Dynamics Method Research Articles

Molecular Dynamics Simulation of Complex Reactivity with the Rapid Approach for Proton Transport and Other Reactions (RAPTOR) Software Package.

Simulating chemically reactive phenomena such as proton transport on nanosecond to microsecond and beyond time scales is a challenging task. Ab initio methods are unable to currently access these time scales routinely, and traditional molecular dynamics methods feature fixed bonding arrangements that cannot account for changes in the system's bonding topology. The Multiscale Reactive Molecular Dynamics (MS-RMD) method, as implemented in the Rapid Approach for Proton Transport and Other Reactions (RAPTOR) software package for the LAMMPS molecular dynamics code, offers a method to routinely sample longer time scale reactive simulation data with statistical precision. RAPTOR may also be interfaced with enhanced sampling methods to drive simulations toward the analysis of reactive rare events, and a number of collective variables (CVs) have been developed to facilitate this. Key advances to this methodology, including GPU acceleration efforts and novel CVs to model water wire formation are reviewed, along with recent applications of the method which demonstrate its versatility and robustness.

All-natural and triple-inspired Janus electrospun fibers with integrated functions for high-performance liquid food packaging

The liquid barrier is a central component of functional liquid packaging materials and is crucial for encapsulating liquid food. To develop high-performance liquid packaging materials for the long-term storage of liquid food, a strong and stable liquid barrier and the simultaneous integration of diverse functionalities must be realized. In this study, inspired by mussel adhesion proteins, nanoparticles are synthesized through oxidative self-polymerization. Furthermore, electrostatic spinning is used for creating multifunctional electrospun fibers for liquid food packaging, which is inspired by the superhydrophobicity of lotus leaf surface and structures of red blood cells. A unique Janus structure with a thin hydrophilic layer and a thick hydrophobic layer prevents liquid food penetration for 12 (EHN/KN electrospun fibers) and 17 days (KN/EHN electrospun fibers). The liquid infiltration mechanism of Janus electrospun fibers is elucidated using the multibody dissipative particle dynamics method, emphasizing their efficacy in avoiding liquid penetration. Moreover, multifunctional KN/EHN electrospun fibers exhibit remarkable characteristics such as water resistance (water contact angle > 150°), UV-blocking (∼100 %), degradability (70 days in soil), biosafety (∼100 %), antioxidation (> 90 %), antimicrobial (∼100 %), grapes and meat freshness retention properties. Thus, this study provides insights into sustainable, high-performance liquid food packaging for enhanced preservation.

Computational fluid dynamics numerical simulation of flue gas emission from stack and tower integration system of coal-fired power plant

ABSTRACT The method of Computational Fluid Dynamics (CFD) simulation has been extensively employed in the stack and tower integration technology (STIT) research; however, a significant number of studies overlooked the impact of thermal buoyancy on the external flow field of cooling tower. In light of this, an improved approach is proposed in this study. A model of a cooling tower and its surrounding flow field was established, and its reliability was confirmed too. Based on our model, the performance of three enhancement strategies under various crosswind speeds and ambient temperatures was simulated. The results indicate that all three enhancement strategies can effectively simulate the effects of thermal buoyancy. In the simulations, the elevation of the flue gases increased from 306 m to either 426 m or 476 m. In the present study, ambient conditions characterized by crosswind speeds below 4 m/s and temperatures below 297.15 K were deemed suitable for the dispersion of stack and tower integration (STI) flue gases. A power function distribution was identified between crosswind speed and the mean height of the plume, while a linear relationship was observed between ambient temperature and the mean height of the plume.

Turbomachines seal flow resistance enhancement and leakage reduction based on flow control method with bow-shaped auxiliary teeth

Improving sealing performance without clearance reduction is important for the economic and safety operation of modern turbomachines. For this purpose, this study proposes the bow-shaped auxiliary teeth to reduce the leakage. One bow-shaped auxiliary tooth is installed after each seal tooth to guide the leakage jet towards the side wall of seal tooth. Then the leakage jet attaches itself to the inner wall of cavity. The Computational Fluid Dynamics method is used to calculate the flow field in the new seal. Results show that flow impingements, flow deflections, and enhanced vena contraction effect increase the leakage flow resistance and reduce the leakage velocity. The application of the bow-shaped auxiliary teeth reduces the leakage flow rate by 43.8–46.3 % compared with the labyrinth seal. Geometry parameters analysis shows that reducing the axial distance between seal tooth and bow-shaped auxiliary tooth, and increasing the central angle of bow-shaped auxiliary tooth are beneficial for leakage reduction. With the increase in the radius of bow-shaped auxiliary tooth, the leakage firstly decreases and then changes a little.

