scholarly journals A Simulation Study on the Interaction Between Pollutant Nanoparticles and the Pulmonary Surfactant Monolayer

2019 ◽  
Vol 20 (13) ◽  
pp. 3281 ◽  
Author(s):  
Kai Yue ◽  
Xiaochen Sun ◽  
Jue Tang ◽  
Yiang Wei ◽  
Xinxin Zhang
Keyword(s):  
Surface Tension ◽  
Structural Properties ◽  
Pulmonary Surfactant ◽  
Fine Particulate Matter ◽  
Membrane System ◽  
Cholesterol Content ◽  
Intermolecular Forces ◽  
Coarse Grained ◽  
Dynamic Simulations ◽  
The Impact

A good understanding of the mechanism of interaction between inhaled pollutant nanoparticles (NPs) and the pulmonary surfactant monolayer is useful to study the impact of fine particulate matter on human health. In this work, we established coarse-grained models of four representative NPs with different hydrophilicity properties in the air (i.e., CaSO4, C, SiO2, and C6H14O2 NPs) and the pulmonary surfactant monolayer. Molecular dynamic simulations of the interaction during exhalation and inhalation breathing states were performed. The effects of NP hydrophilicity levels, NP structural properties, and cholesterol content in the monolayer on the behaviors of NP embedment or the transmembrane were analyzed by calculating the changes in potential energy, NP displacement, monolayer orderliness, and surface tension. Results showed that NPs can inhibit the ability of the monolayer to adjust surface tension. For all breathing states, the hydrophobic C NP cannot translocate across the monolayer and had the greatest influence on the structural properties of the monolayer, whereas the strongly hydrophilic SiO2 and C6H14O2 NPs can cross the monolayer with little impact. The semi-hydrophilic CaSO4 NP can penetrate the monolayer only during the inhalation breathing state. The hydrophilic flaky NP shows the best penetration ability, followed by the rod-shaped NP and spherical NP in turn. An increase in cholesterol content of the monolayer led to improved orderliness and decreased fluidity of the membrane system due to enhanced intermolecular forces. Consequently, difficulty in crossing the monolayer increased for the NPs.

scholarly journals Coarse Grained Molecular Dynamic Simulations for the Study of TNF Receptor Family Members' Transmembrane Organization

2021 ◽  
Vol 8 ◽  
Author(s):  
Mauricio P. Sica ◽  
Cristian R. Smulski
Keyword(s):  
Force Field ◽  
Higher Order ◽  
Coarse Grained ◽  
Structural Basis ◽  
Tnf Receptor ◽  
Dynamic Simulations ◽  
Rich Domain ◽  
Martini Force Field ◽  
The Impact ◽  
Homotypic Interactions

The Tumor Necrosis Factor (TNF) and the TNF receptor (TNFR) superfamilies are composed of 19 ligands and 30 receptors, respectively. The oligomeric properties of ligands, both membrane bound and soluble, has been studied most. However, less is known about the oligomeric properties of TNFRs. Earlier reports identified the extracellular, membrane-distal, cysteine-rich domain as a pre-ligand assembly domain which stabilizes receptor dimers and/or trimers in the absence of ligand. Nevertheless, recent reports based on structural nuclear magnetic resonance (NMR) highlight the intrinsic role of the transmembrane domains to form dimers (p75NTR), trimers (Fas), or dimers of trimers (DR5). Thus, understanding the structural basis of transmembrane oligomerization may shed light on the mechanism for signal transduction and the impact of disease-associated mutations in this region. To this end, here we used an in silico coarse grained molecular dynamics approach with Martini force field to study TNFR transmembrane homotypic interactions. We have first validated this approach studying the three TNFR described by NMR (p75NTR, Fas, and DR5). We have simulated membrane patches composed of 36 helices of the same receptor equidistantly distributed in order to get unbiassed information on spontaneous proteins assemblies. Good agreement was found in the specific residues involved in homotypic interactions and we were able to observe dimers, trimers, and higher-order oligomers corresponding to those reported in NMR experiments. We have, applied this approach to study the assembly of disease-related mutations being able to assess their impact on oligomerization stability. In conclusion, our results showed the usefulness of coarse grained simulations with Martini force field to study in an unbiased manner higher order transmembrane oligomerization.

scholarly journals Microscale distribution and dynamic surface tension of pulmonary surfactant normalize the recruitment of asymmetric bifurcating airways

