Effects of density on flow in a nano channel using a molecular-continuum hybrid method

Kim, Youngjin,Jeong, Myunggeun,Zhou, Wenjing,Tao, Wen Quan,Ambrosia, Matthew Stanley,Ha, Man Yeong Elsevier 2017 Computers & fluids Vol.156 No.-

<P><B>Abstract</B></P> <P>A molecular-continuum hybrid method was developed to simulate micro- and nano-scale fluid flows that cannot be predicted using continuum fluidics. Molecular dynamics simulation was used near stationary solid surfaces, and Navier-Stokes equations were used in other regions. We carried out Couette flow simulation using this hybrid method and validated the results by comparing them with the analytical solution. We also studied the dependence of the velocity slip and slip length on the surface energy, liquid density, and roughness for a liquid channel flow with and without nano-structures on the solid surface. The behavior of the liquid near the solid wall changed with the surface energy as well as the liquid density. The variation of the velocity slip and slip length according to the surface energy also depended on the liquid density as well as the surface roughness. We compared the required computational time obtained from the molecular-continuum hybrid method with that obtained from full molecular dynamics simulation under the same computational condition, giving much shorter computational time for the case using the molecular-continuum hybrid method than that for full molecular dynamics simulation.</P> <P><B>Highlights</B></P> <P> <UL> <LI> The velocity slip and slip length decrease with increasing the surface energy. </LI> <LI> The locking boundary condition is enhanced with the structure. </LI> <LI> The trends of <I>u<SUB>s</SUB> </I> and <I>L<SUB>s</SUB> </I> at each liquid density are changed on the smooth surface. </LI> <LI> The trends at each liquid density differ between the rough and smooth surface. </LI> </UL> </P>

A comprehensive molecular dynamics study of a single polystyrene chain in a good solvent

Sajad Rasouli,Mohammad Reza Moghbeli,Sousa Javan Nikkhah 한국물리학회 2018 Current Applied Physics Vol.18 No.1

In this study, molecular characteristics of polystyrene (PS) was calculated measuring its dilute-solution properties in toluene at 288.15 K via molecular dynamics (MD) simulations. The solution models consisted of PS chains with different number of repeating units all of which were in a dilute regime. In order to investigate the compatibility between the polymer and the solvent molecules, interaction energy and Flory-Huggins (FH) interaction parameter were estimated. The simulation results indicate that increasing the chain repeating units enhanced the interaction between the solute and the solvent. Additionally, the chain dimensions were evaluated calculating the radius of gyration (Rg) and end-to-end distance, r0. To determine the dynamic behavior of the chains in the solutions, mean square displacement (MSD) and diffusivity coefficient were calculated. The simulation results indicated that the chain rigidity at low molecular weight and chain flexibility with increasing the molecular weight influenced chains dynamic behavior and diffusivity. Moreover, radial distribution function (RDF) illustrated the effect of steric hindrance of the chains in dilute solution on capturing the solvent molecules. In addition, solution viscosity was calculated by performing non-equilibrium molecular dynamics simulation (NEMD). The obtained results of chain characteristics and viscosity showed a good agreement with experimental results published previously. This agreement confirms the accuracy of the applied simulation method to characterize the dilute solutions and the chains characteristics.

MD 시뮬레이션을 이용한 실린더 형태 나노와이어의 접촉면적에 관한 연구

김현준(Hyun-Joon Kim) 한국트라이볼로지학회 2016 한국트라이볼로지학회지 (Tribol. Lubr.) Vol.32 No.1

Contact between solid surfaces is one of the most important factors that influence dynamic behavior in micro/nanoscale. Although numerous theories and experimental results on contact behavior have been proposed, a thorough investigation for nanomaterials is still not available owing to technical difficulties. Therefore, molecular dynamics simulation was performed to investigate the contact behavior of nanomaterials, and the application of conventional contact theories to nanoscale was assessed in this work. Particularly, the contact characteristics of cylindrical nanowires were examined via simulation and contact theories. For theoretical analysis, various contact models were utilized and work of adhesion, Hamaker constant and elastic modulus those are required for calculation of the models were obtained from both indentation simulation and tensile simulation. The contact area of the cylindrical nanowire was assessed directly through molecular dynamics simulation and compared with the results obtained from the theories. Determination of the contact area of the nanowires was carried out via simulation by counting each atom, which is within the equilibrium length. The results of the simulation and theoretical calculations were compared, and it was estimated that the discrepancy in the results calculated between the simulation and the theories was less than 10 except in the case of the smallest nanowires. As the result, it was revealed that contact models can be effectively utilized to assess the contact area of nanomaterials.