Improving the sealing performance of honeycomb seal by drilling double wall-holes

A novel double-wall-hole honeycomb seal (D-WHHCS) is proposed in this paper. D-WHHCS is designed based on a traditional honeycomb seal (HCS) by drilling double holes in the honeycomb sidewalls. The leakage characteristics of D-WHHCS are investigated via the computational fluid dynamics (CFD) method. The sealing performance of D-WHHCS under different seal clearances, wall hole positions, operating pressures and rotating speeds is studied. The sealing mechanism of D-WHHCS is revealed. The results show that D-WHHCS has better sealing performance than HCS under all the considered operating conditions, with a maximum leakage reduction of 3.95%. A fluid concentration effect when the axial cavity number (N) = 14 is observed in D-WHHCS, which causes a 9.16% improvement in the maximum turbulent kinetic energy compared with HCS at the outlet extension. A large vortex in the cavities of D-WHHCS with N = 14 is guided by the jets at the centerlines of the drilling hoes. The average turbulent dissipation in the cavities of D-WHHCS is a maximum increase of 95.30%, even though the vortexes in the cavities with N = 13 are weakened by the counteractive effect of two jets. The leakage reduction performance of D-WHHCS decreases with increasing clearance. An abnormal low-pressure region is produced in the first cavity because the intensive jet covers the first two cavities and suppresses the throttling effect of the first-stage honeycomb cavity. The leakage of D-WHHCS further decreases along with holes closing to rotor surface.

Transient simulation of the electrical hysteresis in a metal/polymer/metal nanostructure.

The time-dependent quantum transportation through a metal/polymer/metal system is theoretically investigated on the basis of a Su-Schrieffer-Heeger model combined with the hierarchical equations of motion formalism. Using a non-adiabatic dynamical method, the evolution of the electron subspace and lattice atoms with time can be obtained. It is found that the calculated transient currents vary with time and reach stable values after a response time under the bias voltages. However, the stable current as the system reaches its dynamical steady state exhibits a discrepancy between two sweep directions of the bias voltage, which results in pronounced electrical hysteresis loops in the current-voltage curve. By analyzing the evolution of instantaneous energy eigenstates, the occupation number of the instantaneous eigenstates, and the lattice of the polymer, we show that the formation of excitons and the delay of their annihilation are responsible for the hysteretic current-voltage characteristics, where electron-phonon interactions play the key factor. Furthermore, the hysteresis width and amplitude can also be modulated by the strength of the electron-phonon coupling, level-width broadening function, and temperature. We hope these results about past condition-dependent switching performance at a sweep voltage can provide further insight into some of the basic issues of interest in hysteresis processes in conducting polymers.

Study on the adsorption/desorption characteristics and dynamic diffusion mechanism of rare earth hydrated ions on the kaolinite (001) surface

Coal gangue (CG) contains abundant rare earth elements (REEs), which is a potential REE resource. REEs are mainly present in clay minerals as hydrates. The adsorption, desorption, and diffusion of REEs-hydrates on the surface of clay minerals are the key to regulating the leaching effect of REEs. The paper focuses on the typical clay minerals kaolinite and REEs-hydrates and combines quantum mechanics and molecular dynamics methods to systematically study the adsorption, desorption, and dynamic diffusion behavior of REEs-hydrates in acid solution. The research results indicate that stable REEs-hydrates La(H2O)9 and Y(H2O)7 are formed, with ion bonds between REEs and water molecules. La(H2O)9 and Y(H2O)7 mainly interact with the kaolinite (001) surface through hydrogen bonding. Competitive adsorption is formed between water molecules, hydrated hydrogen ions, and REEs-hydrates. Water molecules and hydrated hydrogen ions occupy the adsorption active sites of REEs-hydrates and form a dense water molecular layer on the surface. The distance between H3O+ and REEs-hydrates and the number of H3O+ in the solvent layer affect the desorption and diffusion behavior of hydrates. The bonding law, dynamic desorption, and diffusion mechanism of REEs-hydrates can provide meaningful references for selective leaching of REEs from CG.

