Emitted Molecules Research Articles

Weapons against Themselves: Identification and Use of Quorum Sensing Volatile Molecules to Control Plant Pathogenic Fungi Growth.

Quorum sensing (QS) is often defined as a mechanism of microbial communication that can regulate microbial behaviors in accordance with population density. Much is known about QS mechanisms in bacteria, but fungal QS research is still in its infancy. In this study, the molecules constituting the volatolomes of the plant pathogenic fungi Fusarium culmorum and Cochliobolus sativus have been identified during culture conditions involving low and high spore concentrations, with the high concentration imitating overpopulation conditions (for QS stimulation). We determined that volatolomes emitted by these species in conditions of overpopulation have a negative impact on their mycelial growth, with some of the emitted molecules possibly acting as QSM. Candidate VOCs related to QS have then been identified by testing the effect of individual volatile organic compounds (VOCs) on mycelial growth of their emitting species. The antifungal effect observed for the volatolome of F. culmorum in the overpopulation condition could be attributed to ethyl acetate, 2-methylpropan-1-ol, 3-methylbutyl ethanoate, 3-methylbutan-1-ol, and pentan-1-ol, while it could be attributed to longifolene, 3-methylbutan-1-ol, 2-methylpropan-1-ol, and ethyl acetate for C. sativus in the overpopulation condition. This work could pave the way to a sustainable alternative to chemical fungicides.

Estimating real driving emissions from multi-axis differential optical absorption spectroscopy (MAX-DOAS) measurements at the A60 motorway near Mainz, Germany

Abstract. In urban areas, road traffic is a dominant source of nitrogen oxides (NOx=NO+NO2). Although the emissions from individual vehicles are regulated by the European emission standards, real driving emissions often exceed these limits. In this study, two multi-axis differential optical absorption spectroscopy (MAX-DOAS) instruments on opposite sides of the motorway were used to measure the NO2 absorption caused by road traffic at the A60 motorway close to Mainz, Germany. In combination with wind data, the total NOx emissions for the occurring traffic volume can be estimated. Hereto, the ozone-dependent photochemical equilibrium between NO and NO2 is considered. We show that for 10 May 2019 the measured emissions exceed the maximum expected emissions calculated from the European emission standards for standardised test cycles by a factor of 11±7. One major advantage of the method used here is that MAX-DOAS measurements are very sensitive to the integrated NO2 concentration close to the surface. Thus, all emitted NO2 molecules are detected independently from their altitude, and therefore the whole emission plume originating from the nearby motorway is captured, which is a key advantage compared to other approaches such as in situ measurements.

Molecular dynamics simulation for hydrogen recycling on tungsten divertor for neutral transport analysis

In magnetic field confinement plasma devices such as the International Thermonuclear Experimental Reactor (ITER), hydrogen atoms and molecules are emitted from plasma-facing materials by hydrogen recycling. The effect of the recycled hydrogen in edge plasma can be investigated by neutral transport analysis. In this paper, in order to obtain the boundary condition at the tungsten divertor for neutral transport simulation, a molecular dynamics simulation is performed to investigate the emission ratio of hydrogen atoms and molecules, the emission angle, the translational energy of emitted hydrogen atoms and molecules, and the vibrational and rotational energies of emitted hydrogen molecules. Moreover, from the simulation results, it is also found that the number of emitted hydrogen molecules increases as the ratio of the number of hydrogen and tungsten atoms (H/W) in the material increases, although the H/W dependence of the number of emitted hydrogen atoms is not significant in the range of our simulation, 0.49 ≤ H/W ≤ 1.37. The elementary process of the emission of hydrogen is also investigated by trajectory analysis. The analysis reveals that the hydrogen atom travels on the surface of the tungsten material and remains there for a while because it is trapped on the surface of the tungsten material.

Molecular dynamics simulation model of hydrogen recycling on carbon divertor for neutral transport analysis in large helical device

AbstractTo perform the neutral‐transport simulation with processes in which hydrogen molecules contribute to the reaction such as molecular assisted recombination, the parameters of emitted neutral particles at the wall such as the energy distributions and the form (atom or molecule) of emitted neutral particles are necessary as a boundary condition of the calculation. Therefore, in order to provide information of recycled hydrogen on the divertor to neutral‐transport code, molecular dynamics simulation of a hydrogen atom injection into a carbon material is performed to obtain the distributions of emission angle and translational energy of emitted hydrogen atoms and molecules. The distributions of rotational and vibrational energies are also investigated in the case of molecular hydrogen emission. Moreover, the quantum rotational state J, and vibrational state v are estimated from the classical value obtained by the simulation.