Molecular dynamics simulation of carbon molecular sieve preparation for air separation

Elham Yaghoobpour,ALI AHMADPOUR,Nafiseh Farhadian,Mojtaba Shariaty-Niassar 한국화학공학회 2015 Korean Journal of Chemical Engineering Vol.32 No.3

Carbon deposition process on activated carbon (AC) in order to produce carbon molecular sieve (CMS)was simulated using molecular dynamics simulation. The proposed activated carbon for simulation includes microporeswith different characteristic diameters and lengths. Three different temperatures of 773 K, 973 K, and 1,273 K wereselected to investigate the optimum deposition temperature. Simulation results show that the carbon deposition processat 973 K creates the best adsorbent structure. While at lower temperature some micropore openings are blockedwith carbon atoms, at higher temperature the number of deposited carbons on the micropores does not change significantly. Also, carbon deposition process confirms the pseudo-second-order kinetic model with an endothermic behavior. To evaluate the sieving property of adsorbent products, nitrogen and oxygen adsorption on the initial and finaladsorbent products are examined. Results show that there is not any considerable difference between the equilibriumadsorption amounts of nitrogen and oxygen on the initial and final adsorbents especially at low pressure (P<10 atm). Although, adsorption kinetics curves of these gases change significantly after the carbon deposition process in comparisonwith the initial sample. These observations indicate that the final adsorbent has high selectivity towards oxygencompared with the nitrogen, so it can be called a carbon molecular sieve. All simulated results are in good agreementwith experiments.

Mechanical Behavior of PMMA/SiO2 Multilayer Nanocomposites: Experiments and Molecular Dynamics Simulation

Xiangshi Zhen,Liyan Zhang,Meinong Shi,Li Li,Lisheng Cheng,Zhiwei Jiao,Weimin Yang,Yumei Ding 한국고분자학회 2020 Macromolecular Research Vol.28 No.3

Poly(methyl methacrylate) (PMMA)/nano-silica (nano-SiO2) nanocomposite film with 256 layers containing different amounts of nano-SiO2 was manufactured by a new type of micro-nano multilayer co-extrusion technology. The structure, morphology and mechanical properties of PMMA/nano-SiO2 nanocomposite films were investigated through Fourier transform infrared spectroscopy (FTIR), scanning electron microscope (SEM) and tensile test. Besides, molecular dynamics simulation was adopted to study the dispersion and content effect on mechanical properties of PMMA/nano-SiO2 nanocomposite film. It is demonstrated that the tensile strength and the elongation at break of the composites improved with increasing nano-SiO2 content from 0 to 5 wt%, which was in good agreement with the Molecular Dynamics simulation. And the nanofiller dispersion in the multilayer nanocomposite film was better than that in the single-layer film with equivalent thickness under the effect of torsion lamination. Overall, the best performance was found for the nanocomposites of PMMA with nano-SiO2 content of 3.5 wt%.

Molecular Dynamics Simulation of Charged Liquid/Vapour Interface

( T. Funakawa ),( W. Balachandran ) 한국액체미립화학회 2005 한국액체미립화학회 학술강연회 논문집 Vol.2005 No.-

The paper discusses the instability mechanism of charged liquid/vapour interface using 3D Molecular Dynamics (MD) simulation. The equilibrium liquid/vapour interface was created in a rectangular simulation box, in which the periodical boundary condition is applied in all directions. The surface tension, the normal pressure, the bulk viscosity, and the shear viscosity were calculated respectively in both charged and uncharged conditions in order to determine the cause of the instability. The instability mechanisms were analyzed by comparison of the charged and uncharged simulation results. Ethane molecule was chosen as a sample fluid in this study. The Electron Bubble (EB), which is known as the main charge carrier of insulating liquids, represents an ion producing the electric field in the liquid/vapor interface. The 2CLJ potential was used for the calculation of the molecular interactions. The Coulomb and the polarization potentials were used to consider the EB effects on the molecules. The separation distance between methyl sites in the ethane molecule was constrained to be constant by the Rattle Algorithm. The reduction of the surface tension was confirmed in the condition when the liquid/vapour interface was charged. The reduction phenomenon appears to be induced by the shear stress increasing in the liquid/vapour interface due to the molecular aggregation effects by the EBs in the liquid phase.

Analysis of phase transition, structural and dynamical properties of R290 using molecular dynamics simulation

Md. Sarwar Alam,Ji Hwan Jeong 대한기계학회 2020 JOURNAL OF MECHANICAL SCIENCE AND TECHNOLOGY Vol.34 No.10

Propane (R290), a hydrocarbon refrigerant, is an excellent choice of cooling fluids for use in refrigeration and air conditioning systems considering the environmental point of view and system performance. The phase transition phenomenon and structural and dynamic properties of R290 were analyzed through a molecular dynamics (MD) simulation. The densities, isobaric heat capacities and viscosities were computed and the variations of density, volume, potential energy and the nucleation process were examined to investigate the effects of condensation temperature on the phase transition rate. The mean square displacement and velocity autocorrelation function for different temperatures were simulated for dynamical analysis. Radial distribution functions were investigated to get insight into the structural analysis at the atomic level. Shear viscosity and isobaric heat capacity obtained by the present simulation showed a good agreement with the REFPROP data. The structural analysis revealed that the phase transition of R290 did not affect its intramolecular structure.

