A Basic Study of the CNT-Biomolecule Conjugation by Molecular Dynamics Analysis

2008 ◽  
Vol 381-382 ◽  
pp. 361-364
Author(s):  
S.M. Kim ◽  
Hyun Kyu Kweon
Keyword(s):  
Molecular Dynamics ◽  
Carbon Nanotube ◽  
Molecular Dynamics Simulation ◽  
Van Der Waals ◽  
Van Der Waals Force ◽  
Dynamics Simulation ◽  
Water Molecules ◽  
Basic Study ◽  
Hydrophobic Force ◽  
Simulation Results

This study is about the underlying conjugation mechanism between carbon nanotube and biomolecule by molecular dynamics. In order to know about the conjugation mechanism between carbon nanotube and biomolecule, molecular dynamics simulation between carbon nanotube and water molecules was taken first and then molecular dynamics simulation between biomolecules and water molecules was taken. At simulation between carbon nanotube and water molecules, kinetic energy and potential energy became decreased with time and it means that the distance between carbon nanotube and water molecules becomes distant with time by van der Waals force and hydrophobic force. Simulation results between biomolecules and water molecules are also same as the results of carbon nanotube and water molecules simulation. From these two simulations, the conjugation mechanism between carbon nanotube and biomolecules can be predicted. Also, from simulation results between carbon nanotube and biomolecules, the distance between carbon nanotube and biomolecules becames close and it supports previous two simulation results. From these results, we can know that biomolecules enter into the carbon nanotube's cavity because of van der Waals force and hydrophobic force.

Molecular dynamics simulation of a hydrated phospholipid bilayer

1994 ◽  
Vol 344 (1309) ◽  
pp. 239-260 ◽  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Complex Systems ◽  
Phospholipid Bilayer ◽  
Dynamics Simulation ◽  
Water Molecules ◽  
Hydrocarbon Chains ◽  
Membrane Bound ◽  
Simulation Results ◽  
Well Data

A hydrated bilayer of the phospholipid 1,2-dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC) has been studied in the course of a molecular dynamics simulation. Comparison of the simulation results with experiment indicates that generally the two agree well. Data are presented concerning all the major system regions, including the hydrocarbon chains, the glycerol region, the lipid headgroups and the hydrating water molecules. The simulations suggest that this model can be extended to the study of more complex systems of greater biochemical interest, such as membrane bound proteins.

INVESTIGATION FOR MOLECULAR ATTRACTION IMPACT BETWEEN CONTACTING SURFACES IN MICRO-GEARS

2013 ◽  
Vol 27 (27) ◽  
pp. 1350150
Author(s):  
PING YANG ◽  
XIALONG LI ◽  
YANFANG ZHAO ◽  
HAIYING YANG ◽  
SHUTING WANG ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Van Der Waals ◽  
Research Work ◽  
Van Der Waals Force ◽  
Computational Method ◽  
Gear Train ◽  
Dynamics Simulation ◽  
Geometrical Properties ◽  
Molecular Attraction

The aim of this research work is to provide a systematic method to perform molecular attraction impact between contacting surfaces in micro-gear train. This method is established by integrating involute profile analysis and molecular dynamics simulation. A mathematical computation of micro-gear involute is presented based on geometrical properties, Taylor expression and Hamaker assumption. In the meantime, Morse potential function and the cut-off radius are introduced with a molecular dynamics simulation. So a hybrid computational method for the Van Der Waals force between the contacting faces in micro-gear train is developed. An example is illustrated to show the performance of this method. The results show that the change of Van Der Waals force in micro-gear train has a nonlinear characteristic with parameters change such as the modulus of the gear and the tooth number of gear etc. The procedure implies a potential feasibility that we can control the Van Der Waals force by adjusting the manufacturing parameters for gear train design.

scholarly journals Does the single-walled carbon nanotube affect the rate constant of binding of biotin to streptavidin? Molecular dynamics simulation perspective

2019 ◽  
Vol 44 (3) ◽  
pp. 234-243
Author(s):  
Orkide Soltani ◽  
Mohammad Reza Bozorgmehr ◽  
Mohammad Momen-Heravi
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Carbon Nanotube ◽  
Molecular Dynamics Simulation ◽  
Complex Formation ◽  
Van Der Waals ◽  
Dynamics Simulation ◽  
Electrostatic Forces ◽  
Single Walled Carbon Nanotube ◽  
Arrhenius Dependence

