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This study utilizes molecular dynamics simulations to explore the tribological behavior of rough surfaces across various lubrication regimes—boundary, mixed, and elastohydrodynamic (EHL)—at the nanoscale. The analysis not only highlights the distinct interactions between asperity contacts and lubricant films but also introduces novel insights into how lubricant film thickness and surface roughness interplay to dictate frictional dynamics. The analysis reveals that in dry contact, surface roughness quickly stabilizes despite an initial increase in contact area, indicating a dominant role of asperity interlocking that influences frictional resistance. Transitioning to boundary lubrication, the presence of a lubricant layer modifies the contact mechanics, leading to a slower root mean square (RMS) reduction of surface roughness and a more gradual increase in friction force, emphasizing the lubricant's protective effect against asperity flattening. Nevertheless, under lower loads, this protective effect can lead to increased frictional forces compared to dry contact due to higher final roughness. Mixed lubrication maintains a near-constant contact area after initial contact, with any variations in friction force primarily occurring in the early cycles due to rapid asperity flattening. In the EHL regime, the formation of a complete lubricant film between surfaces results in the lowest friction forces, dominated by viscous shear rather than direct asperity contact. Unique to this study is the quantification of these effects under realistic roughness conditions (RMS of 1.2 nm). These regime-specific behaviors underline the nuanced interplay between RMS, contact area, and friction forces, and enhance our understanding of the fundamental principles guiding the design of lubrication strategies for advanced mechanical systems. [ABSTRACT FROM AUTHOR]

Three α-dicarbonyl compounds, methylglyoxal (MGO), diacetyl (DA) and glyoxal (GO) were common highly reactive glycosylation intermediates that can cause damage to biological macromolecules (e. g. DNA) in the body. The interaction properties of MGO, DA and GO with calf thymus DNA (ctDNA) were determined by multispectral methods combined with computer simulation techniques. Analysis of UV spectra indicated that MGO, DA and GO binding to ctDNA spontaneously were mainly driven by van der Waals forces and hydrogen bonding, and the energy distribution in molecular dynamics simulations supported this conclusion. The binding constants of MGO, DA and GO with ctDNA at 25 ℃ were close to those of classical groove-binders, with corresponding values of 2.99×10³, 1.96×10³ and 1. 05×10³ L·mol-1, respectively. NaCl, single and double-stranded DNA, thermal denaturation, viscosity and CD spectroscopy experiments demonstrated that MGO, DA and GO were all bound to ctDNA via groove binding. Molecular docking visualization showed that MGO, DA and GO were bound in the AT-rich minor groove region of DNA, with DT7 and DA18 being the active sites of binding. Molecular dynamics simulations of the MGO-ctDNA complex had higher root mean square deviation, radius of gyration, and root mean square fluctuation values than free DNA, indicating that the binding of MGO loosened and tended to destabilise parts of the DNA structure. Gel electrophoresis experiments showed that MGO, DA and GO could damage plasmid DNA in the presence of lysine and Cu2+, and MGO and GO even completely disrupted the superhelical morphology of DNA. [ABSTRACT FROM AUTHOR]

HIV-1 maturation is the final step in the retroviral lifecycle that is regulated by the proteolytic cleavage of the Gag precursor protein. As a first-in-class HIV-1 maturation inhibitor (MI), bevirimat blocks virion maturation by disrupting capsid-spacer peptide 1 (CA-SP1) cleavage, which acts as the target of MIs. Previous alterations of beesioside I (1) produced (20S,24S)-15ꞵ,16ꞵ-diacetoxy-18,24; 20,24-diepoxy-9,19-cyclolanostane-3ꞵ,25-diol 3-O-3′,3′-dimethylsuccinate (3, DSC), showing similar anti-HIV potency compared to bevirimat. To ascertain the binding modes of this derivative, further modification of compound 1 was conducted. Three-dimensional quantitative structure–activity relationship (3D-QSAR) analysis combined with docking simulations and molecular dynamics (MD) were conducted. Five new derivatives were synthesized, among which compound 3b showed significant activity against HIV-1NL4-3 with an EC50 value of 0.28 µM. The developed 3D-QSAR model resulted in great predictive ability with training set (r2 = 0.99, q2 = 0.55). Molecular docking studies were complementary to the 3D-QSAR analysis, showing that DSC was differently bound to CA-SP1 with higher affinity than that of bevirimat. MD studies revealed that the complex of the ligand and the protein was stable, with root mean square deviation (RMSD) values <2.5 Å. The above results provided valuable insights into the potential of DSC as a prototype to develop new antiviral agents. [ABSTRACT FROM AUTHOR]

