Molecular dynamics simulations on the interactions between nucleic acids and a phospholipid bilayer

Recently,lipid nanoparticles(LNPs)have been extensively investigated as non-viral carriers of nucleic acid vaccines due to their high transport efficiency,safety,and straightforward production and scalability.However,the molecular mechanism underlying the interactions between nucleic acids and phospholipid bilayers within LNPs remains elusive.In this study,we employed the all-atom molecular dynamics simulation to investigate the interactions between single-stranded nucleic acids and a phospholipid bilayer.Our findings revealed that hydrophilic bases,specifically G in single-stranded RNA(ssRNA)and single-stranded DNA(ssDNA),displayed a higher propensity to form hydrogen bonds with phospholipid head groups.Notably,ssRNA exhibited stronger binding energy than ssDNA.Furthermore,divalent ions,particularly Ca2+,facilitated the binding of ssRNA to phospholipids due to their higher binding energy and lower dissociation rate from phospholipids.Overall,our study provides valuable insights into the molecular mechanisms underlying nucleic acidphospholipid interactions,with potential implications for the nucleic acids in biotherapies,particularly in the context of lipid carriers.

Study of the Relationship Between New Ionic Interaction Parameters and Salt Solubility in Electrolyte Solutions Based on Molecular Dynamics Simulation

Studying the relationship between ionic interactions and salt solubility in seawater has implications for seawater desalination and mineral extraction.In this paper,a new method of expressing ion-to-ion interaction is proposed by using molecular dynamics simulation,and the relationship between ion-to-ion interaction and salt solubility in a simulated seawater water-salt system is investigated.By analyzing the variation of distance and contact time between ions in an electrolyte solution,from both spatial and temporal perspectives,new parameters were proposed to describe the interaction between ions:interaction distance(ID),and interaction time ratio(ITR).The best correlation between characteristic time ratio and solubility was found for a molar ratio of salt-to-water of 10:100 with a correlation coefficient of 0.96.For the same salt,a positive correlation was found between CTR and the molar ratio of salt and water.For type 1-1,type 2-1,type 1-2,and type 2-2 salts,the correlation coefficients between CTR and solubility were 0.93,0.96,0.92,and 0.98 for a salt-to-water molar ratio of 10:100,respectively.The solubility of multiple salts was predicted by simulations and compared with experimental values,yielding an average relative deviation of 12.4%.The new ion-interaction parameters offer significant advantages in describing strongly correlated and strongly hydrated electrolyte solutions.

EVOLUTION AND INTERACTION OFδ-WAVES IN THE ZERO-PRESSURE GAS DYNAMICS SYSTEM

Evolution and interaction of plane waves of the multidimensional zero-pressure gas dynamics system leads to the study of the corresponding one dimensional system.In this paper,we study the initial value problem for one dimensional zero-pressure gas dynamics system.Here the first equation is the Burgers equation and the second one is the continuity equation.We consider the solution with initial data in the space of bounded Borel measures.First we prove a general existence result in the algebra of generalized functions of Colombeau.Then we study in detail special solutions withδ-measures as initial data.We study interaction of waves originating from initial data concentrated on two point sources and interaction with classical shock/rarefaction waves.This gives an understanding of plane-wave interactions in the multidimensional case.We use the vanishing viscosity method in our analysis as this gives the physical solution.

Multi-Body Dynamics Modeling of Heavy Goods Vehicle-Rail Interaction

Based on the principle of vehicle-track coupling dynamics, SIMPACK multi-body dynamics software is used to establish a C80 wagon line-coupled multi-body dynamics model with 73 degrees of freedom. And the reasonableness of the line-coupled dynamics model is verified by using the maximum residual acceleration, the nonlinear critical speed of the wagon. The experimental results show that the established vehicle line coupling dynamics model meets the requirements of vehicle line coupling dynamics modeling.