Finding an effective distance between T-cell and B-cell using S/W ARQ in an immune system communication

In this paper, we present the effective distance between T-cell and B-cell in an immune system using Stop and Wait (S/W) Automatic Repeat Request (ARQ). The concentration of the molecules can be increased by increasing the transmitting number of molecules but it may reduce the performance of communication due to higher collision or interference with other molecules. It is also reported in the literature that the concentration of the emitted molecules reduces if the distance from Transmitter (Tx) to Receiver (Rx) increases. Thus, this paper mainly focuses on enhancing the receiver's capture probability and higher successful complete transmission of the desired molecules by obtaining the effective distance from T-cell to B-cell. In order to find the effective distance, T-cell transmits the molecules 1 (Interleukins-2) to B-cell, upon successful reception of molecules 1, antibodies (molecules 2) transmit back to T-cell. Then, the effective distance of an immune system can be obtained after T-cell detects the concentration of the molecules 2 with respect to time. Different schemes of S/W ARQ protocols have implemented in Molecular Communication (MC) but it requires retransmission of duplicate copies due to the lack of addressing an effective distance. Thus, the simulations are performed in MATLAB and the results obtain higher capture probability and also successful complete transmission of the desired molecules.

Performance Enhancement of Diffusion-Based Molecular Communication.

Inter-Symbol Interference (ISI) is one of the challenges of bio-inspired diffusion-based molecular communication. The degradation of the remaining molecules from a previous transmission is the solution that biological systems use to mitigate this ISI. While most prior work has proposed the use of enzymes to catalyze the molecules degradation, enzymes also degrade the molecules carrying the information, which drastically decreases the signal strength. In this paper, we propose the use of photolysis reactions, which use the light to instantly transform the emitted molecules so they no longer be recognized after their detection. The light will be emitted in an optimal time, allowing the receiver to detect as many molecules as possible, which increases both the signal strength and ISI mitigation. A lower bound expression on the expectation of the observed molecules number at the receiver is derived. Bit error probability expression is also formulated, and both expressions are validated with simulation results, which show a visible enhancement when using photolysis reactions. The performance of the proposed method is evaluated using Interference-to-Total-Received molecules metric (ITR) and the derived bit error probability.

Molecular SIMS Ionization Probability Studied with Laser Postionization: Influence of the Projectile Cluster

The formation probability of (quasi-)molecular secondary ions released from an organic film under bombardment with a 20 keV cluster ion beam is investigated using combined time-of-flight secondary ion and neutral mass spectrometry (ToF-SIMS/SNMS) experiments. The emitted neutral molecules are postionized after their ejection using strong-field photoionization in an intense short infrared laser pulse. Comparing the (quasi)-molecular secondary ion signal with that of the corresponding neutral molecules, the ionization probability of sputtered intact coronene and guanine molecules is determined. The results are compared between two different projectile cluster ions, namely (i) C60+ and (ii) Arn+ with n ∼ 1000. It is shown that both projectiles deliver different SNMS spectra, indicating pronounced differences in the collision-induced fragmentation of the emitted molecules. For guanine, the ionization probability obtained with both projectiles is of the same order of magnitude (∼10–3), with the fullerene cluster producing a slightly larger ionization efficiency than the rare gas cluster. For coronene, on the other hand, a substantially lower ionization efficiency is found for the gas cluster projectile.

A new diagnostic for tropospheric ozone production

Abstract. Tropospheric ozone is important for the Earth's climate and air quality. It is produced during the oxidation of organics in the presence of nitrogen oxides. Due to the range of organic species emitted and the chain-like nature of their oxidation, this chemistry is complex and understanding the role of different processes (emission, deposition, chemistry) is difficult. We demonstrate a new methodology for diagnosing ozone production based on the processing of bonds contained within emitted molecules, the fate of which is determined by the conservation of spin of the bonding electrons. Using this methodology to diagnose ozone production in the GEOS-Chem chemical transport model, we demonstrate its advantages over the standard diagnostic. We show that the number of bonds emitted, their chemistry and lifetime, and feedbacks on OH are all important in determining the ozone production within the model and its sensitivity to changes. This insight may allow future model–model comparisons to better identify the root causes of model differences.

