer electrolyte membranes. We have demonstrated that the anharmonic two-state empirical valence bond model is capable of describing efficiently excess proton transport through the Grotthuss hopping mechanism within the simplicity of the theoretical framework. To explore the long-time diffusion behavior in perfluorosulfonic acid membranes with statistical certainty, simulations that are longer than 10 ns are needed.

Molecular Dynamics Simulation of Proton Transport in Polymer Electrolyte Membrane.

We have performed a detailed analysis of proton solvation and transport properties in hydrated Nafion using molecular dynamics simulation. The revised empirical valence bond (EVB) method was developed in order to treat the excess proton transport through the Grotthuss mechanism. The new EVB model predicts a significantly enhanced transport in comparison with previous hopping models as well as the classical hydronium diffusion, which largely improves the agreement with the available experimental data.

A modified two-state empirical valence bond model for proton transport in aqueous solutions.

A detailed analysis of the proton solvation structure and transport properties in aqueous solutions is performed using classical molecular dynamics simulations. A refined two-state empirical valence bond (aTS-EVB) method, which is based on the EVB model of Walbran and Kornyshev and the anharmonic water force field, is developed in order to describe efficiently excess proton transport via the Grotthuss mechanism. The new aTS-EVB model clearly satisfies the requirement for simpler and faster calculation, because of the simplicity of the two-state EVB algorithm, while providing a better description of diffusive dynamics of the excess proton and water in comparison with the previous two-state EVB models, which significantly improves agreement with the available experimental data.

Effect of bound state of water on hydronium ion mobility in hydrated Nafion using molecular dynamics simulations.

We have performed a detailed analysis of the structural properties of the sulfonate groups in terms of isolated and overlapped solvation shells in the nanostructure of hydrated Nafion membrane using classical molecular dynamics simulations. Our simulations have demonstrated the correlation between the two different areas in bound water region, i.e.