Dynamic modeling of cavitation bubble clusters:Effects of evaporation,condensation,and bubble-bubble interaction

We present a dynamic model of cavitation bubbles in a cluster,in which the effects of evaporation,condensation,and bubble-bubble interactions are taken into consideration.Under different ultrasound conditions,we examine how the dynamics of cavitation bubbles are affected by several factors,such as the locations of the bubbles,the ambient radius,and the number of bubbles.Herein the variations of bubble radius,energy,temperature,pressure,and the quantity of vapor molecules are analyzed.Our findings reveal that bubble-bubble interactions can restrict the expansion of bubbles,reduce the exchange of energy among vapor molecules,and diminish the maximum internal temperature and pressure when bursting.The ambient radius of bubbles can influence the intensities of their oscillations,with clusters comprised of smaller bubbles creating optimal conditions for generating high-temperature and high-pressure regions.Moreover,an increase in the number of bubbles can further inhibit cavitation activities.The frequency,pressure and waveform of the driving wave can also exert a significant influence on cavitation activities,with rectangular waves enhancing and triangular waves weakening the cavitation of bubbles in the cluster.These results provide a theoretical basis for understanding the dynamics of cavitation bubbles in a bubble cluster,and the factors that affect their behaviors.

Subpicosecond laser ablation behavior of a magnesium target and crater evolution:Molecular dynamics study and experimental validation

The micro-ablation processes and morphological evolution of ablative craters on single-crystal magnesium under subpicosecond laser irradiation are investigated using molecular dynamics(MD) simulations and experiments.The simulation results exhibit that the main failure mode of single-crystal Mg film irradiated by a low fluence and long pulse width laser is the ejection of surface atoms,which has laser-induced high stress.However,under high fluence and short pulse width laser irradiation,the main damage mechanism is nucleation fracture caused by stress wave reflection and superposition at the bottom of the film.In addition,Mg[0001] has higher pressure sensitivity and is more prone to ablation than Mg[0001].The evolution equation of crater depth is established using multi-pulse laser ablation simulation and verified by experiments.The results show that,under multiple pulsed laser irradiation,not only does the crater depth increase linearly with the pulse number,but also the quadratic term and constant term of the fitted crater profile curve increase linearly.

Capturing the non-equilibrium state in light–matter–free-electron interactions through ultrafast transmission electron microscopy

Ultrafast transmission electron microscope(UTEM) with the multimodality of time-resolved diffraction, imaging,and spectroscopy provides a unique platform to reveal the fundamental features associated with the interaction between free electrons and matter. In this review, we summarize the principles, instrumentation, and recent developments of the UTEM and its applications in capturing dynamic processes and non-equilibrium transient states. The combination of the transmission electron microscope with a femtosecond laser via the pump–probe method guarantees the high spatiotemporal resolution, allowing the investigation of the transient process in real, reciprocal and energy spaces. Ultrafast structural dynamics can be studied by diffraction and imaging methods, revealing the coherent acoustic phonon generation and photoinduced phase transition process. In the energy dimension, time-resolved electron energy-loss spectroscopy enables the examination of the intrinsic electronic dynamics of materials, while the photon-induced near-field electron microscopy extends the application of the UTEM to the imaging of optical near fields with high real-space resolution. It is noted that light–free-electron interactions have the ability to shape electron wave packets in both longitudinal and transverse directions, showing the potential application in the generation of attosecond electron pulses and vortex electron beams.

Numerical Study on the Aerodynamic and Fluid−Structure Interaction of An NREL-5MW Wind Turbine

A 5-MW wind turbine has been modeled and analyzed for fluid-structure interaction and aerodynamic performance.In this study, a full-scale model of a 5-MW wind turbine is first developed based on a computational fluid dynamics(CFD) approach, in which the unsteady, noncompressible Reynolds Averaged Navier-Stokes(RANS) method is used. The main focus of the study is to analyze the tower shadow effect on the aerodynamic performance of the wind turbine under different inlet flow conditions. Subsequently, the finite element model is established by considering fluid/structure interactions to study the structural stress, displacement, strain distributions and flow field information of the structure under the uniform wind speed. Finally, the fluid-structure interaction model is established by considering turbulent wind and the tower shadow effect. The variation rules of the dynamic response of the one-way and two-way fluid-structure interaction(FSI) models under different wind speeds are analyzed, and the numerical calculation results are compared with those of the centralized mass model. The results show that the tower shadow effect and structural deformation are the main factors affecting the aerodynamic load fluctuation of the wind turbine, which in turn affects the aerodynamic performance and structural stability of the blades. The structural dynamic response of the coupled model shows significant similarity, while the structural displacement response of the former exhibits less fluctuation compared with the conventional centralized mass model. The one-way fluid-structure interaction(FSI)model shows a higher frequency of stress-strain and displacement oscillations on the blade compared with the two-way FSI model.

