Significance Interactions between proteins normally depend on a range of noncovalent contacts. Under challenging conditions, such as with mechanical force or over long time periods, noncovalent interactions break. Unbreakable protein–protein interactions, linked by covalent bonding, provide many opportunities for robust connection of molecular building blocks, including for biomaterials, enzymes, and vaccines. When evaluating unbreakable interactions, it is important to consider whether reaction happens quickly even at low concentrations. Here we establish a genetically encoded peptide that reacts with its genetically encoded protein partner with a speed close to the limit set by diffusion. We apply a range of biophysical methods to understand the dynamics required for this interaction, demonstrating applicability to rapid and specific detection in a range of species. Much of life’s complexity depends upon contacts between proteins with precise affinity and specificity. The successful application of engineered proteins often depends on high-stability binding to their target. In recent years, various approaches have enabled proteins to form irreversible covalent interactions with protein targets. However, the rate of such reactions is a major limitation to their use. Infinite affinity refers to the ideal where such covalent interaction occurs at the diffusion limit. Prototypes of infinite affinity pairs have been achieved using nonnatural reactive groups. After library-based evolution and rational design, here we establish a peptide–protein pair composed of the regular 20 amino acids that link together through an amide bond at a rate approaching the diffusion limit. Reaction occurs in a few minutes with both partners at low nanomolar concentration. Stopped flow fluorimetry illuminated the conformational dynamics involved in docking and reaction. Hydrogen–deuterium exchange mass spectrometry gave insight into the conformational flexibility of this split protein and the process of enhancing its reaction rate. We applied this reactive pair for specific labeling of a plasma membrane target in 1 min on live mammalian cells. Sensitive and specific detection was also confirmed by Western blot in a range of model organisms. The peptide–protein pair allowed reconstitution of a critical mechanotransmitter in the cytosol of mammalian cells, restoring cell adhesion and migration. This simple genetic encoding for rapid irreversible reaction should provide diverse opportunities to enhance protein function by rapid detection, stable anchoring, and multiplexing of protein functionality.
In this paper, the nonlinear coupled system of partial differential equations named the Wu–Zhang system investigated by applying the new auxiliary equation method. The Wu–Zhang system help us to investigate the various nonlinear wave propagation phenomena physically including the width and amplitude of solitons, physically form of shock, traveling and solitary wave structures in fiber optics, fluid dynamics, plasma physics, nonlinear optics, these nonlinear wave equations play significant role in these phenomenas. In this regard, the dispersive long wave is described by the Wu–Zhang system, from which a number of solitons and solitary wave structure are formally extracted as an accomplishment. On the basis of the computational program Mathematica, soliton and many other solitary wave results have been obtained with the ability to use an analytical approach. Consequently, various solutions in solitons and solitary waves are generated in rational, trigonometric, and hyperbolic functions and displayed within contour, two–dimension and three–dimension plotting by using the numerical simulation. The soliton solutions are obtained including bright and dark solitons, anti–kink wave solitons, peakon bright and dark solitons, kink wave soliton, periodic wave solitons, solitary wave structure, and other mixed solitons. In order to comprehend the significance of investigating various nonlinear wave phenomena in engineering and science, including soliton theory, nonlinear optics, fluid mechanics, material energy, water wave mechanics, mathematical physics, signal transmission, and optical fibers, all research outcomes are required. With precise analytical results, shed light that the applied approach to be more powerful, dependable, and accurate.
Nonlinear evolution equations (NLEEs) have a wide range of applications in various fields, including physics, engineering, biology, economics, and more. These equations are used to describe complex systems that change over time, where the state or behavior of the system not only depends on the current situation, but may also be related to the past. A deep understanding of the solutions to NLEEs is of great significance for predicting and controlling the behavior of complex systems. The (3 + 1)-dimensional Kadomtsev-Petviashvili-Boussinesq-like (KPB-like) equation represents a partial differential equation that describes nonlinear wave phenomena in multi-dimensional spaces. This model is commonly employed in fields such as fluid dynamics, plasma physics, and nonlinear optics to study wave behaviors. This paper investigates the KPB-like equations, which have meaningful physical implications in describing nonlinear wave phenomena. Hirota bilinear method is employed to derive the bilinear form for the KPB-like equation and 1-soliton, 2-soliton, lump, and travelling wave solutions are studied to this kind of nonlinear model. In addition, the chaotic behaviors of soliton and lump solutions are explored via applying the Duffing chaotic system. To have a better understanding of dynamic structures, 3D, line, density and contour map plots of begotten results are displayed. Our results indicate the directness and effectiveness of the applied method for analyzing high-dimensional differential equations that arise in nonlinear science.
