Intermolecular Collisions Research Articles

Molecular dynamics study on the conversion mechanism between momentum and energy components in gas-surface interaction

With the rapid development of micro-nano technology and aerospace technology, researches related to rarefied gas flows have received more and more attention. For micro-/nanoscale systems and spacecraft in a rarefied environment, the reduction in the frequency of intermolecular collisions in the flow field makes the interaction between gas molecules and the solid surface develop into a major factor affecting the flow state. However, the mechanism of gas-surface interaction in rarefied flow has not been fully revealed due to its microscopic nature and physical complexity, and the existing simulation methods cannot accurately reflect the effect of this process on the flow state. In this paper, molecular beam method is adopted to simulate the scattering process of argon molecules on platinum surface, and the impacts of incident velocity, angle and wall roughness on the momentum and energy conversion mechanism are explored. By simulating the molecular scattering process under the two incident angles of <inline-formula><tex-math id="M3">\begin{document}$ 5^{\circ} $\end{document}</tex-math><alternatives><graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="2-20201192_M3.jpg"/><graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="2-20201192_M3.png"/></alternatives></inline-formula> and <inline-formula><tex-math id="M4">\begin{document}$ 75^{\circ}$\end{document}</tex-math><alternatives><graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="2-20201192_M4.jpg"/><graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="2-20201192_M4.png"/></alternatives></inline-formula>, the following conclusions are obtained. When colliding with the wall at an angle close to vertical, both components of the momentum of the gas molecules are lost. The normal energy transfers to the tangential direction, and when the molecular velocity is not less than 2.0, the transfer rate is not significantly affected by the incident energy of the molecule and the surface roughness. The total energy loss of gas molecules after scattering becomes significant with the increase of incident velocity, and it is not sensitive to changes of surface roughness. When the gas molecules are incident at <inline-formula><tex-math id="M5">\begin{document}$ 75^{\circ} $\end{document}</tex-math><alternatives><graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="2-20201192_M5.jpg"/><graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="2-20201192_M5.png"/></alternatives></inline-formula>, the roughness of the surface has a significant impact on the conversion mechanism of molecular momentum and energy. After colliding with a smooth wall, the momentum and energy values of the gas molecules remain basically unchanged, only the direction of the momentum is reversed. The motion state of molecules is close to the mirror reflection, and the conversion between momentum and energy components is not obvious. The introduction of roughness enhances the degree of accommodation between gas molecules and metal surface, and promotes the transfer of molecular tangential momentum and kinetic energy to the normal direction. When incident at a large polar angle, as opposed to the small-angle cases, the total energy loss of molecules is not sensitive to changes of incident velocity, it goes up significantly with the surface roughness increasing. The research in this article not only explores the gas-surface interaction mechanism, but also provides a useful reference for the high-fidelity simulation of rare gas flow and the development of appropriate gas-surface interaction models.

On the conservative property of particle-based Fokker–Planck method for rarefied gas flows

The Fokker–Planck-type approximation of the full Boltzmann equation has aroused intense research interest due to its potential for the stochastic particle simulation of rarefied gas flows. The ellipsoidal statistical Fokker–Planck (ES-FP) model treats the evolution of molecular velocity as a continuous stochastic process, and it satisfies the basic requirements for a proper gas-kinetic model including the H-theorem and an adjustable Prandtl number. The ES-FP model can be numerically implemented with computational particles in a Monte Carlo manner. Two different particle ES-FP schemes are presented. The first scheme utilizes the exact stochastic integral solution of the Langevin equations corresponding to the ES-FP equation and couples free-molecular moves and intermolecular collisions. The second scheme is designed to enforce the conservation of momentum and energy during the numerical simulation based on the decoupled algorithm and the analysis of the specific conditions for the conservative property. Numerical tests are conducted to demonstrate the performances of different schemes. In the simulation of a homogeneous gas system, the ES-FP scheme without enforcement of conservation leads to unphysical variation in the momentum and loss in energy, whereas the conservative ES-FP scheme strictly maintains the momentum and energy of the system. For the Mach 6 flows over the leading edge of a flat plate and over a round-nosed blunt body, the non-conservative ES-FP scheme underestimates the shock angle and the shock standoff distance, makes inaccurate predictions of aerodynamic force and heating, and produces low-temperature anomalies in front of the shock waves. In comparison with the results given by the direct simulation Monte Carlo method, the results of the conservative ES-FP simulations show satisfactory accuracy for the flow fields as well as the distributions of pressure, friction, and heat flux on the wall surfaces.