Molecular Dynamics Simulations of the Interactions Between Konjac Glucomannan and Soy Protein Isolate

The interactions between konjac glucomannan（KGM） and soy protein isolate （SPI） were studied with the method of molecular dynamics simulation. Part representative structures segments of KGM and SPI were used as mode, and the force-field was FF03. The stability and sites of KGM/SPI interactions in water were researched at 363 K with the following results： the potential energy （EPOT） of the mixed gel dropped, while that of single KGM gel increased. The surface area （SA） of KGM in the mixed system was decreased to 401.41 from 1 267.54 Az, and that of SPI to 484.94 from 1 943.28 A2. The sum potential energy of KGM and soy protein in the mixed system was decreased to -13 402.41 from -5 768.56 kcal mol^-1. The variations of two parameters showed that the stability of compound gel KGM/SPI was improved, which was consistent with the previous studies. The sites of interactions in the mixed gel were the -OH groups on C（2） in KGM mannose and glucose, and the amide linkage group on Histidine, Asparagine and Leucine in SPI. The hydrogen bond was formed directly or indirectly by the bridge of waters.

Comparative study on wheel-rail dynamic interactions of side-frame cross-bracing bogie and sub-frame radial bogie

Improving freight axle load is the most effective method to improve railway freight capability; based on the imported technologies of railway freight bogie, the 27 t axle load side-frame cross-bracing bogie and sub-frame radial bogie are developed in China. In order to analyze and compare dynamic interactions of the two newly developed heavy-haul freight bogies, we establish a vehi- cle-track coupling dynamic model and use numerical calculation methods for computer simulation. The dynamic performances of the two bogies are simulated separately at various conditions. The results show that at the dipped joint and straight line running conditions, the wheel-rail dynamic interactions of both bogies are basically the same, but at the curve negotiation condition, the wear and the lateral force of the side-frame cross-bracing bogie are much higher than that of the sub-frame radial bogie, and the advantages become more obvious when the curve radius is smaller. The results also indicate that the sub- frame radial bogie has better low-wheel-rail interaction characteristics.

Molecular Dynamics Simulations of the Interactions between Konjac Glucomannan and Carrageenan

The interactions between konjac glucomannan and carrageenan were studied with the method of molecular dynamics simulation. Part representative structure segments of KGM and two unit structures of κ-carrageenan （Fig. 2） were used as mode, and the force-field was AMBER2. The stability and sites of konjac glucomannan/carrageenan interactions in water were researched at 373 K with the following results： the potential energy （EPOT） of the mixed gel was dropped, while those of single-konjac glucomannan gel and single carrageenan were increased. The surface area （SA） of KGM in the mixed system was decreased to 1002.2A^°^2, and that of carrageenan to 800.9 A^°^2. The variations of two parameters showed that the stability of compound gel konjac glucomannan/carrageenan was improved, which is consistent with the previous studies. The sites of interactions in the mixed gel were the -OH groups on C（2）, C（4） and C（6）, the acetyl group in KGM mannose, and the -OH group on C（6） in carrageenan. The hydrogen bond was formed directly or indirectly by the bridge of waters.

Torsional Characteristics of Single Walled Carbon Nanotube with Water Interactions by Using Molecular Dynamics Simulation

The torsional characteristics of single walled carbon nanotube(SWCNT) with water interactions are studied in this work using molecular dynamics simulation method. The torsional properties of carbon nanotubes(CNTs) in a hydrodynamic environment such as water are critical for its key role in determining the lifetime and stability of CNT based nano-fluidic devices. The effect of chirality, defects and the density of water encapsulation is studied by subjecting the SWCNT to torsion. The findings show that the torsional strength of SWCNT decreases due to interaction of water molecules and presence of defects in the SWCNT. Additionally,for the case of water molecules encapsulated inside SWCNT, the torsional response depends on the density of packing of water molecules. Our findings and conclusions obtained from this paper is expected to further compliment the potential applications of CNTs as promising candidates for applications in nano-biological and nano-fluidic devices.