Molecular Dynamics Simulation on Solidification Microstructure and Tensile Properties of Cu/SiC Composites

The shape of ceramic particles is one of the factors affecting the properties of metal matrix composites. Exploring the mechanism of ceramic particles affecting the cooling mechanical behavior and microstructure of composites provides a simulation basis for the design of high-performance composites. In this study, molecular dynamics methods are used for investigating the microstructure evolution mechanism in Cu/SiC composites containing SiC particles of different shapes during the rapid solidification process and evaluating the mechanical properties after cooling. The results show that the spherical SiC composites demonstrate the highest degree of local ordering after cooling. The more ordered the formation is of face-centered-cubic and hexagonal-close-packed structures, the better the crystallization is of the final composite and the less the number of stacking faults. Finally, the results of uniaxial tensile in three different directions after solidification showed that the composite containing spherical SiC particles demonstrated the best mechanical properties. The findings of this study provide a reference for understanding the preparation of Cu/SiC composites with different shapes of SiC particles as well as their microstructure and mechanical properties and provide a new idea for the experimental and theoretical research of Cu/SiC metal matrix composites.

Investigating the effects of temperature on thermal and mechanical properties of polyurethane/polycaprolactone/graphene oxide nanocomposites: focusing on creating a smart polymer nanocomposite via molecular dynamics method

Polycaprolactone, a biodegradable polyester renowned for its biocompatibility, controlled degradation capability, and processability, finds application across diverse industrial sectors. Graphene oxide has been utilised to strengthen polymers and rectify any existing issues. This research aims to investigate the effects of temperature on the thermal and mechanical properties of polyurethane/polycaprolactone/graphene oxide nanocomposites, focusing on creating a smart polymer nanocomposite via the molecular dynamic method. The research is innovative as it investigates the nanocomposite's thermal behaviour and strength in detail. Additionally, the use of molecular dynamics methods to achieve the goal of creating a smart polymer nanocomposite represents an innovative approach that contributes to the advancement of nanocomposite materials. The results show that raising the initial temperature to 350 K decreased heat flux and thermal conductivity to 681.85 W/m2 and 0.82 W/m.K, respectively, while increasing the structure volume to 27364 nm3. Additionally, as the Temp increased from 300 to 350 K, the ultimate strength and Young's modulus values decreased from 72.59–68.22 MPa and 6.63–6.36 MPa, respectively. In general, this research provided valuable insights into understanding and evaluating the attributes of polyurethane/polycaprolactone/graphene oxide polymer nanocomposite through molecular dynamic simulations.

Microscopic mechanism and effect analysis of polymer modifiers on embrittlement and viscosity behaviour of asphalt

To support the research and development of asphalt binder with low embrittlement point in cold areas, the microscopic mechanism and effect of polymer modifier on embrittlement and viscosity of asphalt were analysed by molecular dynamics method. The mixed molecular models of three polymer modified asphalt commonly used in cold areas and the interactive molecular models of each component of asphalt and modifier were established. The micromechanical properties of high-content polymer modified asphalt were studied by three important indices, namely brittleness point, shear viscosity and elastic modulus, and the interaction behaviour of each component of asphalt and modifier molecules was analysed by the layer model. The following conclusions were obtained: The brittleness point of modified asphalt can be decreased by increasing the polymer modifier content, with a notable reduction of 25.54 % observed when the content reaches 7.5 %. However, this is accompanied by a subsequent increase in shear viscosity at mixing temperatures, with the highest increase reaching 16.9 %. At low temperature environment, the diffusion rate of the modifier is closely related to its own type, temperature and the type of asphalt components, and in different modified asphalt, the law of the diffusion rate of each asphalt component is not completely consistent, so it is necessary to fully consider the influence of the proportion of asphalt components, and choose the modifier sensitive to the corresponding components. The above research results have an important guiding role in the scientific formulation of the design and test scheme of low-brittleness-point asphalt binder and the completion of the research and development of low-brittleness-point asphalt binder for cold areas.

Study of the factors influencing the life cycle cost of green buildings using SEM-SD method

ABSTRACT The recent surge in carbon emissions from the building sector has raised significant environmental concerns. While green building practices have proven effective, their widespread adoption has been hindered by high costs. This study aims to explore the factors impacting the life cycle costs of green buildings, with the aim of achieving “double carbon” reduction. Through an analysis of 42 articles, 24 factors were distilled based on expert opinion. After collecting 322 data through questionnaires, a model of the factors influencing the life cycle cost of green buildings was constructed using structural equation modeling, and a cost simulation study was carried out through the system dynamics method in the practical case to examine how the cost changed. The findings highlight the pivotal role of planning and design, implementation, and operation and maintenance phases. Notably, green building design programs, green construction programs, and the property management level stand out as critical factors emerged as critical factors. These insights can inform strategies to reduce the cost of green buildings, thereby fostering energy conservation and emission reduction in the construction industry.