Double-Stranded DNA Matrix for Photosensitization Switching

Photosensitization, originated from the activation of triplet states, is the basis of many photodynamic applications, but often competes with a series of nonradiative processes. Herein, we communic...

Coupling the molecular motion and collision processes in numerical simulations

The molecular motion and collision processes are usually decoupled in the traditional molecular simulations, where the simulation process is divided into a series of time steps and the two processes are sequentially executed during each time step. The numerical errors in transport properties and flow-field solutions will become noticeable when the time step is much larger than the mean time interval between intermolecular collisions. The limitation of using small time step can be relaxed for multiscale problems by using coupled algorithm that allows the molecular motions and collisions to happen simultaneously. This coupling idea was proposed in the DSBGK method that however focused on the discussion of variance reduction. The same coupling idea has been also implemented in the recent USP-ESBGK method that focused on the advantage of using a coupled algorithm. As this is a significant advancement in particle simulation, we present the similarity analysis between the two methods in the coupling spirit as well as the difference in the detailed implementations.

Study of intermolecular interactions in the binary mixtures containing cyclic ethers and benzyl amine at different temperatures

Densities and speed of sound have been reported for the binary mixtures containing benzyl amine and cyclic ethers (1,3-dioxolane, 1,4-dioxane, THF, 2-MTHF) at three different temperatures ( T = 303.15 K, 308.15 K and 313.15 K) and at atmospheric pressure. The experimental data of densities and speed of sound has been further utilised to calculate excess molar volume ( V m E ) and excess molar isentropic compression ( K S . m E ). The excess properties have been fitted to Redlich–Kister equation. Further, theoretical results have also been discussed by using Prigogine–Flory–Patterson (PFP) theory, Intermolecular free length theory (FLT) and collision frequency theory (CFT). FTIR studies have also been added to justify the results.

The structure of shock waves propagating through heavy noble gases: temperature dependence

The structure of planar shock waves propagating through argon, xenon, and krypton is calculated using the direct simulation Monte Carlo method for Mach numbers 2, 5, and 10. The upstream temperature considered in the present paper varies from 30 to 8000 K, depending on the gas species and Mach number. Both quantum and classical approaches to the intermolecular collisions based on ab initio potential are used. The distributions of density and temperature inside the shock wave are reported. The density slope is calculated as a function of the upstream temperature and Mach number with the numerical error less than $$0.5\%$$ . The dependence of the density slopes on the upstream temperature is studied. It is shown that the slope behaviors of the heavy gases are qualitatively similar to each other, but they are completely different from those for helium.

Molecular dynamics study on scattering characteristics of nitrogen molecules from platinum surface by molecular beam method

Rarefied gas flow has received wide attention due to the booming of micro/nano-electromechanical systems and aerospace engineering. Under such rarefied conditions, the frequency of intermolecular collisions is sharply reduced, so the impacts of interactions between gas molecules and the wall surface on flow states become non-negligible. Owing to the complexity of theoretical research and the poor reproducibility of experimentation, molecular dynamics simulation has developed into an effective method to study the interplay between gases and solid surfaces. In this study, molecular dynamics simulations on the scattering process of nitrogen molecules from a platinum surface are conducted in a three-dimensional system. The dependences of scattering angle distributions and momentum/energy variations on the incident velocity, angles, and surface roughness are obtained. The results of this paper are not only an attempt to reveal the mechanisms of gas–surface interactions but can also be used as necessary reference data for the development of appropriate gas–surface interaction models.