Protist Interactions and Seasonal Dynamics in the Coast of Yantai, Northern Yellow Sea of China as Revealed by Metabarcoding

Facilitated by the high-throughput sequencing(HTS)technique,the importance of protists to aquatic systems has been widely acknowledged in the last decade.However,information of protistan biotic interactions and seasonal dynamics is much less known in the coast ecosystem with intensive anthropic disturbance.In this study,year-round changes of protist community composition and diversity in the coastal water of Yantai,a city along the northern Yellow Sea in China,were investigated using HTS for the V4 region of 18S rDNA.The interactions among protist groups were also analyzed using the co-occurrence network.Data analyses showed that Alveolata,Chlorophyta,and Stramenopiles are the most dominant phytoplanktonic protists in the investigated coastal area.The community composition displayed strong seasonal variation.The abundant families Dino-Group-I-Clade-1 and Ulotrichales_X had higher proportions in spring and summer,while Bathycoccaceae exhibited higher ratios in autumn and winter.Alpha diversities(Shannon and Simpson)were the highest in autumn and the lowest in spring(ANOVA test,P<0.05).Nutrients(SiO42−,PO43−),total organic carbon(TOC),and pH seemed to drive the variation of alpha diversity,while temperature,PO43−and TON were the most significant factors influencing the whole protist community.Co-variance network analyses reveal frequent co-occurrence events among ciliates,chlorophytes and dinoflagellate,suggesting biotic interactions have been induced by predation,parasitism and mixotrophy.

An experimental study on the effects of friction modifiers on wheel-rail dynamic interactions with various angles of attack

By modifying friction to the desired level,the application of friction modifiers(FMs)has been considered as a promising emerging tool in the railway engineering for increasing braking/traction force in poor adhesion conditions and mitigating wheel/rail interface deterioration,energy consumption,vibration and noise.Understanding the effectiveness of FMs in wheel–rail dynamic interactions is crucial to their proper applications in practice,which has,however,not been well explained.This study experimentally investigates the effects of two types of top-of-rail FM,i.e.FM-A and FM-B,and their application dosages on wheel–rail dynamic interactions with a range of angles of attack(AoAs)using an innovative well-controlled V-track test rig.The tested FMs have been used to provide intermediate friction for wear and noise reduction.The effectiveness of the FMs is assessed in terms of the wheel–rail adhesion characteristics and friction rolling induced axle box acceleration(ABA).This study provides the following new insights into the study of FM:the applications of the tested FMs can both reduce the wheel–rail adhesion level and change the negative friction characteristic to positive;stick–slip can be generated in the V-Track and eliminated by FM-A but intensified by FM-B,depending on the dosage of the FMs applied;the negative friction characteristic is not a must for stick–slip;the increase in ABA with AoA is insignificant until stick–slip occurs and the ABA can thus be influenced by the applications of FM.

Modal interactions in primary and subharmonic resonant dynamics of imperfect microplates with geometric nonlinearities

This paper analyses the modal interactions in the nonlinear, size-dependent dynamics of geometrically imperfect microplates. Based on the modified couple stress theory,the equations of motion for the in-plane and out-of-plane motions are obtained employing the von Kármán plate theory as well as Kirchhoff＇s hypotheses by means of the Lagrange equations. The equations of motions are solved using the pseudo-arclength continuation technique and direct timeintegration method. The system parameters are tuned to the values associated with modal interactions, and then nonlinear resonant responses and energy transfer are analysed.Nonlinear motion characteristics are shown in the form of frequency-response and force-response curves, time histories, phase-plane portraits, and fast Fourier transforms.

Electron Dynamics and Characteristics of Attosecond Electromagnetic Emissions in Relativistic Laser-Plasma Interactions

Generation of attosecond electromagnetic （EM） pulses and the associated electron dynamics are studied using particle-in-cell simulations of relativistic laser pulses interacting with over-dense plasma foil targets. The inter- action process is found to be so complicated even in the situation of utilizing driving laser pulses of only one cycle. Two electron bunches closely involved in the laser-driven wavebreaking process contribute to attosecond EM pulses through the coherent synchrotron emission process whose spectra are found to follow an exponential decay rule. Detailed investigations of electron dynamics indicate that the early part of the reflected EM emission is the high-harmonics produced through the relativistic oscillating mirror mechanism. High harmonics are also found to be generated through the Bremsstrahlung radiation by one electron bunch that participates in the wavebreaking process and decelerates when it experiences the local wavebreaking-generated high electrostatic field in the moving direction.