Muhammad Bilal Riaz, Adil Jhangeer, Syeda Sarwat Kazmi
This article explores the examination of the widely employed zig-zag optical lattice model for cold bosonic atoms, which is commonly utilized to depict nonlinear wave in fluid mechanics and plasma physics. The focus is on obtaining soliton solutions in optics and investigating their physical properties. A wave transformation is initially applied to convert a partial differential equation (PDE) into an ordinary differential equation (ODE). Soliton solutions are subsequently obtained through the application of two distinct methods, namely the generalized logistic equation method and the Sardar sub-equation method. These solutions include bright, dark, combined dark-bright, chirped type solitons, bell-shaped, periodic, W-shape, and kink solitons. In this paper, the solutions derived from two analytical approaches were compared to enhance the understanding of the behavior of the discussed nonlinear model. The obtained solutions have significant implications across various fields such as plasma physics, fluid dynamics, optics, and communication technology. Furthermore, 3D and 2D graphs are generated to depict the physical phenomena of the derived solutions by assigning appropriate constant parameters. The qualitative evaluation of the undisturbed planar system involves the analysis of phase portraits within bifurcation theory. Subsequently, the introduction of an outward force is carried out to induce disruption, and chaotic phenomena are unveiled. The detection of chaotic trajectory in the perturbed system is achieved through 3D plots, 2D plots, time scale plots, and Lyapunov exponents. Furthermore, stability analysis of the examined model is addressed under distinct initial conditions. Finally, the sensitivity assessment of the model under consideration is carried out using the Runge–Kutta method. The results of this study are innovative and have not been previously investigated for the system under consideration. The results obtained underscore the reliability, simplicity, and effectiveness of these techniques in analyzing a variety of nonlinear models found in mathematical physics and engineering disciplines.
This study explores the fractional form of modified Korteweg-de Vries-Kadomtsev-Petviashvili equation. This equation offers the physical description of how waves propagate and explains how nonlinearity and dispersion may lead to complex and fascinating wave phenomena arising in the diversity of fields like optical fibers, fluid dynamics, plasma waves, and shallow water waves. A variety of solutions in different shapes like bright, dark, singular, and combo solitary wave solutions have been extracted. Two recently developed integration tools known as generalized Arnous method and enhanced modified extended tanh-expansion method have been applied to secure the wave structures. Moreover, the physical significance of obtained solutions is meticulously analyzed by presenting a variety of graphs that illustrate the behaviour of the solutions for specific parameter values and a comprehensive investigation into the influence of the nonlinear parameter on the propagation of the solitary wave have been observed. Further, the governing equation is discussed for the qualitative analysis by the assistance of the Galilean transformation. Chaotic behavior is investigated by introducing a perturbed term in the dynamical system and presenting various analyses, including Poincare maps, time series, 2-dimensional 3-dimensional phase portraits. Moreover, chaotic attractor and sensitivity analysis are also observed. Our findings affirm the reliability of the applied techniques and suggest its potential application in future endeavours to uncover diverse and novel soliton solutions for other nonlinear evolution equations encountered in the realms of mathematical physics and engineering.