Thermosensitive nanocomposite gel loaded zinc phthalocyanine for photodynamic therapy

The purpose of this work was first to propose a thermosensitive hydrogel incorporating Zn phthalocyanine loaded mixed micelles for drug delivery. The mixed micelles was prepared easily by dialysis method and the thermosensitive hydrogel was prepared by “cold method” using Pluronic F127 as hydrogel matrix. The properties of sol and gel transition caused by F127 temperature response enables the drug loaded micellar hydrogel(DLM-Gel) to gel in situ gelification upon injection providing long-term retention within the tumor. Sodium deoxycholate (SDC) and D-alpha tocopheryl polyethylene glycol succinate (TPGS) were utilized as micelles materials. Micelles resulted in a mean particle size around 106 nm, spherical morphology and loading efficiency up to 92%. The DLM-Gel displayed a three-dimensional network structure, which helps to stabilize ZnPc molecules because it can reduce the rotation and intermolecular collision of the ZnPc molecules, leading to the enhancement of fluorescence intensity and 1O2 generation. The production of 1O2 from DLM-Gel was more efficient than micelles under the same laser irradiation condition. The DLM-Gel was more photostable than free ZnPc and micelles in the timescale typically used in photodynamic therapy(PDT), only a small photobleaching event(16.91%) was observed after 20 min of light irradiation. Rheology studies demonstrated that DLM-Gel has the potential to be injected at room temperature and to adapt to the deformation of surrounding tissues during human motion. The in vitro drug release studies of DLM-Gel demonstrated slower drug release than mixed micelles. Phototoxicity experiments in A549 cells showed that DLM-Gel had significante toxicity.Therefore the injective micellar hydrogels is a potential drug delivery system for PDT.

Sublimation and deposition in gaseous mixtures

The sublimation and deposition behaviors of the Helium-Argon mixture is analyzed numerically in the temperature range where Helium is only in gaseous state while Argon can sublimate and deposit on its own solid phase. The McCormack model is implemented to model the Boltzmann collision term. Three kinds of potential are used for simulation of the intermolecular collisions: Hard Sphere, Lennard-Jones potential, and ab initio. The matrices of the kinetic coefficients have been obtained for different values of the rarefaction parameters and molar fraction of non-sublimating gas. The influence of the intermolecular potential on the kinetic coefficients as well as on the gas macroscopic profiles has been analyzed.

An improved chemical reaction optimization algorithm for solving the shortest common supersequence problem

The shortest common supersequence (SCS) problem is a classical NP-hard problem, which is normally solved by heuristic algorithms. One important heuristic that is inspired by the process of chemical reactions in nature is the chemical reaction optimization (CRO) and its algorithm known as CRO_SCS. In this paper we propose a novel CRO algorithm, dubbed IMCRO, to solve the SCS problem efficiently. Two new operators are introduced in two of the four reactions of the CRO: a new circular shift operator is added to the decomposition reaction, and a new two-step crossover operator is included in the inter-molecular ineffective collision reaction. Experimental results show that IMCRO achieves better performance on random and real sequences than well-known heuristic algorithms such as the ant colony optimization, deposition and reduction, enhanced beam search, and CRO_SCS. Additionally, it outperforms its baseline CRO_SCS for DNA instances, averaging a SCS length reduction of 1.02, with a maximum length reduction of up to 2.1.

The influence of collisions and thermal escape in Callisto's atmosphere

A molecular kinetic method is applied to simulate intermolecular collisions and thermal escape in single and multi-component Callisto-like atmospheres. The 1D atmospheres at noon and midnight are composed of radiolytically produced volatiles (CO2, O2, H2) which are assumed to permeate the regolith and thermally desorb. The escaping H2 is shown to have a critical effect on the atmosphere as it is the dominant collision partner, it cools the background gases producing non-isothermal profiles, and its diffusion through the O2 and CO2 affects the vertical structure. Therefore, at the densities inferred from observations, molecular collisions must be included when describing the structure of and escape from Callisto's atmosphere.

The state of coating–substrate interfacial region formed during TiO2 coating deposition by Gas Injection Magnetron Sputtering technique

