Regimes of Flow over Complex Structures of Endothelial Glycocalyx: A Molecular Dynamics Simulation Study

Flow patterns on surfaces grafted with complex structures play a pivotal role in many engineering and biomedical applications. In this research, large-scale molecular dynamics (MD) simulations are conducted to study the flow over complex surface structures of an endothelial glycocalyx layer. A detailed structure of glycocalyx has been adopted and the flow/glycocalyx system comprises about 5,800,000 atoms. Four cases involving varying external forces and modified glycocalyx configurations are constructed to reveal intricate fluid behaviour. Flow profiles including temporal evolutions and spatial distributions of velocity are illustrated. Moreover, streamline length and vorticity distributions under the four scenarios are compared and discussed to elucidate the effects of external forces and glycocalyx configurations on flow patterns. Results show that sugar chain configurations affect streamline length distributions but their impact on vorticity distributions is statistically insignificant, whilst the influence of the external forces on both streamline length and vorticity distributions are trivial. Finally, a regime diagram for flow over complex surface structures is proposed to categorise flow patterns

Large-scale molecular dynamics simulation of flow under complex structure of endothelial glycocalyx

In this research, large-scale molecular dynamics (MD) simulations were conducted to study the fluid dynamics inside the endothelial glycocalyx layer. A work flowchart regarding constructing the flow/glycocalyx system, undertaking production simulation using the MD method and post-processing was proposed. Following the flowchart, physiological and accelerating flow cases were simulated to reveal velocity and shear stress distributions over the dendritic (tree-like) structure of the glycocalyx, thereby contributing to understanding of the influence of biomolecular complex structures on flow profiles. Besides, the selection of thermostat algorithm was discussed. Results have shown that when the forcing is below a critical value, the velocity fluctuates around a zero mean along the height in the presence of the dendritic glycocalyx. When the forcing is larger than a critical value, the bulk flow was accelerated excessively, departing from the typical physiological flow. Furthermore, distributions of shear stress magnitude among three sub-regions in the ectodomain indicate that shear stress is enhanced near the membrane surface but is impaired in the sugar-chain-rich region due to the flow regulation by sugar chains. Finally, comparisons of velocity evolutions under two widely used thermostats (Lowe-Andersen and Berendsen thermostats) imply that the Lowe-Andersen algorithm is a suitable thermostat for flow problems

A reactive molecular dynamics simulation study of methane oxidation assisted by platinum/graphene-based catalysts

Platinum-decorated functionalized graphene sheet (Pt@FGS) is a promising nanoparticle additive for catalytic fuel combustion. In this study, four cases involving pure methane oxidation and methane oxidation in the presence of various Pt/graphene-based nanoparticle catalysts are investigated using the reactive force field molecular dynamics (ReaxFF MD) simulations to reveal catalytic mechanisms and kinetics of methane oxidation. The results demonstrate that Pt@FGS is the most effective catalyst among all the nanoparticle candidates involved in this research. Compared with pure methane oxidation, the combination of Pt and FGS in the Pt@FGS reaction improves the catalytic activity by dramatically lowering the activation energy by approximately 73%. Additionally, the catalytic methane oxidation is initiated by the cleavage of C. H bond and the production of hydroxyl. The observed H transfer process suggests that enhanced dehydrogenation of Pt@FGS and interatomic exchanges activate the catalytic cycle and dominate the catalytic process. Moreover, FGS can be further oxidized mostly at the edge of the sheet to increase the functionality. In summary, this research sheds light on the catalytic mechanisms for enhanced fuel combustion in the presence of Pt@FGS

Study of mechanisms for electric field effects on ethanol oxidation via reactive force field molecular dynamics

Molecular dynamics simulations based on reactive force fields (ReaxFF) were conducted to study the effects of an external electric field with varying electric field strengths on ethanol oxidation reactions. Time evolutions of the reactants and intermediate species indicate that imposition of the electric field has modified the reaction pathways in addition to changing the reaction rate in a non-linear way. Intermediates of ethanol oxidation reactions with and without the electric field are identified and quantified. For the first time, reaction pathways of ethanol oxidation with and without an imposed electric field are scrutinized at the atomic scales. The reaction pathways without the electric field are consistent with previous experimental and numerical studies, which validate the present approach. Reaction pathways under varying electric field strengths, on the other hand, show some common pathways but also unique pathways associated with different strengths of the imposed electric field. The ReaxFF-based molecular dynamics method provides new insight into mechanisms for the effects of an electric field with varying electric field strengths on ethanol oxidation reactions. The present research demonstrates that ReaxFF-based reactive molecular dynamics is a valuable tool for detailed study of reaction mechanisms of hydrocarbon or oxygenated fuels, which complements commonly used experimental and computational techniques

