Molecular dynamics simulation of formation and control of nanodroplets in piezoelectric nanoejection systems

In this paper, the formation of nanodroplets in piezoelectric nanoejection processes is investigated by non-equilibrium molecular dynamics simulation. By compressing liquid propane molecules with various specific pushing periods of oscillation, the phenomena of liquid thread breakup and droplet formation are simulated. The simulation results revealed that various features aid the piezoelectric nanoejection system. Two breakup shapes including double-cone and long tail structures were found in this process. To analyse the ejection process in detail, 2D contour plots and thermal properties for various pushing periods are shown and discussed in this paper. The results show that the sizes of nanodroplets are linear depending on the pushing periods. The findings show a new control factor and mechanism for nanodroplet formation through piezoelectric nanoejection processes.     

Dynamic ejection behaviour of water molecules passing through a nano-aperture nozzle

This study used molecular dynamics (MD) simulation to investigate the passage of water molecules through a composite graphene/Au nano-nozzle. Our focus was on the degree to which system temperature, extrusion speed, and nozzle diameter affect jet dynamics and the associated transient phenomena. Our findings show that high pressure and spatial confinement cause the nanojet from a small nozzle diameter (1.0?nm) to bend and twist, whereas the jets from a nozzle with a diameter of 1.5?nm present columns of greater stability. At 100?K, the H₂O nanojet froze at the outlet of the nozzle in the form of condensed icicles. At 500?K, the H₂O nanojet formed a loose spray and gaseous clusters. High extrusion speed of 55.824?m/s produced recirculating flow downstream from the nanojet with the appearance of an erupting volcano, which further prompted the jet column to thicken. Lower extrusion speeds produced jets with flow velocity insufficient to overcome the capillary force at the outlet of the nozzle, which subsequently manifests as unstable fluctuations in the flow rate.

• HIGHLIGHTS

• Water molecules through a composite graphene/Au nano-nozzle forming a nanojet is investigated.

• High pressure and spatial confinement cause the nanojet from a small nozzle diameter (≤1.0?nm) to bend and twist.

• High extrusion speed (≧55.824?m/s) produced recirculating flow downstream from the nanojet.

• Figure abstract: Schematic of the H₂O nano-jet through a nano-nozzle of graphene/Au

     

Evaporation and Condensation at a Liquid Surface of Methanol

Abstract

Evaporation and condensation processes at a liquid surface of methanol were investigated at room temperature with a microcanonical molecular dynamics computer simulation technique. The condensation coefficient (the number ratio of condensed molecules to incident ones) was estimated by comparing two types of autocorrelation functions, and found to be less than unity, which is in qualitative agreement with experiments. A variety of complex dynamic phenomena were observed at the surface.     

下呼吸道重开的生物流体力学研究:实验模拟

实验模拟了受阻塞肺下呼吸道重开的生物力学问题。呼吸是玻璃直圆管,以具有生物流体性质的机油作为阻塞液。实验给同了在压强差作用下阻塞液柱前陈面以及主粘液柱气泡前阵面的位置和速度曲线。结果表明,它们受外加压强,管直径,阻塞液以及初始阻塞液长度的影响。较高的外加中、阻塞液粘度较你攻管径较粗有利于呼吸道的重开。     

Molecular Dynamics Simulation of Behaviours of Non-Polar Droplets Merging and Interactions with Hydrophobic Surfaces

This paper presents a molecular dynamics simulation of the behaviours of non-polar droplets merging and also the fluid molecules interacting with a hydrophobic surface. Such behaviours and transport phenomena are popular in general microchannel flow boiling and two-phase flow. The droplets are assumed to be composed of Lennards-Jones type molecules. Periodic boundary conditions are applied in three coordinate directions of a 3-D system, where there exist two liquid droplets and their vapour. The two droplets merge when they come within the prescribed small distance. The merging of two droplets apart from each other at different initial distances is tested and the possible larger （or critical） non-dimensional distance, in which droplets merging can occur, is discussed. The evolution of the merging process is simulated numerically by employing the Molecular Dynamics （MD） method. For interactions with hydrophobic solid wall, a system with fluid confined between two walls is used to study the wetting phenomena of fluid and solid wall. The results are compared with those of hydrophilic wall to show the unique characteristics of hydrophobic interactions by microscopic methods.     