Enabling Energy Efficient Molecular Communication via Molecule Energy Transfer

Molecular communication via diffusion (MCvD) is inherently an energy efficient transportation paradigm, which requires no external energy during molecule propagation. Inspired by the fact that the emitted molecules have a finite probability to reach the receiver, this letter introduces an energy efficient scheme for the information molecule synthesis process of MCvD via a simultaneous molecular information and energy transfer (SMIET) relay. With this SMIET capability, the relay can decode the received information as well as generate its emission molecules using its absorbed molecules via chemical reactions. To reveal the advantages of SMIET, approximate closed-form expressions for the bit error probability and the synthesis cost of this two-hop molecular communication system are derived and then validated by particle-based simulation. Interestingly, by comparing with a conventional relay system, the SMIET relay system can be shown to achieve a lower minimum bit error probability via molecule division, and a lower synthesis cost via molecule type conversion or molecule division.

Sensor array detection of malaria volatile signature in a murine model

The relationship between malaria infection and volatile compounds has been claimed mainly on the basis that they are believed to be an attractant for mosquitoes. However, since the association of emitted molecules with diseases has been observed for many pathologies, malaria-related volatile compounds are a potential diagnostic tool. The recent confirms of this hypothesis prompts the development of sensors for an effective exploitation of these potentialities.On these bases, we investigated the alteration of volatile compounds in a malaria murine model. For the scope, the total “volatilome” of Plasmodium berghei-infected mice was compared with that of non-infected animals. Gas chromatographic analysis of the sampled air reveals the existence of a pattern of compounds that, collectively considered, detects malaria infection. Finally, an array of porphyrins functionalized quartz microbalance gas sensors was applied to sort non-infected from infected mice. The application of a classification model to the sensor data provided more than 80% of correct identification with errors confined to mice with a low parasitemia level. Noteworthy, the sensor array was trained on data collected months before to run the tests. These results provide, although limited to a murine model, a first evidence of the potentialities of gas sensor technology for malaria diagnosis.

Effective inter‐symbol interference mitigation with a limited amount of enzymes in molecular communications

AbstractIn molecular communication via diffusion (MCvD), the inter‐symbol interference (ISI) is a well‐known severe problem that deteriorates both data‐rate and link reliability. ISI mainly occurs because of the slow and highly random propagation of the messenger molecules, which causes the emitted molecules from the previous symbols to interfere with molecules from the current symbol. An effective way to mitigate the ISI is using enzymes to degrade undesired molecules. Prior work on ISI mitigation by enzymes has assumed an infinite amount of enzymes randomly distributed around the molecular channel. Taking a different approach, this paper assumes an MCvD channel with a limited amount of enzymes. The main question this paper addresses is how to deploy these enzymes in an effective structure so that ISI mitigation is maximized. To find an effective MCvD channel environment, this study considers optimization of the shape of the transmitter node, the deployment location and structure, the size of the enzyme deployed area, and the half‐lives of the enzymes. It also analyzes the dependence of the optimum size of the enzyme area on the distance and half‐life. Lastly, the paper yields interesting results regarding the actual shape of the enzyme region itself.

Performance Analysis of Diffusion-Based Molecular Communications With Memory

In this paper, the comprehensive delay and performance analyses of the $M$ -ary molecular communications with memory are presented. By taking into account any level of channel memory, the type-based and concentration-based modulation schemes are introduced and analyzed. In the type-based modulation, information symbols are encoded through different molecule types. In the concentration-based modulation, various concentration levels of one molecule type are used to encode information symbols. For both modulation schemes, the delay distributions of the molecular symbols are derived, and then, the symbol error probabilities are developed. The given distributions and the error probability expressions are validated through extensive simulation experiments. After showing that the derived expressions are valid, the performance of the modulation schemes is evaluated. The performance evaluations reveal that by properly selecting the parameters such as slot time and number of emitted molecules, the performance can be improved in both type and concentration-based molecular communication as the channel memory is increased. Furthermore, it is shown that the type-based molecular communication outperforms the concentration-based molecular communication.

Arrival modelling for molecular communication via diffusion

The arrival of molecules in molecular communication via diffusion obeys, by its nature, the binomial distribution, considering the hitting probability as the success probability. It is, however, hard to work with the binomial cumulative distribution function (CDF) when considering consecutively sent symbols as it is necessary to add the distribution. Therefore, in the literature, two approximations of the binomial distribution are used. In the present reported work, the Gaussian and Poisson approximations of the binomial model of the molecule arrival process have been analysed. Considering the distance and the number of emitted molecules, the regions in which the Poisson or Gaussian model is better in terms of root mean squared error of CDFs are investigated and the regions using numerical simulations are confirmed.