The interaction of biotin and streptavidin in the presence and absence of a carbon nanotube was studied by molecular dynamics simulation. With respect to the Arrhenius dependence of the rate constants with temperature, those of streptavidin–biotin complex formation ([Formula: see text]) and streptavidin–biotin complex dissociation ([Formula: see text]) were calculated from molecular dynamics simulation trajectories. Nanotube has reduced the amount of and k1and k1. However, the biotin position in streptavidin does not change much. The results obtained from MMPBSA calculations show that the contribution of the van der Waals forces to both systems (in the absence and presence of the nanotube) was greater than that of electrostatic forces. The presence of the nanotube also led to the reduction of van der Waals and electrostatic forces in the interaction of biotin with streptavidin. However, this reduction was greater for electrostatic forces. In the absence of a nanotube, there are four hydrogen bonds between streptavidin and biotin, which are related to the residues Ser27, Tyr43, Ser45 and Ser88. In the presence of the nanotube, the hydrogen bonding of biotin with Ser45 is removed.

Molecular Dynamics Simulation of the Hydrogen Bonding Structure of Water Molecules Inside Carbon Nanotube

2013 ◽  
Author(s):  
Ning Zhang ◽  
Cong Chen ◽  
Yujing Feng ◽  
Qingnan Pang ◽  
Weizhong Li
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Carbon Nanotube ◽  
Molecular Dynamics Simulation ◽  
Hydrogen Bonds ◽  
Dynamics Simulation ◽  
Water Molecules ◽  
Structure Of Water ◽  
Bonding Structure ◽  
Single File

The structure of water molecules inside (6, 6) carbon nanotube under two different conditions are studied using molecular dynamics simulation. The structural and thermodynamic properties of the single-file water chain along the nanotube help to determine the hydrogen bonds between water molecules inside the channel. The properties of the systems show that induced pressure and ionic environment have similar effects on the structure of the inner water molecules. However, the Na+ and Cl− ions lead the number of hydrogen bonds inside the nanotube to fluctuate a little more greatly than that under the induced pressure.

scholarly journals Diamond Needles Actuating Triple-Walled Carbon Nanotube to Rotate via Thermal Vibration-Induced Collision

2019 ◽  
Vol 20 (5) ◽  
pp. 1140
Author(s):  
Hui Li ◽  
Aiqin Wang ◽  
Jiao Shi ◽  
Yongjian Liu ◽  
Gao Cheng
Keyword(s):  
Molecular Dynamics ◽  
Carbon Nanotube ◽  
Molecular Dynamics Simulation ◽  
Theoretical Analysis ◽  
Potential Application ◽  
Boundary Effect ◽  
Rotational Frequency ◽  
Dynamics Simulation ◽  
Simulation Results ◽  
Rotational Direction

A rotary nanomotor is an essential component of a nanomachine. In the present study, a rotary nanomotor from wedged diamonds and triple-walled nanotubes was proposed with the consideration of boundary effect. The outer tubes and mid-tubes were used as nanobearing to constrain the inner tube. Several wedges of the diamond were placed near the inner tube for driving the inner tube to rotate. At a temperature lower than 300 K, the inner tube as the rotor had a stable rotational frequency (SRF). It is shown that both the rotational direction and the value of SRF of the rotor depended on the temperature and thickness of the diamond wedges. The dependence was investigated via theoretical analysis of the molecular dynamics simulation results. For example, when each diamond wedge had one pair of tip atoms (unsaturated), the rotational direction of the rotor at 100 K was opposite to that at 300 K. At 500 K, the rotating rotor may stop suddenly due to breakage of the diamond needles. Some conclusions are drawn for potential application of such a nanomotor in a nanomachine.

The Study on Young's Modulus of Multilayered Cu/Ni Multilayered Nano Thin Films by Molecular Dynamics Simulation

2014 ◽  
Vol 513-517 ◽  
pp. 113-116
Author(s):  
Jen Ching Huang ◽  
Fu Jen Cheng ◽  
Chun Song Yang
Keyword(s):  
Thin Film ◽  
Thin Films ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Strain Rate ◽  
Young’S Modulus ◽  
Potential Function ◽  
Dynamics Simulation ◽  
System Temperature ◽  
Simulation Results

The Youngs modulus of multilayered nanothin films is an important property. This paper focused to investigate the Youngs Modulus of Multilayered Ni/Cu Multilayered nanoThin Films under different condition by Molecular Dynamics Simulation. The NVT ensemble and COMPASS potential function were employed in the simulation. The multilayered nanothin film contained the Ni and Cu thin films in sequence. From simulation results, it is found that the Youngs modulus of Cu/Ni multilayered nanothin film is different at different lattice orientations, temperatures and strain rate. After experiments, it can be found that the Youngs modulus of multilayered nanothin film in the plane (100) is highest. As thickness of the thin film and system temperature rises, Youngs modulus of multilayered nanothin film is reduced instead. And, the strain rate increases, the Youngs modulus of Cu/Ni multilayered nanothin film will also increase.

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