2017 ◽  
Vol 122 (5) ◽  
pp. 1167-1178 ◽  
Author(s):  
Eiichiro Yamaguchi ◽  
Liam P. Nolan ◽  
Donald P. Gaver
Keyword(s):  
Surface Tension ◽  
Lung Injury ◽  
Pulmonary Surfactant ◽  
Dynamic Surface Tension ◽  
Dependent Manner ◽  
Dynamic Surface ◽  
Ventilator Induced Lung Injury ◽  
Large Influence ◽  
The Impact

We investigate the influence of bifurcation geometry, asymmetry of daughter airways, surfactant distribution, and physicochemical properties on the uniformity of airway recruitment of asymmetric bifurcating airways. To do so, we developed microfluidic idealized in vitro models of bifurcating airways, through which we can independently evaluate the impact of carina location and daughter airway width and length. We explore the uniformity of recruitment and its relationship to the dynamic surface tension of the lining fluid and relate this behavior to the hydraulic (PHyd) and capillary (PCap) pressure drops. These studies demonstrate the extraordinary importance of PCap in stabilizing reopening, even in highly asymmetric systems. The dynamic surface tension of pulmonary surfactant is integral to this stability because it modulates PCap in a velocity-dependent manner. Furthermore, the surfactant distribution at the propagating interface can have a very large influence on recruitment stability by focusing surfactant preferentially to specific daughter airways. This implies that modification of the surfactant distribution through novel modes of ventilation could be useful in inducing uniformly recruited lungs, aiding in gas exchange, and reducing ventilator-induced lung injury. NEW & NOTEWORTHY The dynamic surface tension of pulmonary surfactant is integral to the uniformity of asymmetric bifurcation airway recruitments because it modulates capillary pressure drop in a velocity-dependent manner. Also, the surfactant distribution at the propagating interface can have a very large influence on recruitment stability by focusing surfactant preferentially to specific daughter airways. This implies that modification of the surfactant distribution through novel modes of ventilation could be useful in inducing uniformly recruited lungs, reducing ventilator-induced lung injury.

scholarly journals Impact of pathogenic mutations of the GLUT1 glucose transporter on channel dynamics using ConsDYN enhanced sampling

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 322
Author(s):  
Halima Mouhib ◽  
Akiko Higuchi ◽  
Sanne Abeln ◽  
Kei Yura ◽  
K. Anton Feenstra
Keyword(s):  
Conformational Changes ◽  
Glucose Transporter ◽  
Pathogenic Mutation ◽  
Deficiency Syndrome ◽  
Coarse Grained ◽  
Strong Impact ◽  
Conformational States ◽  
Dynamic Simulations ◽  
Pathogenic Mutations ◽  
The Impact

Background: The solute carrier (SLC) family of membrane proteins is a large class of transporters for many small molecules that are vital for the cell. Several pathogenic mutations are reported in the glucose transporter subfamily SLC2, causing Glut1-deficiency syndrome (GLUT1DS1, GLUT1DS2), epilepsy (EIG2) and cryohydrocytosis with neurological defects (Dystonia-9). Understanding the link between these mutations and transporter dynamics is crucial to elucidate their role in the dysfunction of the underlying transport mechanism. Methods: Predictions from SIFT and PolyPhen provided an impression of the impact upon mutation in the highly conserved RXGRR motifs, but no clear differentiation could be made by these methods between pathogenic and non-pathogenic mutations. Therefore, to identify the molecular effects on the transporter function, insight from molecular dynamic simulations is required. We studied a variety of pathogenic and non-pathogenic mutations, using a newly developed coarse-grained simulation approach ‘ConsDYN’, which allows the sampling of both inward-open and outward-occluded states. To guarantee the sampling of large conformational changes, we only include conserved restraints of the elastic network introduced upon coarse-graining, which showed similar reference distances between the two conformational states (≤1 Å difference). Results: We capture the ‘conserved dynamics’ between both states using ConsDYN. Simultaneously, it allowed us to considerably lower the computational costs of our study. This approach is sufficiently sensitive to capture the effect of different mutations, and our results clearly indicate that the pathogenic mutation in GLUT1, G91D, situated at the highly conserved RXGRR motif between helices 2 and 3, has a strong impact on channel function, as it blocks the protein from sampling both conformational states.  Conclusions: Using our approach, we can explain the pathogenicity of the mutation G91D when we observe the configurations of the transmembrane helices, suggesting that their relative position is crucial for the correct functioning of the GLUT1 protein.

