• 제목/요약/키워드: Molecular-Dynamics Simulation

검색결과 540건 처리시간 0.027초

분자동역학기법을 이용한 나노 임프린트 리소그래피 공정에서의 고분자 변형모사 (Deformation of Polymer Resist in NIL Process by Molecular Dynamic Simulation)

  • 우영석;이우일
    • 대한기계학회:학술대회논문집
    • /
    • 대한기계학회 2007년도 춘계학술대회A
    • /
    • pp.337-342
    • /
    • 2007
  • In this study, molecular dynamics simulation of nano imprint lithography in which patterned stamp is pressed onto amorphous polyethylene(PE) surface are performed to study the behaviour of polymer. Force fields including bond, angle, torsion, and Lennard Jones potential are used to describe the inter-molecular and intra-molecular force of PE molecules and stamp, substrate. Periodic boundary condition is used in horizontal direction and canonical NVT ensemble is used to control the system temperature. As the simulation results, the behaviour of polymer is investigated during the imprinting process. The mechanism of polymer deformation is studied by means of inspecting the surface shape, volume, density, atom distribution. Deformation of the polymer resist was found for various of the stamp geometry and the alignment state of the polymer molecules.

  • PDF

Molecular Dynamics Simulation on thermodynamic and Structural Properties of Liquid Hydrocarbons : Normal Alkanes

  • Im, Won-Pil;Won, Young-Do
    • Bulletin of the Korean Chemical Society
    • /
    • 제15권10호
    • /
    • pp.852-856
    • /
    • 1994
  • A series of aliphatic hydrocarbons, methane to hexane in the liquid state, are modeled with the molecular mechanical potential parameters treating all hydrogen degrees of freedom explicitly. Thermodynamic properties (heat capacities and heats of vaporization) are calculated from relatively short (20ps) molecular dynamics trajectories. The liquid state structures are also examined through various radial distribution functions. Molecular dynamics simulations reproduce experimentally measured properties within a few percent errors, thus indicate that the present set of all-hydrogen parameters is suitable for simulating macromolecular systems in bulk.

Targeting of integrin αvβ3 with different sequence of RGD peptides: A molecular dynamics simulation study

  • Azadeh Kordzadeh;Hassan Bardania;Esmaeil Behmard;Amin Hadi
    • Advances in nano research
    • /
    • 제15권2호
    • /
    • pp.105-111
    • /
    • 2023
  • Integrin αvβ3 is one of the receptors expressed in cancer cells. RGD peptides have the potential to target integrin αvβ3 (receptor), which can increase drug delivery efficiency. In this study, 55 different RGD dimer motifs were investigated. At first, the binding energy between RGD peptides and the receptor was calculated using molecular docking. Then, three RGD peptides with the strongest binding energy with the receptor were selected, and their dynamic adsorption on the receptor was simulated by molecular dynamics (MD). The obtained results showed that a sequence that has RGD at the beginning and end with tryptophan (TRP) has strong Lennard-Jones (LJ) and electrostatic interactions with Integrin αvβ3 and has changed the conformation of receptor significantly, which analyzed by root mean square deviation (RMSD) and radius of gyration.

분자 동역학 모사를 이용한 Fe(100) 표면의 스퍼터링 해석 (Sputtering of Fe(100) Substrate Due to Energetic Ion Bombardments: Investigation with Molecular Dynamics Simulations)

  • 김동호
    • 한국표면공학회지
    • /
    • 제39권2호
    • /
    • pp.76-81
    • /
    • 2006
  • Molecular dynamics simulations were carried out to investigate physical sputtering of Fe(100) substrate due to energetic ion bombardments. Repulsive interatomic potentials at short internuclear distances were determined with ab initio calculations using the density functional theory. Bohr potentials were fitted to the ab initio results on diatomic pairs (Ar-Fe, Fe-Fe) and used as repulsive screened Coulombic potentials in sputtering simulations. The fitted-Bohr potentials improve the accuracy of the sputtering yields predicted by molecular dynamics for sputtering of Fe(100), whereas Moliere and ZBL potentials were found to be too repulsive and gave relatively high sputtering yields. In spite of assumptions and limitations in this simulation work, the sputtering yields predicted by the molecular dynamics method were in fairly good accordance with the obtainable experimental data in absolute values as well as in manner of the variation according to the Incident energy. Threshold energy for sputtering of Fe(100) substrate was found to be about 40 eV. Additionally, distributions of kinetic energies of sputtered atoms and their original depths could be obtained.

분자동역학을 이용한 다공성 물질 건조공정 멀티스케일 시뮬레이션(2부: 미시 물성) (Multi-scale simulation of drying process for porous materials using molecular dynamics (part 2: material properties))

  • 백성민;금영탁
    • 한국결정성장학회지
    • /
    • 제15권4호
    • /
    • pp.162-167
    • /
    • 2005
  • 건조공정 중인 다공성 물질의 물성은 재료의 비균질성 즉 전위, 입자, 입계, 균열, 기공과 같은 미시적인 결함인자들의 영향을 받는다. 따라서 다공성 물질의 건조공정을 전산 시뮬레이션하기 위해서는 원자 스케일 해석을 통한 미시적 물성을 알아야 한다. 본 연구에서는 분자동역학 시뮬레이션을 이용하여 원자 모델을 구성하고 원자 상호간 거동을 예측하여 재료의 미시적 물성을 계산하였다. 이렇게 구한 탄성계수, 열팽창계수, 체적 열용량은 실험 및 이론에 기초한 결과들과 비교하여 검증하였다.