Hydrodynamics and mass transfer of CO2 in water in a tubular photobioreactor

Microalgae cultivation has received growing importance because of its potential applications in CO₂ bio‐fixation, wastewater treatment and biofuel production. In this regard, proper design of photobioreactors is crucial for large‐scale commercial applications. The hydrodynamics of a photobioreactor has great influence on the transfer of CO₂ from gas phase to liquid phase. Considering the facts, the present research focused on studying the gas holdups and mass transfer from the gas to liquid phase in a tubular photobioreactor at various superficial liquid velocities ranging from 8.4 to 22.4 cm/s and superficial gas velocities ranging from 3.66 to 8.1 cm/s. It was found that the gas holdups were radially distributed. The highest gas holdups were observed at the center zone while the lowest holdups are found near the reactor wall. CO₂ mass transfer coefficient in the photobioreactor was also estimated under different superficial liquid velocities (0.206, 0.355 and 0.485 cm/s) and gas velocities (0.67, 1.16 and 1.37 cm/s). The overall mass transfer coefficient was estimated by fitting the experimental data and comparing results with an unsteady state differential mole balance equation solved by Runge‐Kutta‐Gill method. Model predictions were comparable to experimental results.     

Conformational transition and mass transfer in extraction of proteins by AOT–alcohol–isooctane reverse micellar systems

We examined quantitatively the effect of alcohols on protein and reverse micellar structure. We used circular dichroism (CD) to compare the effects of various alcohols on the protein structure, and percolation phenomena to evaluate the effects of various alcohols on reverse micellar structure. Upon the addition of alcohols to the bulk aqueous phase, proteins were denatured significantly, depending on the alcohol species and concentration, suggesting that use of alcohol directly to the stripping solution is not effective in back-extraction processes of proteins. In the present study, a new method, a small amount of alcohol is added to the surfactant–organic solution to improve the back-extraction behaviors of proteins. Practically, in the back-extraction process, the alcohols suppressing the cluster formation of reverse micelles (high value of β_t), remarkably improved the back-extraction behavior of proteins. In addition, the same alcohol molecules showed a positive effect on the rate and fraction of protein back-extraction. From a result of the CD measurement of the back-extracted proteins, it was known that the alcohols added to reverse micellar solution allowed the proteins to back-extract safely without causing structural changes. These results show that the values of β_t, defined by the variation of percolation processes, and the back-extraction behaviors of proteins have a good relationship, suggesting that the back-extraction processes were controlled by the micellar–micellar and protein–micellar interactions.     

The risk and intensity of sperm ejection in female birds

The way females utilize the gametes of different males has important consequences for sexual selection, sexual conflict, and intersexual coevolution in natural populations. However, patterns of sperm utilization by females are difficult to demonstrate, and their functional significance remains unclear. Here, we experimentally study sperm ejection in the fowl Gallus gallus domesticus, where females eject preferentially the sperm of socially subordinate males. We study two measures of sperm ejection, (i) the probability that an ejaculate is ejected ("risk") and (ii) the proportion of semen ejected ("intensity"), and show that both measures are strongly nonrandom with respect to characteristics of the ejaculate, the male, and the female. Sperm ejection neutralized on average 80% of an ejaculate, and while larger ejaculates suffered a higher ejection risk, smaller ejaculates suffered more intense ejection. After controlling for ejaculate volume, we found socially subdominant males suffered higher ejection intensity. After controlling for male and ejaculate effects, we found ejection risk increased and intensity declined as females mated with successive males. Collectively, these results reveal that sperm ejection risk and intensity are at least partly actively caused by female behavior and generate independent selective pressures on male and ejaculate phenotypes.     

Two- and three-phase mixing in a concentric draft tube gas-lift fermentor

Two- and three-phase mixing studies were carried out in a 44-L concentric draft tube gas-lift fermentor. It was proposed to use the fermentor for the production of solvents using immobilized bacteria. Bubble size, gas holdup, liquid velocities, circulation, and mixing times were determined for various superficial gas velocities in distilled water, starch, carboxymethyl cellulose, and ethanol solutions. The observed trends for two phase mixing were similar to other studies but the results were found to be more sensitive to liquid properties. This was possibly due to the large value of downcomer to riser area used in this study. Mixing in three phases highlighted the difficulty in predicting the effect of adding solids to the gas-liquid system. Results showed that the gas-lift fermentor was ideally suited to dealing with three phases but more work is necessary before accurate models can be developed to account for the effect of solids.     