Multiscale Molecular Dynamics Simulation of Nanobio Membrane in Interaction With Protein

2013 ◽  
Author(s):  
Negin Maftouni ◽  
Mehriar Amininasab ◽  
MohammadReza Ejtehadi ◽  
Farshad Kowsari
Keyword(s):  
Molecular Dynamics ◽  
Surface Tension ◽  
Molecular Dynamics Simulation ◽  
Lipid Membranes ◽  
Lateral Pressure ◽  
Lipid Membrane ◽  
Intermolecular Forces ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Multiscale Approach

One of the most important biological components is lipid nanobio membrane. The lipid membranes of alive cells and their mechanical properties play an important role in biophysical investigations. Some proteins affect the shape and properties of the nanobio membrane while interacting with it. In this study a multiscale approach is experienced: first a 100ns all atom (fine-grained) molecular dynamics simulation is done to investigate the binding of CTX A3, a protein from snake venom, to a phosphatidylcholine lipid bilayer, second, a 5 micro seconds coarse-grained molecular dynamics simulation is carried out to compute the pressure tensor, lateral pressure, surface tension, and first moment of lateral pressure. Our simulations reveal that the insertion of CTX A3 into one monolayer results in an asymmetrical change in the lateral pressure and distribution of surface tension of the individual bilayer leaflets. The relative variation in the surface tension of the two monolayers as a result of a change in the contribution of the various intermolecular forces may be expressed morphologically and lead to deformation of the lipid membrane.

Simulation of the Impact of Higher Ammonia Recycle Loads Caused by Upgrading Anaerobic Sludge Digesters

2005 ◽  
Vol 40 (4) ◽  
pp. 491-499 ◽  
Author(s):  
Jeremy T. Kraemer ◽  
David M. Bagley
Keyword(s):  
Anaerobic Digestion ◽  
Biogas Production ◽  
Treatment Plant ◽  
Anaerobic Sludge ◽  
Content Increase ◽  
Limited Information ◽  
Dynamic Simulations ◽  
Treatment Train ◽  
Temperature Liquid ◽  
The Impact

Abstract Upgrading conventional single-stage mesophilic anaerobic digestion to an advanced digestion technology can increase sludge stability, reduce pathogen content, increase biogas production, and also increase ammonia concentrations recycled back to the liquid treatment train. Limited information is available to assess whether the higher ammonia recycle loads from an anaerobic sludge digestion upgrade would lead to higher discharge effluent ammonia concentrations. Biowin, a commercially available wastewater treatment plant simulation package, was used to predict the effects of anaerobic digestion upgrades on the liquid train performance, especially effluent ammonia concentrations. A factorial analysis indicated that the influent total Kjeldahl nitrogen (TKN) and influent alkalinity each had a 50-fold larger influence on the effluent NH3 concentration than either the ambient temperature, liquid train SRT or anaerobic digestion efficiency. Dynamic simulations indicated that the diurnal variation in effluent NH3 concentration was 9 times higher than the increase due to higher digester VSR. Higher recycle NH3 loads caused by upgrades to advanced digestion techniques can likely be adequately managed by scheduling dewatering to coincide with periods of low influent TKN load and ensuring sufficient alkalinity for nitrification.

scholarly journals The Impact of the Electric Field on Surface Condensation of Water Vapor: Insight from Molecular Dynamics Simulation

Nanomaterials ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 64 ◽  
Author(s):  
Qin Wang ◽  
Hui Xie ◽  
Zhiming Hu ◽  
Chao Liu
Keyword(s):  
Molecular Dynamics ◽  
Water Vapor ◽  
Electric Field ◽  
Intermolecular Forces ◽  
Dynamics Simulation ◽  
Water Molecules ◽  
Attraction Force ◽  
Condensation Rate ◽  
Shape Transformation ◽  
The Impact

In this study, molecular dynamics simulations were carried out to study the coupling effect of electric field strength and surface wettability on the condensation process of water vapor. Our results show that an electric field can rotate water molecules upward and restrict condensation. Formed clusters are stretched to become columns above the threshold strength of the field, causing the condensation rate to drop quickly. The enhancement of surface attraction force boosts the rearrangement of water molecules adjacent to the surface and exaggerates the threshold value for shape transformation. In addition, the contact area between clusters and the surface increases with increasing amounts of surface attraction force, which raises the condensation efficiency. Thus, the condensation rate of water vapor on a surface under an electric field is determined by competition between intermolecular forces from the electric field and the surface.

