Optical measurements of cavitation in tribological contacts

The paper describes the use of a white light interformeter to measure the cavitation bubble and oil film thickness in a tribological contact and compares the results to theory. It is found that oil film thickness is best predicted by the theory proposed by Coyne and Elrod.

Cavitation bubble measurement in tribological contacts using digital holographic microscopy

The use of advanced measurement techniques such as the digital holography method described in this paper improves the understanding of the cavitation phenomenon in tribological contacts such as the sliding contact of the piston ring–cylinder liner conjunction. The paper describes the use of digital holography measurement technique to measure cavitation bubble formation and thickness. The position of observed lubricant film rupture preceding the cavitation region is compared with some commonly predicted boundary often used with Reynolds equation. The experimental results indicate that the Reynolds and Elrod boundary conditions are the most suitable for the investigated sliding contact conditions

Cavitation bubble measurement in tribological contacts using digital holographic microscopy

The use of advanced measurement techniques such as the digital holography method described in this paper improves the understanding of the cavitation phenomenon in tribological contacts such as the sliding contact of the piston ring–cylinder liner conjunction. The paper describes the use of digital holography measurement technique to measure cavitation bubble formation and thickness. The position of observed lubricant film rupture preceding the cavitation region is compared with some commonly predicted boundary often used with Reynolds equation. The experimental results indicate that the Reynolds and Elrod boundary conditions are the most suitable for the investigated sliding contact conditions

Molecular Dynamics Simulations Reveal Inhomogeneity-Enhanced Stacking of Violanthrone-78-Based Polyaromatic Compounds in <i>n</i>‑Heptane–Toluene Mixtures

We elucidated the effect of inhomogeneity in solutes on the aggregation of our representative polyaromatic (PA) compounds through a series of molecular dynamics simulations. Two kinds of solutes, a single type of PA compounds and a mixture of four types of PA compounds, were simulated in toluene, <i>n</i>-heptane, and heptol (mixture of toluene and <i>n</i>-heptane). The geometries of the resultant aggregates were quantified using gyradius ratios. Our results revealed that in toluene, while a single type of PA compound can only form short-cylinder-like aggregates, by having a solute mixture, parallel stacking of PA cores is enhanced, leading to the formation of one-dimensional (1D) rod-like structure. The enhanced stacking is caused by collective arrangement of the PA molecules; i.e., PA compounds of different types appear in an alternating manner in the aggregate. In addition, while the aggregated geometries of a single type of PA compounds were found to be affected by the composition of the solvents, the existence of the 1D structure formed by mixture seems to be insensitive to the solvents. On the other hand, the longest range of stacking is achieved by having a small amount of toluene (“good” solvent) in <i>n</i>-heptane (“bad” solvent)

Molecular Dynamics Investigation on the Aggregation of Violanthrone78-Based Model Asphaltenes in Toluene

In order to investigate the aggregation mechanisms of asphaltenes in toluene, a series of molecular dynamics simulations were performed on Violanthrone78-based model asphaltenes with different aliphatic/aromatic ratios. Our simulation results show that the attraction between poly-aromatic cores is the main driving force for asphaltene aggregation in toluene, and that the extent of aggregation is independent of the aliphatic/aromatic ratios. On the other hand, analysis of the aggregated structures indicates that long side chains do hinder the formation of large direct parallel stacking structures. In contrast with water as a solvent, toluene exhibits attractive interactions with both the aliphatic and aromatic regions of the asphaltenes, hence reducing the size and stability of the asphaltene aggregates. Our findings help to elucidate, at a molecular level, the different solubility behaviors of asphaltenes in toluene and in water

Probing the Effects of Lipid Substitution on Polycation Mediated DNA Aggregation: A Molecular Dynamics Simulations Study

Understanding the molecular mechanism of DNA aggregation and condensation is of importance to DNA packaging in cells, and applications of gene delivery therapy. Modifying polycations such as polyethylenimine with lipid substitution was found to improve the performance of polycationic gene carriers. However, the role of the lipid substitution in DNA binding and aggregation is not clear and remains to be probed at the molecular level. In this work, we elucidated the role of lipid substitution through a series of all-atom molecular dynamics simulations on DNA aggregation mediated by lipid modified polyethylenimine (lmPEI). We found that the lipids associate significantly with one another, which links the lmPEIs and serves as a mechanism of aggregating the DNAs and stabilizing the formed polyplex. In addition, some lipid tails on the lmPEIs stay at the periphery of the lmPEI/DNA polyplex and may provide a mechanism for hydrophobic interactions. The enhanced stability and hydrophobicity might contribute to better cellular uptake of the polyplexes