Ethanol oxidation with high water content: A reactive molecular dynamics simulation study

Ethanol is a potential alternative to conventional fossil fuels. However, the required dewatering process to produce anhydrous ethanol is extremely energy-intensive and expensive. A promising solution is the direct use of hydrous ethanol for combustion applications, which can dramatically reduce the production cost. Many researchers have undertaken experiments demonstrating the feasibility and advantages of burning hydrous ethanol solely as a fuel. In this study, molecular dynamics (MD) simulation with the reactive force field (ReaxFF) is employed to investigate the fundamental reaction mechanisms of hydrous ethanol oxidation in comparison with the ethanol oxidation under fuel-air condition in order to understand the effects of water addition on ethanol oxidation. The results show that the reaction rate of ethanol oxidation is faster in water than in nitrogen environment and the presence of water advances the ionisation process and accelerates the radical production rate thereby enhancing the oxidation reaction. Additionally, it is suggested that the water content plays a vital role in reactions at low temperatures but that effect can be ignored at high temperatures. The detailed reaction pathways and time evolution of relevant key species indicate that H2O promotes many reactions involving OH generation and these OH radicals also facilitate its reactions with C1& C2intermediates as well as the dehydrogenation of C1& C2intermediates. Similarly, CO production is reduced in hydrous ethanol oxidation as a result of CO reaction with OH converting the CO to CO2ultimately. Therefore, it is the addition of water that promotes the OH production due to the chemical effect of H2O leading to the enhancement of ethanol oxidation and reduction of CO production. In summary, this research provides the scientific base for the direct use of hydrous ethanol as a fuel for combustion systems with a low cost

Declining malaria transmission differentially impacts on the maintenance of humoral immunity to Plasmodium falciparum in children

BACKGROUND We investigated the poorly understood impact of declining malaria transmission on maintenance of antibodies to P. falciparum merozoite antigens and infected erythrocytes (IEs), including functional immunity. METHODS In a 3-year longitudinal cohort of 300 Kenyan children, antibodies to different merozoite AMA1 and MSP2 alleles, IE surface antigens, and antibody functional activities were quantified. RESULTS Over a period in which malaria transmission declined markedly, AMA1 and MSP2 antibodies decreased substantially; estimated half-lives of antibody duration were 0.8 and 1-3 years, respectively. However, 69-74% of children maintained their sero-positivity to AMA1 alleles and 42-52% to MSP2 alleles. Levels and prevalence of anti-merozoite antibodies were consistently associated with increasing age and concurrent parasitaemia. Antibodies promoting opsonic phagocytosis of merozoites declined rapidly (half-life 0.15 years). In contrast, complement-fixing antibodies to merozoites did not decline and antibodies to IE surface antigens expressing virulent phenotypes were much better maintained (half-life 4-10 years). CONCLUSIONS A decline in malaria transmission is associated with reduction in naturally-acquired immunity. However, loss of immunity is not universal; some key functional responses and antibodies to IEs were better maintained and these may continue to provide some protection. Findings have implications for malaria surveillance and control measures and informing vaccine development

Rhabdastrellic Acid-A Induced Autophagy-Associated Cell Death through Blocking Akt Pathway in Human Cancer Cells

BACKGROUND: Autophagy is an evolutionarily conserved protein degradation pathway. A defect in autophagy may contribute to tumorigenesis. Autophagy inducers could have a potential function in tumor prevention and treatment. METHODOLOGY/PRINCIPAL FINDINGS: Our results showed that Rhabdastrellic acid-A, an isomalabaricane triterpenoid isolated from the sponge Rhabdastrella globostellata, inhibited proliferation of human cancer cell lines Hep3B and A549 and induced caspase-independent cell death in both the cell lines. Further investigation showed that Rhabdastrellic acid-A induced autophagy of cancer cells determined by YFP-LC3 punctation and increased LC3-II. The pretreatment with autophagy inhibitor 3-MA inhibited Rhabdastrellic acid-A-induced cell death. Knockdown of autophagy-related gene Atg5 inhibited Rhabdastrellic acid-A-induced cell death in A549 cells. Also, phospho-Akt and its downstream targets significantly decreased after treatment with Rhabdastrellic acid-A in both cancer cell lines. Transfection of constitutive active Akt plasmid abrogated autophagy and cell death induced by Rhabdastrellic acid-A. CONCLUSIONS/SIGNIFICANCE: These results suggest that Rhabdastrellic acid-A could induce autophagy-associated cell death through blocking Akt pathway in cancer cells. It also provides the evidence that Rhabdastrellic acid-A deserves further investigation as a potential anticancer or cancer preventive agent