This manuscript presents the nature of interaction of energetic plasmoids, generated in the Gas Injection Magnetron Sputtering (GIMS) technique, with the surface of substrate or the coating–substrate system. We expected that the plasma generated by a dynamic injection of gas (GIMS) is better ionized than the plasma generated in stationary pressure in its standard range for magnetron sputtering. The GIMS technique operates under conditions that may favor the plasma species to retain their kinetic energy, limiting the probability of intermolecular collisions events. In this experiment, the frequency of injecting small amounts of gas was used as a parameter to control the pressure amplitudes, thus achieving the conditions of plasma generation from stationary, through quasi-stationary, to pulsed oscillations of pressure. The optical emission spectroscopy (OES) was used to evaluate the state of deposition environment in GIMS. Investigation showed that the plasma spectrum consists of higher population of ions in the conditions of high amplitude of pressure oscillations. The phase content of a titanium dioxide coating, deposited under various conditions of plasma generation, also depends on the energetic state of plasma. Raman spectroscopy proved that the stationary condition favors the anatase phase as the nucleation phase, while with the increase in the non-equilibrium of plasma, the metastable rutile phase is more expected. The effects of strong impingement of energetic species were observed, causing crystallization of the amorphous phase of coatings, with sputtering of the substrate surface and the formation of a specific type of coating–substrate interfacial region.

Potential energy surface of interaction of two diatomic molecules for air flows simulation at intermediate temperatures

The paper studies the potential energy surface (PES) of interaction between two rigid diatomic molecules (N2–N2, N2–O2, O2–O2). The dependence of energy on the angles of mutual orientation of the two molecules is carefully described (18000 DFT calculations for each pair) so that the obtained PES would be suitable for detailed simulation of the rotational excitation and relaxation in intermolecular collisions in air. The DFT results were fitted by proposed multi-particle interaction model with good accuracy. Corresponding force field was calculated and tested on two problems (simulation of the equilibrium state and the adiabatic rotational relaxation), its software implementation is attached to the paper and one can use it for molecular dynamics calculations.

Gyroscopic effect in intermolecular collision with the C60 fullerene molecule

The work is devoted to the study of the gyroscopic phenomena of a rotating C60 fullerene molecule on interaction with a moving particle. To determine the precession characteristics of the C60 fullerene molecule, the pairwise interaction model of nonpolar Lennard-Jones molecules was used. The rotational motion of fullerene was described by the dynamic Euler equations. The influence of the angular velocity and direction of rotation of the fullerene molecule on the deviation from the initial position is investigated.

Multiple temperature model of nonlinear coupled constitutive relations for hypersonic diatomic gas flows

The rotational energy of diatomic gases would be activated by the process of intermolecular collisions in high-temperature hypersonic flows. In this paper, a multi-temperature nonlinear coupled constitutive model has been proposed for simulating the transfer of energy between translational and rotational motions in hypersonic non-equilibrium flows. In this model, the nonlinear coupled constitutive equations are modified by introducing a rotational energy relaxation model and a changeable viscosity ratio related to local temperature. To confirm its accuracy, the new model is applied to investigate steady shock wave structures and high-speed gas flows around a cylinder and across a flat plate. The computational results are compared with the multi-temperature Navier–Stokes (NS) equations, the direct simulation Monte Carlo (DSMC) solutions, and the experiment data. The final results show the new model would reproduce the NS results at low Knudsen numbers but behave quite differently from the NS results as the non-equilibrium degree is enhanced. The new model is in better agreement with the DSMC solutions and the experimental data than the NS solutions in the far-from-equilibrium regions, which demonstrates the potential of the new relaxation model in the simulation of hypersonic non-equilibrium flows.

Discrete unified gas kinetic scheme for all Knudsen number flows. IV. Strongly inhomogeneous fluids.

This work is an extension of the discrete unified gas kinetic scheme (DUGKS) from rarefied gas dynamics to strongly inhomogeneous dense fluid systems. The fluid molecular size can be ignored for dilute gases, while the nonlocal intermolecular collisions and the competition of solid-fluid and fluid-fluid interactions play an important role for surface-confined fluid flows at the nanometer scale. The nonequilibrium state induces strong fluid structural-confined inhomogeneity and anomalous fluid flow dynamics. According to the previous kinetic model [Guo etal., Phys. Rev. E 71, 035301(R) (2005)10.1103/PhysRevE.71.035301], the long-range intermolecular attraction is modeled by the mean-field approximation, and the volume exclusion effect is considered by the hard-sphere potential in the collision operator. The kinetic model is solved by the DUGKS, which has the characteristics of asymptotic preserving, low dissipation, second-order accuracy, and multidimensional nature. Both static fluid structure and dynamic flow behaviors are calculated and validated with Monte Carlo or molecular dynamics results. It is shown that the flow of dense fluid systems tends to that of rarefied gases as the dense degree decreases or the mean flow path increases. The DUGKS is proved to be applicable to simulate such nonequilibrium dense fluid systems.