Inverting a model of neuro-muscular control to estimate descending activation patterns that generate fast reaching movements.

Reaching movements generally show smooth kinematic profiles that are invariant across varying movement speeds even as interaction torques and muscle properties vary non-linearly with speed. How the brain brings about these invariant profiles is an open question.We develop an analytical inverse dynamics method to estimate descending activation patterns directly from observed joint angle trajectories based on a simple model of the stretch reflex, and of muscle and biomechanical dynamics. We estimate descending activation patterns for experimental data from eight different planar two-joint movements performed at two movement times (fast: 400 msec; slow: 800 msec). The temporal structure of descending activation differed qualitatively across speeds, consistent with the idea that the nervous system uses an internal model to generate anticipatory torques during fast movement. This temporal structure also depended on the co-contraction level of antagonistic muscle groups. Comparing estimated muscle activation and descending activation revealed the contribution of the stretch reflex to movement generation that was found to set in after about 20 percent of movement time.

Numerical Investigation of Interventions to Mitigate Heat Stress: A Case Study in Dubai

Urbanization and changes in microclimate have negative impacts on outdoor thermal comfort, making urban design more important. This study aims to improve outdoor thermal comfort in a local climate zone (LCZ) in Dubai using computational fluid dynamics (CFD) methods. This study evaluates cooling interventions, such as vegetation, architectural, and pavement material, using Reynolds-averaged Navier–Stokes (RANS) equations and the SIMPLE scheme. The results show that a combination of cooling interventions affects the average temperature between 4.44 °C and 6.14 °C. Light-colored ground material has a 5.4 °C cooling effect in the LCZ compared with dark-colored materials. The predicted mean vote (PMV) method is used to compare outdoor thermal comfort and the results show that thermal sensation in the LCZ improves from warm to slightly cool. Lastly, the most effective cooling interventions are, in order, shade structures, trees, chimneys, and bushes.

Numerical investigation of inlet-pipe configurations on fluid dynamics and flow-field characteristics inside filling valve

The filling valve requires high efficiency and stability in the working process, which is closely related to the distribution of the flow characteristics inside the valve. In this study, computational fluid dynamics (CFD) methods were present to analyse the pressure, velocity, and other characteristics of the filling valve under different inlet pipe angles and valve openings. The flow characteristics, which are experimentally measured, are consistent with CFD simulation results. Research shows that the increase in the angle of the inlet pipe can improve the uniformity of the flow field inside the valve, produce a better core flow pattern at the valve outlet, and have better fluid stability. Based on the flow characteristics of the valve, to obtain good filling efficiency and stability, a moderate valve opening of 9 mm should be selected, and the flow coefficient can reach 1.08, which is 1.6 times higher than that of 3 mm, and the angle of the inlet pipe should be appropriately increased. This study provides a reference for the use and optimization of filling valves.

On the thermodynamics of DNA double strand in the Peyrard-Bishop-Dauxois model

The temperature dependence of energy, partition function, entropy and free energy, describing a first-order-like phase transition of a DNA molecule is calculated based on the direct method of molecular dynamics for the classical Peyrard-Bishop-Dauxois model. It is shown that without taking into account the quantum freezing of the degrees of freedom at low temperatures, the relationship between these quantities is not determined. The latent heat of DNA melting is calculated for homogeneous PolyA/PolyT and PolyG/PolyC DNA chains. It is shown that this melting transition corresponds to a sharp temperature dependence of the heat capacity.

MSD-based transient fluid model of liquid circular angular accelerometer for vibration-induced error analysis

This paper investigates the errors induced by linear vibration in the fluidic system of liquid circular angular accelerometers (LCAAs). A two-dimensional mass-spring-damper model is proposed to analyze the pressure difference between both sides of LCAA transducer subjected to linear vibration in both transient and steady states, where the compressibility of fluid is taken into account. The complex flow patterns of fluid are simplified to the positional changes of fluid particles. Springs and dampers are utilized to simulate the forces inside the fluid and between the fluid and the tube wall. Simulations are carried out based on the linear acceleration step excitation to explore the influence of model parameters, LCAA structure parameters and fluid parameters. The proposed model is validated by comparing the characteristics of the simulated pressure difference with their corresponding theoretical values, and is further verified by the comparison with the results from computational fluid dynamics method. Furthermore, the pressure difference under linear acceleration excitations in various forms is analyzed. The results indicate that the abrupt changes in linear acceleration are the primary cause of pressure difference oscillation, and the compressibility of fluid leads to increased pressure difference.