The present work develops a full particle-based model that couples the particle-in-cell plus Monte Carlo collision (PIC-MCC) simulation for plasma dynamics and the direct simulation Monte Carlo (DSMC) method for neutral dynamics in a synergistic iterative manner. This new model overcomes the slow convergence issue in the conventional direct coupling approach caused by the disparity of the time scales between the plasma and neutral dynamics. This model is applied to simulate the behavior of xenon (Xe) and its potential alternatives, krypton (Kr) and argon (Ar), in the discharge chamber of a miniature direct current (DC) ion thruster. The results show that a stable discharge is difficult to achieve for Kr and Ar under the operating conditions optimal for Xe. While increasing the discharge voltage can effectively improve the stability of discharge for Kr and Ar, other common strategies such as changing the magnetic field strength, propellant flow rate, and cathode current are not successful. The propellant utilization efficiency and discharge efficiency are affected by both discharge voltage and propellant flow rate. A maximum utilization efficiency and an optimal discharge efficiency are observed for all three propellants, with the values decreasing in the order of Xe, Kr, and Ar. Moreover, the discharge voltage corresponding to the optimal efficiency is inversely proportional to the square root of the propellant mass, indicating that the ion diffusional loss to the wall, rather than the ionization energy, is the dominant factor affecting the discharge performance for alternative propellants in a miniature DC thruster.
Novel analytical and numerical solutions to the (un)damped Helmholtz-Duffing (H-D) equation for arbitrary initial conditions are derived. Both the analytical (for undamped case) and approximate analytical (for damped case) solutions, are obtained in the form of Weierstrass elliptic function. Also, the soliton solution to the undamped H-D equation is obtained in detail. The semi-analytical solution to the damped H-D equation is compared to the fourth-order Runge–Kutta (RK4) numerical solution. The obtained solution shows an excellent agreement with the numerical simulations but sometimes (according to the values of initial conditions) not on all time interval. Thus, the moving boundary method is utilized to improve the semi-analytical solution. It is found that the improved solution gives good results with high accuracy in the whole time domain. As a realistic application, the obtained solutions are applied to the study of nonlinear oscillations in an electronegative non-Maxwellian dusty plasma. Finally, we conclude that our novel solutions could help us to understand the dynamics of various nonlinear oscillations in engineering and in different branches of sciences such as oscillations in different plasma models.
This work presents an experimental study of a nanosecond repetitively pulsed dielectric barrier discharge interacting with a transient laminar flame propagating in a channel of height near the quenching distance of the flame. The discharge and the flame are of comparable size, and the discharge is favoured at a location where it is coupled with the reaction zone and burnt gas. The primary goal is to determine how the discharge evolves on the time scale of the flame passage, with the evolution driven by the changing gas state produced by the moving flame front. This work complements the large body of work investigating the effect of plasma to modify flame dynamics, by considering the other side of the interaction (how the discharge is modified by the flame). The hot gas produced by the combustion had a strong effect on the discharge, with the discharge preferentially forming in the region of hot combustion products. The per-pulse energy deposited by the discharge was measured and found to increase with the size of the discharge region and applied voltage. The pulse repetition frequency did not have a direct impact on the per-pulse energy, but did have an effect on the morphology and size of the discharge region. Two distinct discharge regimes were observed: uniform and filamentary (microdischarges). Higher pulse repetition frequencies and faster-cooling combustion products were more likely to transition to the filamentary regime, while lower frequencies and slower-cooling combustion products maintained a uniform regime for the entirety of the time the discharge was active. This regime transition was influenced by the ratio of the time scale of fluid motion to the pulse repetition rate (with no noticeable impact caused by the reduced electric field), with the filamentary regime preferentially observed in situations where this ratio was small. This work demonstrates the importance of considering how the discharge properties will change due to combustion processes in applications utilizing plasma assistance for transient combustion systems.
A new combined use of dynamic mode decomposition algorithms is proposed, which is suitable for the analysis of spatiotemporal data from experiments with few observation points, unlike computational fluid dynamics with many observation points. The method was applied to our data from a plasma turbulence experiment. As a result, we succeeded in constructing a quite accurate model for our training data and it made progress in predictive performance as well. In addition, modal patterns from the longer-term analysis help to understand the underlying mechanism more clearly, which is demonstrated in the case of plasma streamer structure. This method is expected to be a powerful tool for the data-driven construction of a reduced-order model and a predictor in plasma turbulence research and also any nonlinear dynamics researches of other applied physics fields.