Research in Turn-on Delay of Semiconductor Lasers

This paper derived out a closed expression describing the time evolution of the carrier density within the turn-on period of a semiconductor laser, for the case that the Auger effect is considered with a term which is proportional to the cube of the carrier density. As a result, an explicit analytical expression for the turn-on delay of the diode laser has also been deduced. Semiconductor laser works by incentives, the use of semiconductor material (both using electronic) transition between can shine in a semiconductor crystal cleavage plane form two parallel reflection mirror as a mirror, and form a resonant cavity, the oscillation, feedback, produce light amplification of radiation, the output laser. Semiconductor laser advantage is small size, light weight, reliable operation, less consumption, high efficiency, etc. Nonradiative recombination (in particular, the Auger effect) and the carrier leakage over the hetero barrier have been reported theoretically as well as experimentally for 1.3 ym wavelength GaInAsP/InP crystals. Most of these works have concentrated on 1.3 pm lasers. As for 1.5-1.6 pm GaInAsP/InP crystals, the effects of the intervallic band absorption were reported, and the nonradiative recombination in relation to the carrier lifetime has been measured. Auger effect is associated with an electron energy reduced at the same time, another higher electron energy transition process. Will launch photoelectron, auger electron (cannot be explained in the photoelectric effect) to atoms and molecules becomes a phenomenon known as auger effect ion of higher order. According to this effect made auger electron spectrometer, has been on the surface physical and chemical reaction kinetics, metallurgy, electron, etc., within the territory of the high sensitivity of detection and rapid analysis. Auger effect is one of the atomic emission result in one or more other electronic (auger electron) is rather than the radiation emitted x-rays (explained in the photoelectric effect), the atoms and molecules become advanced ion physical phenomena, is associated with an electron energy reduced at the same time, the other one (or more) increased electron energy transition process. It named Auger effect because of the French Pierre Victor Auger. In 1925, Pierre Victor Auger on the analysis of the Wilson cloud chamber found after the results of the experiment. Experiments using high energy X-rays to electronic gases, optoelectronics and observed. For electronic measurement shows that the trajectory has nothing to do with the frequency of the photon, this suggests that the mechanism is the atomic internal electronic ionization energy exchange or no radiation transition. Use of basic

크라이오펌프 알곤 회복시간 측정과 알곤 불안정성 분석

크라이오펌프는 응축과 흡착을 통해 기체를 배기하므로 극저온 표면 온도와 증기압이 배기성능에 큰 영향을 미친다. 어느 부분의 온도가 어중간하면 한번 응축했던 기체분자가 방출과 재응축 또는 재흡착을 반복하여 진공용기 압력이 어느 선 이하로 떨어지지 않고 심한 요동을 나타낸다. 어떤 기체나 특정 온도 범위에서 이런 불안정성이 나타날 수 있지만 크라이오펌프를 많이 사용하는 스퍼터 장치의 공정기체인 알곤을 배기할 때 불안정성이 발생하는 것은 좋지 않다. 본 논문에서는 알곤 회복시간 측정실험을 수행하면서 크라이오펌프의 알곤 불안정성의 원인과 대책을 분석했다. Cryopump removes gas molecules by condensation and adsorption. Therefore, cryo-surface temperature and corresponding vapor pressure influence directly the pumping performance. If the surface temperature of any part is neither low nor high, there occurs the desorption of gas molecules condensed or adsorbed, and the emitted molecules can be captured again, which leads to a time-consuming and fluctuating change of the pressure. Though every gas can show such a pressure instability at a specified temperature range, the instability generated in a sputter system using Ar as a working gas and operating with a cryopump is especially undesirable. In this paper the cause of the argon instability is analyzed and corrective is provided through the measurement of the Ar recovery time.

Atom and molecule emission caused by ion impact into a frozen oxygen target: Role of rovibrational excitation

Translational energy distributions of particles sputtered by 750eV Ne+ ion impact into a cryogenic O2 target are studied using molecular-dynamics simulation. When comparing the energy distribution of emitted molecules to a Thompson distribution, good agreement can only be found for energies E with U<E<D, where U is the surface binding and D the dissociation energy of oxygen molecules. At smaller energies, a strong spike contribution enhances the spectrum. At higher energies (≳0.5eV), simulation shows a deficiency in sputtered molecules compared to the Thompson distribution; we show that this can be traced back to the decay of highly rovibrationally excited molecules after emission. Around 2% of the sputtered particles consist of radicals (atomic O). These originate from direct projectile-molecule collisions; they are emitted early in the collision cascade and feature a strong high-energy contribution.