Bi-directional cell-pericellular matrix interactions direct stem cell fate

Modifiable hydrogels have revealed tremendous insight into how physical characteristics of cells’ 3D environment drive stem cell lineage specification. However, in native tissues, cells do not passively receive signals from their niche. Instead they actively probe and modify their pericellular space to suit their needs, yet the dynamics of cells’ reciprocal interactions with their pericellular environment when encapsulated within hydrogels remains relatively unexplored. Here, we show that human bone marrow stromal cells (hMSC) encapsulated within hyaluronic acid-based hydrogels modify their surroundings by synthesizing, secreting and arranging proteins pericellularly or by degrading the hydrogel. hMSC’s interactions with this local environment have a role in regulating hMSC fate, with a secreted proteinaceous pericellular matrix associated with adipogenesis, and degradation with osteogenesis. Our observations suggest that hMSC participate in a bi-directional interplay between the properties of their 3D milieu and their own secreted pericellular matrix, and that this combination of interactions drives fate

Complementation of diverse HIV-1 Env defects through cooperative subunit interactions: a general property of the functional trimer

<p>Abstract</p> <p>Background</p> <p>The HIV-1 Env glycoprotein mediates virus entry by catalyzing direct fusion between the virion membrane and the target cell plasma membrane. Env is composed of two subunits: gp120, which binds to CD4 and the coreceptor, and gp41, which is triggered upon coreceptor binding to promote the membrane fusion reaction. Env on the surface of infected cells is a trimer consisting of three gp120/gp41 homo-dimeric protomers. An emerging question concerns cooperative interactions between the protomers in the trimer, and possible implications for Env function.</p> <p>Results</p> <p>We extended studies on cooperative subunit interactions within the HIV-1 Env trimer, using analysis of functional complementation between coexpressed inactive variants harboring different functional deficiencies. In assays of Env-mediated cell fusion, complementation was observed between variants with a wide range of defects in both the gp120 and gp41 subunits. The former included gp120 subunits mutated in the CD4 binding site or incapable of coreceptor interaction due either to mismatched specificity or V3 loop mutation. Defective gp41 variants included point mutations at different residues within the fusion peptide or heptad repeat regions, as well as constructs with modifications or deletions of the membrane proximal tryptophan-rich region or the transmembrane domain. Complementation required the defective variants to be coexpressed in the same cell. The observed complementation activities were highly dependent on the assay system. The most robust activities were obtained with a vaccinia virus-based expression and reporter gene activation assay for cell fusion. In an alternative system involving Env expression from integrated provirus, complementation was detected in cell fusion assays, but not in virus particle entry assays.</p> <p>Conclusion</p> <p>Our results indicate that Env function does not require every subunit in the trimer to be competent for all essential activities. Through cross-talk between subunits, the functional determinants on one defective protomer can cooperatively interact to trigger the functional determinants on an adjacent protomer(s) harboring a different defect, leading to fusion. Cooperative subunit interaction is a general feature of the Env trimer, based on complementation activities observed for a highly diverse range of functional defects.</p

Visualized exploratory spatiotemporal analysis of hand-foot-mouth disease in southern China

Objectives: In epidemiological research, major studies have focused on theoretical models; however, few methods of visual analysis have been used to display the patterns of disease distribution.Design: For this study, a method combining the space-time cube (STC) with space-time scan statistics (STSS) was used to analyze the pattern of incidence of hand-foot-mouth disease (HFMD) in Guangdong Province from May 2008 to March 2009. In this research, STC was used to display the spatiotemporal pattern of incidence of HFMD, and STSS were used to detect the local aggregations of the disease.Setting: The hand-foot-mouth disease data were obtained from Guangdong Province from May 2008 to March 2009, with a total of 68,130 cases.Results: The STC analysis revealed a differential pattern of HFMD incidence among different months and cities and also showed that the population density and average precipitation are correlated with the incidence of HFMD. The STSS analysis revealed that the most likely aggregation includes the Shenzhen, Foshan and Dongguan populations, which are the most developed regions in Guangdong Province.Conclusion: Both STC and STSS are efficient tools for the exploratory data analysis of disease transmission. STC clearly displays the spatiotemporal patterns of disease. Using the maximum likelihood ratio, the STSS model precisely locates the most likely aggregation