This study presents a comprehensive investigation into Ni X Co 1-x Fe 2 O 4 (x = 0.5) spinel nanoparticles synthesized through a one-pot hydrothermal method using Co(NO 3) 2.6H 2 O and Ni(NO 3) 2.6H 2 O salts. XRD, FTIR, FESEM, and VSM analyses confirmed a cubic structure of Ni X Co 1-x Fe 2 O 4 (x = 0.5) nanoparticles without impurities. These nanoparticles exhibit efficient Zn (II) adsorption characteristics, following Langmuir isotherm and pseudo-second-order kinetics. The maximum adsorption capacity was measured to be 666.67 mg g−1 at pH = 7, with mechanisms involving both electrostatic attraction and cation exchange. Desorption studies indicate more than 75% Zn (II) recovery in an acidic environment (pH = 2) after three cycles. Computational analysis was used to validate the experimental results through Molecular Dynamics simulations, initially focusing on Ni X Co 1-x Fe 2 O 4 (x = 0.5). Further exploration involved variations in x at 0.25 and 0.75 to identify the optimal Ni and Co ratio in this bivalent cation spinel ferrite. Computational analyses reveal the superior performance of Ni X Co 1-x Fe 2 O 4 (x = 0.75) in Zn (II) removal, supported by radial distribution analysis, VdW energy, Coulombic energy, mean square displacement (MSD), root mean square displacement (RMSD), and interaction energy. This comprehensive study provides valuable insights into the adsorption behavior and structural stability of Ni X Co 1-x Fe 2 O 4 nanoparticles, showcasing potential applications in Zn (II) removal. [Display omitted] • One-pot synthesis produced pure Ni₀.₅Co₀.₅Fe₂O₄ spinel nanoparticles with cubic structure and no impurities. • Nanoparticles adsorbed Zn(II) at 666.67 mg/g (pH 7), fitting Langmuir isotherm and pseudo-second-order kinetics. • Molecular Dynamics (MD) simulations found Ni₀.₇₅Co₀.₂₅Fe₂O₄ optimal for Zn(II) removal. • Validated structural stability and performance using experiments and MD simulations, confirmed by various energy parameters. • Ni₀.₇₅Co₀.₂₅Fe₂O₄ nanoparticles show promise for efficient Zn(II) removal in water treatment. [ABSTRACT FROM AUTHOR]

• Water desalination laws and related mechanisms of HCM were investigated by the MD simulations. • Microscopic mechanism of raw water temperature affects HCM membrane flux was clarified. • Diffusion form of free-state water molecules in the membrane micropores of HCM was ascertained. With LAMMPS software, the non-equilibrium molecular dynamics (NEMD) simulations study was conducted for the membrane distillation process with the hydrophobic α-Al 2 O 3 ceramic membrane (HCM). It could further help to explain the macroscopic laws and phenomena that appeared in the membrane distillation tests with HCM. In this study, the average temperature (T r) of raw water and the negative pressure (P con) on the cold side of HCM were taken as the investigation variables to research the microscopic water desalination performance of HCM, transport/diffusion properties of water molecules, and related mechanisms. The results showed that the root means square displacement (MSD) of water molecules on the cold side of HCM positively changed with time by the linear trend. The height of the transmembrane energy barrier mainly depends on the atomic structure of the HCM. The diffusion type of free-state water molecules in the membrane micropores of HCM was the main ballistic-transport-like accompanied by rebound-jump. The influence level of T r on the number of water molecules in the cold side of HCM was much greater than that of P con under the dynamic equilibrium state. The essential reason T r determined the HCM molecular flux was that it changed the hydrogen bond lifetime in the microporous membrane of HCM. [ABSTRACT FROM AUTHOR]

Cysteine dioxygenase (CDO) regulates the concentration of l -cysteine substrate by its oxidation in the body to prevent different diseases, including neurodegenerative and autoimmune diseases. CDO catalyzes the oxidation of thiol group of l -cysteine to l -cysteine sulfinic acid using molecular oxygen. In this study, molecular dynamics simulations were applied to ligand-free CDO, cysteine-bound CDO, and oxygen-bound CDO-cysteine complex which were primarily subjected to the evaluation of their structural and dynamical properties. The simulation data provided significant information not only on the conformational changes of the enzyme after its ligation but also on the co-ligation by sequential binding of l -cysteine and molecular oxygen. It was found that the ligation and co-ligation perturbed the active site region as well as the overall protein dynamics which were analyzed in terms of root mean square deviation, root mean square fluctuation and dynamic cross correlation matrices as well as principal component analysis. Furthermore, oxygen transport pathways were successfully explored by taking various tunnel clusters into account and one of those clusters was given preference based on the throughput value. The bottleneck formed by different amino acid residues was examined to figure out their role in the oxygenation process of the enzyme. The residues forming the tunnel's bottleneck and their dynamics mediated by water molecules were further investigated using radial distribution functions which gave insights into the hydration behavior of these residues. The findings based on the hydration behavior in turn served to explore the water-mediated dynamics of these residues in the modulation of the pathway, including tunnel gating for the oxygen entry and diffusion to the active site, which is essential for the CDO's catalytic function. Molecular dynamics simulations were applied to cysteine dioxygenase and its complexes to investigate their structural and dynamical properties as well as to explore the oxygen tunnels involved in the oxygenation process of the enzyme. [Display omitted] • Evaluation of the structural and dynamical properties. • Exploration of the oxygen transport tunnel. • Evaluation of the hydration behavior of the tunnel residues involved in the oxygen of CDO enzyme. [ABSTRACT FROM AUTHOR]