분자동력학과 몬테카를로의 혼성 분자시뮬레이션에 의한 다가전해질 복잡유체의 미세구조 특성 연구

이현수,전명석 한국화학공학회 2002 Korean Chemical Engineering Research(HWAHAK KONGHA Vol.40 No.5

분자동력학(molecular dynamics)과 몬테카를로(Monte Carlo)의 혼성(hybrid) 알고리즘을 이용하여 harmonic spring 사슬과 하전된 단분자(monomer)들 사이의 Debye-Hu¨ckel potential로 표현된 다가전해질(polyelectrolyte)의 미세구조 특성을 규명하였다. Polyelectrolyte의 단일 사슬에 대해서 기존에 제안된 분자동력학과 몬테카를로의 혼성 알고리즘을 개선하여, polyelectrolyte의 conformation 특성인 끝단거리(end-to-end distance), 선회반경(radius of gyration), 그리고 구조인자(structure factor)를 한층 효율적으로 구할 수 있는 새로운 모사 기법을 개발하였다. 본 연구에서 새로이 개발된 알고리즘에 의한 모사결과와 기존 문헌값과의 비교를 통해 해석 방법의 타당성과 정확성을 검증하였다. 끝단거리와 선회반경간 평균제곱의 비와 구조인자의 계산을 통해, polyelectrolyte 단분자의 하전율(charge fraction)을 대변하는 Bjerrum length λ_β와 용액의 이온화세기에서 결정되어 용매의 screening 정도를 나타내는 Debye length k^-1가 증가함에 따라 사슬이 신장되는 거동을 확인하였다. The microstructural properties of charged polyelectrolytes described by a potential model regarding both the harmonic springs and Debye-Hu¨ckel interaction were investigated by employing a hybrid scheme of molecular dynamics(MD) and Monte Carlo(MC) simulations. Based on the previous hybrid scheme, a novel hybrid scheme has been developed in the present study, with which computational efforts are effectively reduced. We present the conformational properties such as end-to-end distance, radius of gyration and structure factor. It is evident that the simulation results of the present study agree well with the previously reported results. The elongation behavior of the polyelectrolyte chain can successfully be observed by the calculations of the characteristic mean square ratio of end-to-end distance to radius of gyration as well as the structure factor. As the Bjerrum length λ_β and the Debye length k^-1 increase, the polyelectrolyte chain becomes elongated.

Accelerating Molecular Dynamics Simulation Using Graphics Processing Unit

Myung, Hun-Joo,Sakamaki, Ryuji,Oh, Kwang-Jin,Narumi, Tetsu,Yasuoka, Kenji,Lee, Sik Korean Chemical Society 2010 Bulletin of the Korean Chemical Society Vol.31 No.12

We have developed CUDA-enabled version of a general purpose molecular dynamics simulation code for GPU. Implementation details including parallelization scheme and performance optimization are described. Here we have focused on the non-bonded force calculation because it is most time consuming part in molecular dynamics simulation. Timing results using CUDA-enabled and CPU versions were obtained and compared for a biomolecular system containing 23558 atoms. CUDA-enabled versions were found to be faster than CPU version. This suggests that GPU could be a useful hardware for molecular dynamics simulation.

Dynamics of a DNA minicircle: Poloidal rotation and in-plane circular vibration

Kim Minjung,Hong Chi Cheng,Lee Saeyeon,Kim Jun Soo 대한화학회 2022 Bulletin of the Korean Chemical Society Vol.43 No.4

We investigated the dynamics of a 90-base pair-long DNA minicircle with the sequence of (AT)45/(AT)45 using the all-atom molecular dynamics (MD) simulation. The simulation was run for a duration of 5 μs and the internal dynamics was analyzed in terms of the poloidal rotation and the in-plane circular vibration. The poloidal rotation was defined by the directional variation of each base pair relative to the plane of the DNA minicircle, and its correlation time was estimated to be 61 ns. The in-plane circular vibration was measured as the radial distance variation of each base pair from the center-of-mass of the DNA, and the correlation time was 6.3 ns. The characteristic time scales determined for the poloidal rotation and the radial fluctuation suggest that the internal motion of a small DNA minicircle is highly dynamic. This work provides a new set of dynamic information for small DNA minicircles, available for future applications.