CLASSROOM DYNAMICS THROUGH INTERACTIVE ACTIVITIES

课堂活力是作用于教学系统的动力。它直接影响教学活动的开展 ,并推动教学的进程。积极的课堂活力对学习者的精神面貌、学习动机和自我形象的形成会产生良好的影响。从而使学习者对所学的语言、学习的过程和作为学习主体本身持积极的态度。本文对不同学习群体特征及语言教学本质进行了分析 ,提出产生和增进课堂活力的有效途径———双向活动教学。这一方法以英语教学交际理论为基础 ,是我们两年多在中学与大学两种不同层次间开展英语教学研究的初步成果。本文介绍其基本教学原则、侧重点、步骤、双主体作用并展示教学个案 ,使读者了解如何通过双向活动教学营造和增进课堂活力。

Wheel-rail contact model for railway vehicle-structure interaction applications:development and validation

An enhancement in the wheel-rail contact model used in a nonlinear vehicle-structure interaction(VSI)methodology for railway applications is presented,in which the detection of the contact points between wheel and rail in the concave region of the thread-flange transition is implemented in a simplified way.After presenting the enhanced formulation,the model is validated with two numerical applications(namely,the Manchester Benchmarks and a hunting stability problem of a sus-pended wheelset),and one experimental test performed in a test rig from the Railway Technical Research Institute(RTRI)in Japan.Given its finite element(FE)nature,and contrary to most of the vehicle multibody dynamic commercial software that cannot account for the infrastructure flexibility,the proposed VSI model can be easily used in the study of train-bridge systems with any degree of complexity.The validation presented in this work proves the accuracy of the proposed model,making it a suitable tool for dealing with different railway dynamic applications,such as the study of bridge dynamics,train running safety under different scenarios(namely,earthquakes and crosswinds,among others),and passenger riding comfort.

An efficient method for train-track-substructure dynamic interaction analysis by implicit-explicit integration and multi-time-step solution

In this work,a method is put forward to obtain the dynamic solution efficiently and accurately for a large-scale train-track-substructure(TTS)system.It is called implicit-explicit integration and multi-time-step solution method(abbreviated as mI-nE-MTS method).The TTS system is divided into train-track subsystem and substruc-ture subsystem.Considering that the root cause of low effi-ciency of obtaining TTS solution lies in solving the alge-braic equation of the substructures,the high-efficient Zhai method,an explicit integration scheme,can be introduced to avoid matrix inversion process.The train-track system is solved by implicitly Park method.Moreover,it is known that the requirement of time step size differs for different sub-systems,integration methods and structural frequency response characteristics.A multi-time-step solution is pro-posed,in which time step size for the train-track subsystem and the substructure subsystem can be arbitrarily chosen once satisfying stability and precision demand,namely the time spent for m implicit integral steps is equal to n explicit integral steps,i.e.,mI=nE as mentioned above.The numeri-cal examples show the accuracy,efficiency,and engineering practicality of the proposed method.

Application of Computational Fluid Dynamics and Fluid Structure Interaction Techniques for Calculating the 3D Transient Flow of Journal Bearings Coupled with Rotor Systems

Journal bearings are important parts to keep the high dynamic performance of rotor machinery. Some methods have already been proposed to analysis the flow field of journal bearings, and in most of these methods simplified physical model and classic Reynolds equation are always applied. While the application of the general computational fluid dynamics （CFD）-fluid structure interaction （FSI） techniques is more beneficial for analysis of the fluid field in a journal bearing when more detailed solutions are needed. This paper deals with the quasi-coupling calculation of transient fluid dynamics of oil film in journal bearings and rotor dynamics with CFD-FSI techniques. The fluid dynamics of oil film is calculated by applying the so-called ＂dynamic mesh＂ technique. A new mesh movement approacb is presented while the dynamic mesh models provided by FLUENT are not suitable for the transient oil flow in journal bearings. The proposed mesh movement approach is based on the structured mesh. When the joumal moves, the movement distance of every grid in the flow field of bearing can be calculated, and then the update of the volume mesh can be handled automatically by user defined function （UDF）. The journal displacement at each time step is obtained by solving the moving equations of the rotor-bearing system under the known oil film force condition. A case study is carried out to calculate the locus of the journal center and pressure distribution of the journal in order to prove the feasibility of this method. The calculating results indicate that the proposed method can predict the transient flow field of a journal bearing in a rotor-bearing system where more realistic models are involved. The presented calculation method provides a basis for studying the nonlinear dynamic behavior of a general rotor-bearing system.