The secondary structure of guide RNA molecules from Trypanosoma brucei.

RNA editing in kinetoplastid organisms is a mitochondrial RNA processing phenomenon that is characterized by the insertion and deletion of uridine nucleotides into incomplete mRNAs. Key molecules in the process are guide RNAs which direct the editing reaction by virtue of their primary sequences in an RNA-RNA interaction with the pre-edited mRNAs. To understand the molecular details of this reaction, especially potential RNA folding and unfolding processes as well as assembly phenomena with mitochondrial proteins, we analyzed the secondary structure of four different guide RNAs from Trypanosoma brucei at physiological conditions. By using structure-sensitive chemical and enzymatic probes in combination with spectroscopic techniques we found that the four molecules despite their different primary sequences, fold into similar structures consisting of two imperfect hairpin loops of low thermodynamic stability. The molecules melt in two-state monomolecular transitions with Tms between 33 and 39 degrees C and transition enthalpies of -32 to -38 kcal/mol. Both terminal ends of the RNAs are single-stranded with the 3' ends possibly adopting a single-stranded, helical conformation. Thus, it appears that the gRNA structures are fine tuned to minimize stability for an optimal annealing reaction to the pre-mRNAs while at the same time maximizing higher order structural features to permit the assembly with other mitochondrial components into the editing machinery.     

Cavitation phenomena in mechanical heart valves: the role of squeeze flow velocity and contact area on cavitation initiation between two impinging rods

In this study, the closing dynamics of two impinging rods were experimentally analyzed to simulate the cavitation phenomena associated with mechanical heart valve closure. The purpose of this study was to investigate the cavitation phenomena with respect to squeeze flow between two impinging surfaces and the parameter that influences cavitation inception. High-speed flow imaging was employed to visualize and identify regions of cavitation. The images obtained favored squeeze flow as an important mechanism in cavitation inception. A correlation study of the effects of impact velocities, contact areas and squeeze flow velocity on cavitation inception showed that increasing impact velocities results in an increase in the risk of cavitation. It was also shown that for similar impact velocities, regions near the point of impact were found to cavitate later for those with smaller contact areas. It was found that the decrease in contact areas and squeeze flow velocities would delay the onset and reduce the intensity of cavitation. It is also interesting to note that the squeeze flow velocity alone does not provide an indication if cavitation inception will occur. This is corroborated by the wide range of published critical squeeze flow velocity required for cavitation inception. It should be noted that the temporal acceleration of fluid, often neglected in the literature, can also play an important role on cavitation inception for unsteady flow phenomenon. This is especially true in mechanical heart valves, where for the same leaflet closing velocity, valves with a seat stop were observed to cavitate earlier. Based on these results, important inferences may be made to the design of mechanical heart valves with regards to cavitation inception.     

Analysis of deformation behaviour of Al–Ni–Co thin film coated aluminium during nano-indentation: a molecular dynamics study

In the present work, molecular dynamics simulations of AlNiCo metallic film deposition on FCC Al substrate and subsequently nano-indentation on the same specimen considering different indenter velocities have been performed using Embedded Atom Method (EAM) potential. The mechanical properties and deformation behaviour of AlNiCo thin film deposited Al substrate is investigated subjected to simulated nano-indentation test. It has been found that indenter velocity significantly influences the calculated hardness of the thin film coated substrate specimen and faster indentation process increases the hardness of the specimen. This finding has been rationalised by correlating with the generation of various full and partial dislocations and their interactions during the nano-indentation process. Sessile dislocations such as stair-rod and Frank partials are found to aid/help the strain hardening phenomena. Furthermore, the effect of indenter velocity on the pile-up formation during the nano-indentation process is also investigated here and it is observed that the amount of pile-up reduces as indenter velocity increases.     