Phosphine detection in veterinary samples using headspace gas chromatography/tandem mass spectrometry with multiple reaction monitoring.

Determination of phosphine exposure from zinc or aluminum phosphide fumigants continues to be a routine analytical requirement in veterinary forensic toxicology. There is a need for a more reliable and specific method than simple gas chromatography/mass spectrometry (GC/MS) analysis of sample solvent extracts, as GC/MS of extracts on capillary columns used for general screens involves significant interference from air peaks. GC/MS/MS headspace analysis of acid-generated phosphine gas enabled study of the feasibility of devising multiple reaction monitoring (MRM) approaches to the determination of phosphine with greater specificity. Collision-induced dissociation in GC/MS/MS showed that phosphine generated m/z 34 → 31, 32 and 33 ion transitions by sequential proton release as well as minor transitions m/z 34 → 47, 34 → 63 and 63 → 31.5 by intermolecular collisions and double charging. Study of the formation of these product ions enabled development of MRM settings for a highly useful headspace method for phosphine detection. The method was validated over a working range of 5-100 ppm of phosphide generating phosphine gas which enabled retention of regular screen capillary columns without necessitating separation from air components. The method should have adequate sensitivity and reliability for veterinary toxicology laboratories confronting specimens from animals poisoned by crop fumigants.

New Thermodynamics: Temperature, Sun’s Insolation, Thermal, and Blackbody Radiation

The various relationships between the temperature’s witnessed here on Earth, the Sun’s isolation, thermal energy and blackbody radiation are all poorly understood. Herein, the interrelations are examined, and a new theory concerning their relationships is presented. This also puts limitations upon temperature being related to a system’s thermal energy density. It also gives new insights into why inferences based upon infrared spectrometry, do not match those associated with heat capacities. Furthermore, new understandings concerning the inelastic nature of both intermolecular and intramolecular collisions will be proposed. This all will have profound implications to our understanding of thermodynamics, such as what is blackbody radiation, thermal radiation, and temperature, cumulating in profound implications concerning how we view global warming.

New Thermodynamics: Temperature, Sun’s Insolation, Thermal, and Blackbody Radiation

The various relationships between the temperature’s witnessed here on Earth, the Sun’s isolation, thermal energy and blackbody radiation are all poorly understood. Herein, the interrelations are examined, and a new theory concerning their relationships is presented. This also puts limitations upon temperature being related to a system’s thermal energy density. It also gives new insights into why inferences based upon infrared spectrometry, do not match those associated with heat capacities. Furthermore, new understandings concerning the inelastic nature of both intermolecular and intramolecular collisions will be proposed. This all will have profound implications to our understanding of thermodynamics, such as what is blackbody radiation, thermal radiation, and temperature, cumulating in profound implications concerning how we view global warming.

GRSA Enhanced for Protein Folding Problem in the Case of Peptides

Protein folding problem (PFP) consists of determining the functional three-dimensional structure of a target protein. PFP is an optimization problem where the objective is to find the structure with the lowest Gibbs free energy. It is significant to solve PFP for use in medical and pharmaceutical applications. Hybrid simulated annealing algorithms (HSA) use a kind of simulated annealing or Monte Carlo method, and they are among the most efficient for PFP. The instances of PFP can be classified as follows: (a) Proteins with a large number of amino acids and (b) peptides with a small number of amino acids. Several HSA have been positively applied for the first case, where I-Tasser has been one of the most successful in the CASP competition. PEP-FOLD3 and golden ratio simulated annealing (GRSA) are also two of these algorithms successfully applied to peptides. This paper presents an enhanced golden simulated annealing (GRSA2) where soft perturbations (collision operators), named “on-wall ineffective collision” and “intermolecular ineffective collision”, are applied to generate new solutions in the metropolis cycle. GRSA2 is tested with a dataset for peptides previously proposed, and a comparison with PEP-FOLD3 and I-Tasser is presented. According to the experimentation, GRSA2 has an equivalent performance to those algorithms.