SiO gas emission and triple line dynamics of small silicon droplets on quartz

Periodic spreading motions of small silicon melt droplets on quartz (SiO2) have been observed by a video microscope and mass signals of the emitted molecules were thereby recorded simultaneously. The triple line of the droplet expands slowly and retracts spontaneously. The intensity of a mass signal at 44amu is clearly correlated to these changes of the triple line circumference and seems to stem from SiO molecules that are emitted as reaction products from the vicinity of the triple line. The velocity of the triple line has been studied as a function of temperature. Results can be described by an Arrhenius-like behavior with an activation energy of 111±14kJmol−1. For a detailed analysis of the experimental results a model for the oxygen transport through the interfaces and its diffusion through the droplet is presented. It can be used to predict etch profiles on the substrate in the vicinity of the triple line by using well known thermophysical data of silicon and quartz. These theoretical profiles are in good agreement with the experimental profiles that have been measured ex-situ by atomic force microscopy and provide a value for the diffusion constant of D=3.3×10−4cm2s−1 for oxygen in liquid silicon which fits well with the values used in crystal growth simulations.

Calcium-activated chloride channels in the apical region of mouse vomeronasal sensory neurons

The rodent vomeronasal organ plays a crucial role in several social behaviors. Detection of pheromones or other emitted signaling molecules occurs in the dendritic microvilli of vomeronasal sensory neurons, where the binding of molecules to vomeronasal receptors leads to the influx of sodium and calcium ions mainly through the transient receptor potential canonical 2 (TRPC2) channel. To investigate the physiological role played by the increase in intracellular calcium concentration in the apical region of these neurons, we produced localized, rapid, and reproducible increases in calcium concentration with flash photolysis of caged calcium and measured calcium-activated currents with the whole cell voltage-clamp technique. On average, a large inward calcium-activated current of −261 pA was measured at −50 mV, rising with a time constant of 13 ms. Ion substitution experiments showed that this current is anion selective. Moreover, the chloride channel blockers niflumic acid and 4,4′-diisothiocyanatostilbene-2,2′-disulfonic acid partially inhibited the calcium-activated current. These results directly demonstrate that a large chloride current can be activated by calcium in the apical region of mouse vomeronasal sensory neurons. Furthermore, we showed by immunohistochemistry that the calcium-activated chloride channels TMEM16A/anoctamin1 and TMEM16B/anoctamin2 are present in the apical layer of the vomeronasal epithelium, where they largely colocalize with the TRPC2 transduction channel. Immunocytochemistry on isolated vomeronasal sensory neurons showed that TMEM16A and TMEM16B coexpress in the neuronal microvilli. Therefore, we conclude that microvilli of mouse vomeronasal sensory neurons have a high density of calcium-activated chloride channels that may play an important role in vomeronasal transduction.

Strongly reduced fragmentation and soft emission processes in sputtered ion formation from amino acid films under large Arn+ (n ≤ 2200) cluster ion bombardment

The analysis of organic and biological substances by secondary-ion mass spectrometry (SIMS) has greatly benefited from the use of cluster ions as primary bombarding species. Thereby, depth profiling and three-dimensional (3D) imaging of such systems became feasible. Large Ar(n)(+) cluster ions may constitute a further improvement in this direction. To explore this option, size-selected Ar(n)(+) cluster ions with 300 ≤ n ≤ 2200 (bombarding energies 5.5 and 11 keV) were used to investigate the emission of positive secondary ions from four amino acid specimens (arginine, glycine, phenylalanine, and tyrosine) by time-of-flight SIMS. For all cluster sizes, the protonated molecule of the respective amino acid is observed in the mass spectra. With increasing cluster size the number of fragment ions decreases strongly in relation to the intact molecules, to the extent that the fraction of fragment ions amounts to less than 10% in some cases. Such 'soft' emission processes also lead the ejection of dimers and even multimers of the amino acid molecules. In the case of the phenylalanine, secondary ion species composed of up to at least seven phenylalanine moieties were observed. Tentatively, the ionization probability of the emitted molecules is envisaged to depend on the presence of free protons in the emission zone. Their number can be expected to decrease concurrently with the decreasing amount of fragmentation for large Ar(n)(+) cluster ions (i.e. for low energies per cluster atom).

Molecular dynamics modeling of chemical erosion of hydrocarbon films

The erosion of hydrocarbon layers at room temperature due to co-bombardment of energetic (150 eV) argon ions and thermal atomic hydrogen is investigated. Using molecular dynamics simulations a mechanism has been identified explaining the experimentally observed increase of the physical sputtering yield. The surface erosion process is primarily a physical sputtering mechanism, enhanced by the screening effect of hydrogen atoms. This causes emission of unsaturated hydrocarbon molecules from the surface within a few picoseconds after ion impact and a superthermal energy distribution of the emitted molecules.