Removal of hydrocarbons from liquid media by Aspergillus niger van Tieghem

This study investigated the abiliy of Aspergillus niger van Tieghem to utilize crude oil and kerosene. Hydrocarbons are molecules that pose serious environmental problem because of their toxic, carcinogenic or teratogenic properties. The fate of these pollutants in the environment is mainly governed by the biodegradation process. The existence of these phenomena depends on the inherent biodegradability of the pollutant but also the presence of microflora-degrading competent.The microbial strain were isolated and identified from industrial wastewater samples from Sonatrach Skikda (North-east of Algeria), we selected them for their ability to grow in the presence of hydrocarbons. To test the ability to biodegrade the two selected hydrocarbons in 6 days, the study of the evolution of such parameters as the microbial kinetics, pH, the final dry weight of the population, oxygen concentration, and finally, biodegradation rate of crude oil and kerosene was conducted by high performance liquid chromatography (HPLC). A control test was performed to quantify the losses caused by abiotic factors.The filamentous fungus was found to degrade crude oil and kerosene, when previously grown mycelium was incubated 6 days in the Galzy and Slonimski media containing hydrocarbon. The results showed that these organisms were able to utilize crude oil more than kerosene and the degradation rate was 52.01% and 32.67%, respectively. Thus Aspergillus niger van Tieghem plays a major role in the detoxification of polluted natural environments and these capabilities could be explored in bioremediation processes.     

Characterization of HmqF, a protein involved in the biosynthesis of unsaturated quinolones produced by Burkholderia thailandensis

The opportunistic pathogen Burkholderia thailandensis produces a number of structurally similar unsaturated quinolones involved in quorum sensing. However, little is known about the biosynthesis of these unsaturated quinolones. In this study, we have characterized the starting point of the biosynthesis of unsaturated quinolone molecules produced in B. thailandensis. We have shown by using in vitro enzymology, liquid chromatography, and mass spectrometry that protein HmqF is involved in the biosynthesis of unsaturated quinolones produced by B. thailandensis. HmqF consists of three domains: an adenylation domain (A domain), a dehydrogenase domain (DH domain), and an acyl carrier domain (ACP). The three domains (A, DH, and ACP) were cloned and expressed individually in Escherichia coli, and their reactivity was studied using high-performance liquid chromatography (HPLC) and mass spectrometry (MS) based assays. Our in vitro studies show that the A domain catalyzes ATP-dependent activation of medium chain (C6-C14) fatty acids without activation by coenzyme A (CoA). Results from competition assays are consistent with decanoic acid being the preferred substrate. Incubation of the ACP domain with 4'-phosphopantetheine transferase and CoA led to the formation of phosphopantetheinylated ACP (Ppant-ACP). In a Ppant ejection assay using tandem MS (MS/MS), a mass consistent with the mass of a cyclic variant of dephosphorylated Ppant was detected. We further demonstrated that Ppant-ACP could be loaded with medium chain fatty acids in the presence of ATP and the A domain. MS analysis was consistent with the formation of Ppant-ACP thiol esters of the fatty acids. MS/MS Ppant ejection experiments confirmed the loss of 2H in samples of fatty acid-loaded Ppant-ACP in the presence of the DH domain. HPLC analysis of benzyl amide ligation products allowed us to conclude that dehydrogenation produced trans-β,γ-unsaturation in the fatty acid chains. Our results are in good agreement with naturally observed quinolone molecules produced by B. thailandensis, which predominately produce nine-carbon trans-β,γ-unsaturated alkyl chain quinolone molecules.     

Induction of circles of heterogeneous sizes in carcinogen-treated cells: two-dimensional gel analysis of circular DNA molecules.

Extrachromosomal circular DNA molecules are associated with genomic instability, and circles containing inverted repeats were suggested to be the early amplification products. Here we present for the first time the use of neutral-neutral two-dimensional (2D) gel electrophoresis as a technique for the identification, isolation, and characterization of heterogeneous populations of circular molecules. Using this technique, we demonstrated that in N-methyl-N'-nitro-N-nitrosoguanidine-treated simian virus 40-transformed Chinese hamster cells (CO60 cells), the viral sequences are amplified as circular molecules of various sizes. The supercoiled circular fraction was isolated and was shown to contain molecules with inverted repeats. 2D gel analysis of extrachromosomal DNA from CHO cells revealed circular molecules containing highly repetitive DNA which are similar in size to the simian virus 40-amplified molecules. Moreover, enhancement of the amount of circular DNA was observed upon N-methyl-N'-nitro-N-nitrosoguanidine treatment of CHO cells. The implications of these findings regarding the processes of gene amplification and genomic instability and the possible use of the 2D gel technique to study these phenomena are discussed.     