Molecular Modeling and its Experimental Verification for the Catalytic Mechanism of Candida antarctica Lipase B

  • Kwon, Cheong-Hoon;Shin, Dae-Young;Lee, Jong-Ho;Kim, Seung-Wook;Kang, Jeong-Won
    • Journal of Microbiology and Biotechnology
    • /
    • 제17권7호
    • /
    • pp.1098-1105
    • /
    • 2007
  • Quantum mechanical and molecular dynamics simulation analysis has been performed on the model system for CALB (Candida antarctica lipase B) with esters to study the reaction mechanism and conformational preference of catalytic hydrolysis and the esterification reaction. Using quantum mechanical analysis, the ping-pong bi-bi mechanism was applied and energies and 3-dimensional binding configurations of the whole reaction pathways were calculated. Further molecular dynamics simulation analysis was performed on the basis of the transition state obtained from quantum mechanical study to observe the effect of structures of the substrates. Calculation results using substrates of different chain length and chiral configurations were compared for conformational preference. The calculated results showed very small influence on chain length, whereas chiral conformation showed big differences. Calculated results from molecular modeling studies have been compared qualitatively with the experimental data using racemic mixtures of (${\pm}$)-cis-4-acetamido-cyclopent-2-ene-1-ethyl acetate as substrates.

Molecular Dynamics Simulation of Contact Process in AFM/FFM Surface Observation

  • Shimizu, J.;Zhou, L.;Eda, H.
    • 한국윤활학회:학술대회논문집
    • /
    • 한국윤활학회 2002년도 proceedings of the second asia international conference on tribology
    • /
    • pp.61-62
    • /
    • 2002
  • In order to clarify the contact mechanism between specimen surface and probe tip in the surface observation by the AFM (atomic force microscope) or the FFM (friction force microscope), several molecular dynamics simulations have been performed. In the simulation, a 3-dimensional simulation model is proposed where the specimen and the probe are assumed to consist of mono-crystal line copper and a carbon atom respectively and the effect of cantilever stiffness is also taken into considered. The surface observation process on a well-defined Cu{100} is simulated. The influences of cantilever stiffness on the reactive force images and the behavior of probe tip were evaluated. As a resuIt, several phenomena similar to those observed by the actual surface observation experiment, such as double-slip behavior and dispersion in the stick-slip wave period were observed.

  • PDF

분자동역학 전산모사를 이용한 나노임프린트 리소그래피 공정에서의 스탬프-레지스트 간의 상호작용 및 원자분포에 관한 연구 (A study on the stamp-resist interaction mechanism and atomic distribution in thermal NIL process by molecular dynamics simulation)

  • 양승화;조맹효
    • 대한기계학회:학술대회논문집
    • /
    • 대한기계학회 2007년도 춘계학술대회A
    • /
    • pp.343-348
    • /
    • 2007
  • Molecular dynamics study of thermal NIL (Nano Imprint Lithography) process is performed to examine stamp-resist interactions. A layered structure consists of Ni stamp, poly-(methylmethacrylate) thin film resist and Si substrate was constructed for isothermal ensemble simulations. Imposing confined periodicity to the layered unit-cell, sequential movement of stamp followed by NVT simulation was implemented in accordance with the real NIL process. Both vdW and electrostatic potentials were considered in all non-bond interactions and resultant interaction energy between stamp and PMMA resist was monitored during stamping and releasing procedures. As a result, the stamp-resist interaction energy shows repulsive and adhesive characteristics in indentation and release respectively and irregular atomic concentration near the patterned layer were observed. Also, the spring back and rearrangement of PMMA molecules were analyzed in releasing process.

  • PDF

탄소와 구리의 마찰 및 마모에 관한 분자 동역학 시뮬레이션 (Molecular Dynamics Simulation of Friction and Wear Behavior Between Carbon and Copper)

  • 김광섭;강지훈;김경웅
    • Tribology and Lubricants
    • /
    • 제20권2호
    • /
    • pp.102-108
    • /
    • 2004
  • In this paper, friction and wear behaviors between monocrystalline, defect-free copper and carbon on the atomic scale are investigated by using 2-dimensional molecular dynamics simulation. It is assumed that all interatomic forces are given by Morse potential. The deformation of carbon is assumed to be neglected and vacuum condition is also assumed. Average friction and normal forces for various surface conditions, various scratch speeds and scratch depths are obtained from simulations. Changes of wear behaviors for various scratch speeds and surface conditions are investigated by observing snapshots in scratch process. The effects of surface conditions, scratch speeds, and scratch depths on the friction force, normal force, and friction coefficient are also investigated.

카본나노튜브의 포텐셜 함수에 따른 마찰거동에 대한 분자동역학 시뮬레이션 연구 (Study on frictional behavior of carbon nanotube with respect to potential function by molecular dynamics simulation)

  • 김현준;김대은
    • 정보저장시스템학회논문집
    • /
    • 제9권2호
    • /
    • pp.36-41
    • /
    • 2013
  • Frictional behavior of a single carbon nanotube(CNT) was investigated using molecular dynamics simulation. A single CNT aligned horizontally on silver or graphene substrate was modeled to evaluate its frictional behavior such as frictional force and rolling/sliding motion with respect to potential parameter and lattice structure of the substrate. As a result, it was found that friction and rolling was affected by adhesion between two surfaces and period of the rolling depended on lattice distance of the substrate.