This study is essentially an attempt to investigate the effects of trapped ions concentration on the dynamics of dust‐acoustic (DA) periodic travelling waves in dusty plasmas, which consist of dust fluid, trapped ions, and Maxwellian electrons. The physical nature of DA solitary and periodic travelling waves in the plasma model at hand is governed by a Korteweg‐de Vries (KdV) type equation. Bifurcation analysis of the Hamiltonian system is applied to demonstrate the probability of the presence of DA solitary and periodic travelling waves for the KdV type equation. A careful discussion illustrates that non‐linear phenomena of DA solitary and periodic travelling waves are modified due to the presence of the trapped ions concentration. It is found numerically that the negative amplitude of DA periodic travelling waves is amplified, as the trapping parameter that determines the number of the trapped ions is increased. The numerical simulation gives rise to significant highlights on the dynamics of solitary and periodic travelling waves in astrophysical environments such as Saturn's moon Enceladus.
In order to make it possible to control the plasma state and predict the regime transitions via coupling optical and electrical diagnosis in aerospace engineering, we have experimentally investigated the regime transitions under 0.1-15 kPa with an input discharge power of 0-25 W in a parallel-plate electrode configuration. An abnormal glow discharge (AGD), filamentary discharge (FD), and arc discharge (AD) are distinguished using the voltage-current characteristics under different gas pressures. The electron excitation temperature (Te), electron density (Ne), spatial resolutions of Te and Ne, and ionization degree are obtained via optical emission spectroscopy to reveal the transition mechanisms. Thermal instability, characterized by Te, plays a dominant role during the transition from an AGD to an FD. The conclusions are supported by analysis of ionization degree, whereas electronic instability becomes the dominant mechanism in the transition from an FD to an AD. This is related to collision kinetics because of an observed drop in Ne, which is verified by the spatial resolution as well. Moreover, planar laser-induced fluorescence provides further insight into the instantaneous location and relative number variation of Ar 1s5 metastable atoms, which agrees well with the plasma properties mentioned above. In addition, a pressure of 1 kPa with a maximum input power of 17.5 W are specified as suitable working parameters for further study when applied to microthrusters due to its higher Ne and better stability.
This study focuses on a magnetically stabilized gliding arc (MGA) plasma. Two fully coupled flow-plasma models (in 3D and 2D) are presented. The 3D model is applied to compare the arc dynamics of the MGA with a traditional gas-driven gliding arc. The 2D model is used for a detailed parametric study on the effect of the external magnetic field. The results show that the relative velocity between the plasma and feed gas is generated due to the Lorentz force, which can increase the plasma-treated gas fraction. The magnetic field also helps to decrease the gas temperature by enhancing heat transfer and to increase the electron number density. This work shows the potential of an external magnetic field to control the gliding arc behavior, for enhanced gas conversion at low gas flow rates.
The optimal use of atmospheric pressure plasma jets (APPJs) for treatment of surfaces—inorganic, organic and liquid—depends on being able to control the flow of plasma-generated reactive species onto the surface. The typical APPJ is a rare gas mixture (RGM) flowed through a tube to which voltage is applied, producing an RGM plasma plume that extends into the ambient air. The RGM plasma plume is guided by a surrounding shroud of air due to the higher electric field required for an ionization wave (IW) to propagate into the air. The mixing of the ambient air with the RGM plasma plume then determines the production of reactive oxygen and nitrogen species (RONS). The APPJ is usually oriented perpendicular to the surface being treated. However, the angle of the APPJ with respect to the surface may be a method to control the production of reactive species to the surface due to the change in APPJ propagation properties and the resulting gas dynamics. In this paper, we discuss results from computational and experimental investigations addressing two points—propagation of IWs in APPJs with and without a guiding gas shroud as a function of angle of the APPJ with respect to the surface; and the use of this angle to control plasma activation of thin water layers. We found that APPJs propagating out of the plasma tube into a same-gas environment lack any of the directional properties of shroud-guided jets, and largely follow electric field lines as the angle of the plasma tube is changed. Guided APPJs propagate coaxially with the tube as the angle is changed, and turn perpendicularly towards the surface only a few mm above the surface. The angle of the APPJ produces different gas dynamic distributions, which enable some degree of control over the content of RONS transferred to thin water layers.