Molecular Dynamics Simulations for Complexation of DNA with 2 kDa PEI Reveal Profound Effect of PEI Architecture on Complexation

A series of all-atom molecular dynamics (MD) simulations of the complexation between DNA and 2 kDa branched and linear polyethylenimines (PEIs) are reported in this study. The simulations revealed distinct binding modes of branched and linear PEIs to DNA, with branched PEIs adhering to the DNA surface like beads and linear PEIs adhering to the DNA surface like cords. The dynamics of each PEI’s binding state to the DNA during the simulations and how the PEIs neutralize the DNA were quantified. For both branched and linear PEIs, the addition of salt ions similar to physiological conditions were found to have only a small effect on DNA/PEI complexation compared to salt-free conditions. The simulation results reported here will be helpful to understand the mechanism of action for the PEI-based gene carriers

Probing the Effect of Side-Chain Length on the Aggregation of a Model Asphaltene Using Molecular Dynamics Simulations

A series of molecular dynamics simulations were performed to investigate the effect of aliphatic side-chain length on the aggregation behavior of a model asphaltene in water. We found that the extent of aggregation has a nonmonotonic relationship with the side-chain length. Asphaltene molecules with very short or very long side chains can form dense aggregates, whereas those with intermediate chain lengths cannot. Through analysis of the kinetics and driving forces of the aggregation, the role of the side chains in affecting the aggregation behavior was elucidated. Long side chains hinder the formation of parallel stacking structures of the polyaromatic cores while also favoring aggregation through hydrophobic association. The simulation results reported here can be used to propose appropriate means to reduce the extent of aggregation of asphaltene in the presence of water

Probing the Effect of miRNA on siRNA–PEI Polyplexes

Delivery of small interfering RNA (siRNA) for silencing of aberrantly expressed genes is a promising therapy for the treatment of various genetic disorders. Polymeric carriers have been used in the design of efficient delivery systems to generate nanoscale siRNA polyplexes. Despite the great amount of research pursued on siRNA therapeutics, the underlying mechanisms of polyplex dissociation in cytosol are still unclear. The fate of siRNA polyplexes during intracellular stages of delivery and how the endogenous molecules may affect the integrity of polyplexes remains to be explored. In this study, we have focused on miRNA-21 as a representative anionic endogenous molecule and performed gel electrophoresis mobility shift assays, particle size and zeta (ζ)-potential analyses, and a series of all-atom molecular dynamics simulations to elucidate the effect of miRNA on siRNA–PEI polyplexes. We report a slightly better binding to PEI by miRNA than that of siRNA, and speculated that miRNA may disrupt the integrity of preformed siRNA–PEI polyplexes. In contrast to our initial speculation, however, introduction of miRNA to a preformed siRNA–PEI polyplex revealed formation of a miRNA layer surrounding the polyplex through interactions with PEI. The resulting structure is a ternary siRNA–PEI–miRNA complex, where the experimentally determined ζ-potential was found to decrease as a function of miRNA added

DataSheet_1_Genetic basis of local adaptation in the cold-tolerant mangrove Kandelia obovata.zip

Understanding the genetic basis of local adaption is crucial in the context of global climate change. Mangroves, as salt-tolerant trees and shrubs in the intertidal zone of tropical and subtropical coastlines, are particularly vulnerable to climate change. Kandelia obovata, the most cold-tolerant mangrove species, has undergone ecological speciation from its cold-intolerant counterpart, Kandelia candel, with geographic separation by the South China Sea. In this study, we conducted whole-genome re-sequencing of K. obovata populations along China’s southeast coast, to elucidate the genetic basis responsible for mangrove local adaptation to climate. Our analysis revealed a strong population structure among the three K. obovata populations, with complex demographic histories involving population expansion, bottleneck, and gene flow. Genome-wide scans unveiled pronounced patterns of selective sweeps in highly differentiated regions among pairwise populations, with stronger signatures observed in the northern populations compared to the southern population. Additionally, significant genotype-environment associations for temperature-related variables were identified, while no associations were detected for precipitation. A set of 39 high-confidence candidate genes underlying local adaptation of K. obovata were identified, which are distinct from genes under selection detected by comparison between K. obovata and its cold-intolerant relative K. candel. These results significantly contribute to our understanding of the genetic underpinnings of local adaptation in K. obovata and provide valuable insights into the evolutionary processes shaping the genetic diversity of mangrove populations in response to climate change.</p