Molecular dynamics study of the influence of electric fields on water penetration in metal confined nanochannels

Electric field regulation of water penetration in nanochannels is an important method to address membrane fouling issues. Investigating the mechanism of electric field effects on water penetration in metal-confined nanochannels is highly meaningful. This article uses molecular dynamics methods to study the characteristics of water penetration in copper nanochannels. The influence and mechanisms of different types of applied electric fields on the water penetration within the channels were analyzed. The results indicate that applying electric fields in the y and z directions can enhance water penetration efficiency within the channels. Furthermore, a sinusoidal electric field has a greater enhancing effect on water penetration compared to a uniform electric field. Particularly, with a sinusoidal electric field frequency of 50 GHz, favorable water penetration effects were observed, with maximum increases in transport rate and axial diffusion coefficient of 197.5 % and 249.7 % respectively, relative to the absence of an electric field. The sinusoidal electric field exhibited greater capability in accelerating water molecule movement, leading to a rise in system temperature, with a maximum temperature increase of 46.9 %. These findings provide microscopic evidence for the feasibility of electric field regulation of water penetration in nanochannels, offering a theoretical foundation for enhancing nanoconfined water penetration behavior within channels.

Study on Flow Characteristics of Integrated Natural Circulation Reactor Under Inclined Conditions

In order to study the flow characteristics of an integrated natural circulation reactor under inclined conditions, a typical three-dimensional analysis model of natural circulation was established. The natural circulation under inclined conditions was numerically simulated using the computational fluid dynamics method, and the velocity and temperature distribution characteristics of heat exchangers and mixed-flow channels with different inclined angles were analyzed. The results show that as the inclination angle of the heat exchanger flow rate increases, there is a spatial migration phenomenon corresponding to the direction of the average flow rate. A large inclination angle will lead to a serious deterioration of the natural circulation capacity in the lower channel. Under inclined conditions, there is a phenomenon of temperature stratification in the mixed-flow channel.

A study on the effects of long-term radiation exposure on superconducting magnets in MRI-Guided proton therapy

In this publication, we offer the first assessment of the long-term radiation impact on superconducting magnets utilized in MRI-guided proton therapy. We explore both uniform and non-uniform magnetic fields and create three improved therapy plans for shallow (brain), medium (liver), and deep (prostate) targets. The evaluation of radiation damage in superconducting magnets using therapy plans is carried out through the implementation of the Monte Carlo method, molecular dynamics method, and modified NRT model. The results of the three plans show that a large amount of particles do enter the superconducting magnet during the treatment, with a preponderance of photons and neutrons. For superconducting magnets in MRI systems, the closer the coil is to the target area, the greater the radiation damage, and the extent of radiation damage increases with the energy of the incident proton beam. The PKA with high energy can induce temperature fluctuations locally in the superconducting coils, but does not pose a threat to its mechanical properties. Following 20 years of continuous operation, the DPA of the internal coils is about 2.3097E-17, and the maximum dose to insulating layer is about 1.25 Gy. The results of this paper show that MRI-guided proton therapy poses no threat to the long-term operation of superconducting magnets.

Localized Phonon Transport Study of GaN/SiO2 Core/shell Nanowires under Thermal-Stress Coupling.

In order to comprehensively explore the intricate mechanisms of thermo-mechanical interactions, this study employs the molecular dynamics method to investigate the influence of heat flux density, shell thickness and length, as well as stress on the radial interface phonon transport in GaN/SiO2 core/shell nanowire. Additionally, the surface eigenmode decomposition method is employed to analyze the interface phonon dispersion curves. The investigation reveals that with increasing heat flux density, internal thermal stresses intensify, leading to a complex distribution of thermal stresses within the system. Under the influence of thermal stress, the nonlinear acoustic properties interact with phonon scattering, resulting in the pronounced localization of interface phonons. Compressive stress causes an upshift in low-frequency phonons, while tensile stress induces a downward shift in the high-frequency optical branches at the interface. The localized phonon vibrations at the SiO2/GaN interface under nonuniform stress are identified as the primary cause for the abundant presence of nondispersive phonon modes at the radial interface. By elucidating the subtle interplay between lattice vibrations and stress fields, this study offers a novel and profound understanding of thermo-mechanical coupling effects, thereby providing innovative theoretical foundations for the design and performance management of thermoelectric devices.