Pulsed nanosecond discharges at atmospheric pressure produce non-thermal plasmas that can be used in various applications. The dynamics of such discharges are highly dependent on experimental conditions, particularly the propagation medium. In this study, pulsed nanosecond discharges in air in-contact with deionized water are investigated, and the dynamics of plasma emission are studied using an ultrafast imaging technique. Depending on the magnitude of the applied voltage, two discharge modes are observed: (i) highly-organized filaments and (ii) intense and less-organized plasma filaments that superimpose to the organized ones. Based on the acquired 1 ns resolved images, the highly-organized filaments can be considered as plasma dots that propagate at the water surface with velocities in the order of hundreds of km s−1. Detailed analyses of the dots number, by imaging, and of the discharge properties, by current–voltage characteristics, reveal that the charge of each dot is constant (3–5 nC), irrespective of the experimental conditions. After being compared with the plasma bullets, usually produced by jets, the analyzed dots are proposed as plasma quanta.
The production of negative ions is of significant interest for applications including mass spectrometry, particle acceleration, material surface processing, and neutral beam injection for magnetic confinement fusion. Methods to improve the efficiency of the surface production of negative ions, without the use of low work function metals, are of interest for mitigating the complex engineering challenges these materials introduce. In this study we investigate the production of negative ions by doping diamond with nitrogen. Negatively biased (−20 V or −130 V), nitrogen doped micro-crystalline diamond films are introduced to a low pressure deuterium plasma (helicon source operated in capacitive mode, 2 Pa, 26 W) and negative ion energy distribution functions are measured via mass spectrometry with respect to the surface temperature (30 °C to 750 °C) and dopant concentration. The results suggest that nitrogen doping has little influence on the yield when the sample is biased at −130 V, but when a relatively small bias voltage of −20 V is applied the yield is increased by a factor of 2 above that of un-doped diamond when its temperature reaches 550 °C. The doping of diamond with nitrogen is a new method for controlling the surface production of negative ions, which continues to be of significant interest for a wide variety of practical applications.
We propose a theoretical ground for emissive capacitively coupled radio-frequency plasma sheath under low pressure. The rf sheath is assumed to be collisionless, and oscillates with external source. A known sinusoidal voltage instead of current is taken as prerequisite to derive sheath dynamics. Kinetic studies are performed to determine mean wall potential as a function of secondary emission coefficient and applied voltage amplitude, with which the complete mean DC sheath is resolved. Analytical analyses under homogeneous model and numerical analyses under inhomogeneous model are conducted to deduce real time sheath properties including space potential, capacitance and stochastic heating. Obtained results are validated by a continuum kinetic simulation without ionization. The influences of collisionality and ionization induced by secondary electrons are elucidated with a particle-in-cell simulation, which further formalizes proposed theories and inspires future works.
Atmospheric rotating gliding arc (RGA) plasma is proposed as a facile, scalable and catalyst-free approach to synthesize hydrogen (H2) and graphene sheets from coalbed methane (CBM). CH4 is used as a CBM surrogate. Based on previous investigation of discharge properties, product distribution and energy efficiency, the operating parameters such as CH4 concentration, applied voltage and gas flow rate can effectively affect the CH4 conversion rate, selectivity of H2 and properties of generated carbon solid. Nevertheless, the basic properties of RGA plasma and its role in CH4 conversion are scarcely touched. In present work, a 3D RGA model, with a detailed non-equilibrium CH4/Ar plasma chemistry, is developed to validate with the previous experiments of CBM conversion, especially aiming at distribution of H2 and other gas products. Our results demonstrate that dynamics of RGA is derived from the joint effect of electron convection, electron migration and electron diffusion, and is prominently determined by the variation of gas flow rate and applied voltage. Subsequently, a combined experimental and chemical kinetical simulation is performed to analyze the selectivity of gas products in RGA reaction, with the consideration of the formation and loss pathways of crucial targeted substances (such as CH4, C2H2, H2 and H radicals) and corresponding contribution rates. Additionally, the effects of operating conditions on the properties of solid products are investigated by scanning electron microscopy (SEM) and Raman spectroscopy. The results show that increasing the applied voltage and decreasing CH4 concentration will change the solid carbon from initial spherical structure into a folded multi-layer graphene sheets, while the size of graphene sheets is slightly affected by the change of gas flow rate.