scholarly journals Buoyancy control in ammonoid cephalopods refined by complex internal shell architecture

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
David J. Peterman ◽  
Kathleen A. Ritterbush ◽  
Charles N. Ciampaglio ◽  
Erynn H. Johnson ◽  
Shinya Inoue ◽  
...  
Keyword(s):  
Surface Tension ◽  
Water Retention Capacity ◽  
Functional Explanation ◽  
Retention Capacity ◽  
Biomechanical Stress ◽  
Liquid Retention ◽  
3D Printed ◽  
Functional Explanations ◽  
Hydrophilic Coatings ◽  
The Impact

AbstractThe internal architecture of chambered ammonoid conchs profoundly increased in complexity through geologic time, but the adaptive value of these structures is disputed. Specifically, these cephalopods developed fractal-like folds along the edges of their internal divider walls (septa). Traditionally, functional explanations for septal complexity have largely focused on biomechanical stress resistance. However, the impact of these structures on buoyancy manipulation deserves fresh scrutiny. We propose increased septal complexity conveyed comparable shifts in fluid retention capacity within each chamber. We test this interpretation by measuring the liquid retained by septa, and within entire chambers, in several 3D-printed cephalopod shell archetypes, treated with (and without) biomimetic hydrophilic coatings. Results show that surface tension regulates water retention capacity in the chambers, which positively scales with septal complexity and membrane capillarity, and negatively scales with size. A greater capacity for liquid retention in ammonoids may have improved buoyancy regulation, or compensated for mass changes during life. Increased liquid retention in our experiments demonstrate an increase in areas of greater surface tension potential, supporting improved chamber refilling. These findings support interpretations that ammonoids with complex sutures may have had more active buoyancy regulation compared to other groups of ectocochleate cephalopods. Overall, the relationship between septal complexity and liquid retention capacity through surface tension presents a robust yet simple functional explanation for the mechanisms driving this global biotic pattern.

scholarly journals Review of the relationship between aggregates geology and Los Angeles and micro-Deval tests

2021 ◽  
Vol 80 (3) ◽  
pp. 1963-1980
Author(s):  
Solomon Adomako ◽  
Christian John Engelsen ◽  
Rein Terje Thorstensen ◽  
Diego Maria Barbieri
Keyword(s):  
Los Angeles ◽  
Crystal Size ◽  
Grain Shape ◽  
Mechanical Performance ◽  
Pore Space ◽  
Construction Material ◽  
Engineering Properties ◽  
Coarse Grained ◽  
The Impact ◽  
The Relationship

AbstractRock aggregates constitute the enormous volume of inert construction material used around the globe. The petrologic description as igneous, sedimentary, and metamorphic types establishes the intrinsic formation pattern of the parent rock. The engineering properties of these rocks vary due to the differences in the transformation process (e.g. hydrothermal deposits) and weathering effect. The two most common mechanical tests used to investigate the performance of aggregates are the Los Angeles (LA) and micro-Deval (MD) tests. This study reviewed the geological parameters (including mineralogy, grain and crystal size, grain shape, and porosity) and the relationship to Los Angeles and micro-Deval tests. It was found that high content of primary minerals in rocks (e.g. quartz and feldspar) is a significant parameter for performance evaluation. Traces of secondary and accessory minerals also affect the performance of rocks, although in many cases it is based on the percentage. Furthermore, some studies showed that the effect of mineralogic composition on mechanical strength is not sufficient to draw final conclusions of mechanical performance; therefore, the impact of other textural characteristics should be considered. The disposition of grain size and crystal size (e.g. as result of lithification) showed that rocks composed of fine-grain textural composition of ≤ 1 mm enhanced fragmentation and wear resistance than medium and coarse grained (≥ 1 mm). The effect of grain shape was based on convex and concave shapes and flat and elongated apexes of tested samples. The equidimensional form descriptor of rocks somehow improved resistance to impact from LA than highly flat and elongated particles. Lastly, the distribution of pore space investigated by means of the saturation method mostly showed moderate (R = 0.50) to strong (R = 0.90) and positive correlations to LA and MD tests.

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