Enterohepatic circulation in man. A simple method for the determination of duodenal bile acids

A method has been developed for easy sampling of duodenal bile acids. For this purpose Entero-Test was used, an encapsulated nylon thread originally used to estimate enteral parasites. This capsule is swallowed by a fasting subject and one end of the thread is taped at a corner of the month. Four hours after swallowing the thread, it is withdrawn and bile acids are eluted with buffer. The solution is applied to a Sep-Pak C18 cartridge to extract bile acids, which are subsequently analyzed by capillary gas-liquid chromatography and liquid chromatography. In vitro analyses showed that there was no preferential binding to the thread of any bile acid and that binding was pH-independent. A high correlation (r = 0.98) was found between direct analyses of bile and analyses by Entero-Test after in vitro incubation. The values obtained by the Entero-Test were similar to those of duodenal bile simultaneously collected with the normal intubation technique (r = 0.99). Duodenal bile acid composition showed a daily variation. In 11 healthy volunteers the following bile acid composition of unstimulated duodenal juice was found (mean +/- SD; %): choleate 44 +/- 12 (glycine/taurine ratio 1.8), chenodeoxycholate: 29 +/- 6 (G/T ratio 2.3); deoxycholate: 25 +/- 11 (G/T ratio 5.7), lithocholate: 1, ursodeoxycholate: less than 1. The described technique turned out to be an easily applicable method for determination of duodenal bile acids in man. This enables longitudinal studies concerning the factors that determine the bile acid pool composition and its relevance to various diseases.     

Induced inflammatory process in Peripatus acacioi Marcus et Marcus (Onychophora)

The inflammatory response induced by the implant of a suture thread in Peripatus acacioi muscle was characterized under light and transmission electron microscopy (TEM). After 24 and 48 h granulocytes were observed migrating through the connective tissue toward the suture thread. These cells contain cytoplasmic eosinophilic granules as well as free granules near to the thread. There were few spherule cells with eccentric smooth kidney-shaped acidophilic nuclei and basophilic granules. Cells with intermediary characteristics as well as cells with a central basophilic nucleus with scarce acidophilic cytoplasm devoid of granules were also found. Under TEM, the granulocytic coelomocytes show small and homogeneous electron dense granules, while the spherule cells possess spherules that can be heterogeneous, granular, or with myelin figures. An acute induced inflammatory process is described for the first time in Onychophora and contributes to the scarce available literature on the function of the coelomocytes within this group.     

Langevin dynamics simulation of DNA ejection from a phage

We have performed Langevin dynamics simulations of a coarse-grained model of ejection of dsDNA from Φ29 phage. Our simulation results show significant variations in the local ejection speed, consistent with experimental observations reported in the literature for both in vivo and in vitro systems. In efforts to understand the origin of such variations in the local speed of ejection, we have investigated the correlations between the local ejection kinetics and the packaged structures created at various motor forces and chain flexibility. At lower motor forces, the packaged DNA length is shorter with better organization. On the other hand, at higher motor forces typical of realistic situations, the DNA organization inside the capsid suffers from significant orientational disorder, but yet with long orientational correlation times. This in turn leads to lack of registry between the direction of the DNA segments just to be ejected and the direction of exit. As a result, a significant amount of momentum transfer is required locally for successful exit. Consequently, the DNA ejection temporarily slows down exhibiting pauses. This slowing down occurs at random times during the ejection process, completely determined by the particular starting conformation created by prescribed motor forces. In order to augment our inference, we have additionally investigated the ejection of chains with deliberately changed persistence length. For less inflexible chains, the demand on the occurrence of large momentum transfer for successful ejection is weaker, resulting in more uniform ejection kinetics. While being consistent with experimental observations, our results show the nonergodic nature of the ejection kinetics and call for better theoretical models to portray the kinetics of genome ejection from phages.     

On the evolution and dynamics of biological networks.

Large numbers of interacting non-genic molecules regulate metabolism and embryonic morphogenesis through often unspecific mechanisms. This lack of specificity suggests that the prevailing viewpoint, that such ordered processes result from the direct control of genes and their products irrespective of local molecular dynamics, is incomplete. Proposed here is a hypothetical type of control dynamics, called indirect, that is exhibited in natural biological networks of interacting and adapting elements. Evidence in the literature suggests that ordinary interactions among such elements - including organisms, cells and molecules - produce six network phenomena that can be attributed to indirect-control dynamics. Although these hypotheses can be disproved, including by showing that the phenomena can be accounted for by an alternative process, the set of ecological dynamics argued to underlie the phenomena is observable, biologically consistent and universal. In contrast, the direct-control dynamics required by the modern synthesis likely is biologically disadvantageous. This biological view of networks suggests new areas of research.