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.

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.

scholarly journals Interaction Between Edge Dislocation and Single-Layered Graphene in Aluminum Matrix Investigated by Molecular Dynamics Simulation

2022 ◽  
Vol 2152 (1) ◽  
pp. 012034
Author(s):  
Liu Chen ◽  
Zhencheng Li ◽  
Sai Xu ◽  
Aixue Sha
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Mechanical Response ◽  
Aluminum Matrix ◽  
Shear Plane ◽  
Computational Method ◽  
Dynamics Simulation ◽  
Size Dependent ◽  
Graphene Interface ◽  
Dislocation Movement

Abstract The influence of graphene on dislocation movement and subsequent mechanical response of aluminum is investigated by the computational method of molecular dynamics simulation. A Lennard–Jones potential describing Al-C interaction was obtained through ab initio calculation. It was observed that the 2D graphene could reinforce Al matrix similar to the traditional Orowan mechanism. The Al/graphene interface first attract the gliding dislocation to reduce the system energy, which is unlike the grain boundary to repel gliding dislocations through pile-up mechanism. With the increase of stress, dislocation attracted and trapped at the front of graphene could glide along the interface and finally bypass it through climbing when graphene is orientated out of the shear plane. In addition, the strengthening ability of graphene is size dependent, showing a linear relationship between strength increment and graphene size.

scholarly journals The Potential role of Procyanidin as a Therapeutic Agent against SARS-CoV-2: A Text Mining, Molecular Docking and Molecular Dynamics Simulation Approach

2020 ◽  
Author(s):  
Nikhil Maroli ◽  
Balu Bhasuran ◽  
Jeyakumar Natarajan ◽  
Ponmalai Kolandaivel
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Text Mining ◽  
Van Der Waals ◽  
Interaction Network ◽  
Van Der Waals Interactions ◽  
Entity Recognition ◽  
Dynamics Simulation ◽  
Inhibition Mechanism

<p></p><p></p><p>A novel coronavirus (SARS-CoV-2) has caused a major outbreak in human all over the world. There are several proteins interplay during the entry and replication of this virus in human. Here, we have used text mining and named entity recognition method to identify co-occurrence of the important COVID 19 genes/proteins in the interaction network based on the frequency of the interaction. Network analysis revealed a set of genes/proteins, highly dense genes/protein clusters and sub-networks of Angiotensin-converting enzyme 2 (ACE2), Helicase, spike (S) protein (trimeric), membrane (M) protein, envelop (E) protein, and the nucleocapsid (N) protein. The isolated proteins are screened against procyanidin-a flavonoid from plants using molecular docking. Further, molecular dynamics simulation of critical proteins such as ACE2, Mpro and spike proteins are performed to elucidate the inhibition mechanism. The strong network of hydrogen bonds and hydrophobic interactions along with van der Waals interactions inhibit receptors, which are essential to the entry and replication of the SARS-CoV-2. The binding energy which largely arises from van der Waals interactions is calculated (ACE2=-50.21 ± 6.3, Mpro=-89.50 ± 6.32 and spike=-23.06 ± 4.39) through molecular mechanics Poisson-Boltzmann surface area also confirm the affinity of procyanidin towards the critical receptors.</p><p></p><p></p>

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.

scholarly journals Percolated Network of Mixed Nanoparticles with Different Sizes in Polymer Nanocomposites: A Coarse-Grained Molecular Dynamics Simulation

Materials ◽  
2021 ◽  
Vol 14 (12) ◽  
pp. 3301
Author(s):  
Xiuying Zhao ◽  
Yun Nie ◽  
Haoxiang Li ◽  
Haoyu Wu ◽  
Yangyang Gao ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Percolation Threshold ◽  
Polymer Nanocomposites ◽  
Total Concentration ◽  
Research Work ◽  
Antagonistic Effect ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Contrast Effects

The size of real nanoparticles (NPs) is polydisperse which can influence the electrical property of polymer nanocomposites (PNCs). Here, we explored the percolated network of mixed NPs with different sizes (small NPs and big NPs) by adopting a molecular dynamics simulation. The simulated results reveal that the big NPs are adverse to building the percolated network compared to the small NPs. Thus, the percolation threshold becomes higher along with increasing the mixing ratio, which denotes the concentration ratio of big NPs to the total NPs. For a better understanding of it, the dispersion state and the number and the size of clusters are employed to analyze the percolated network, which can explain the percolation threshold well. Furthermore, by adopting the Sun’s theory (Macromolecules, 2009, 42, 459–463), small and big NPs exhibit a weak antagonistic effect in the simulation if their total concentration is fixed. On the one hand, the number of small NPs is larger than that of big NPs at the same concentration. In addition, one big NP can connect to more others than one small NP. These two contrast effects are responsible for it. Interestingly, the shear flow leads to more contact aggregation structure of NPs which is beneficial to build the new percolated networks. Especially, the big NPs play a more important role in forming the percolated network than small NPs. Consequently, the percolation threshold is reduced at a higher shear rate. In total, our research work provides a further understanding of how the mixed NPs with different sizes form the percolated network in polymer matrix.

scholarly journals Molecular-dynamics investigation of molecular flexibility in ligand binding

1992 ◽  
Vol 288 (1) ◽  
pp. 109-116 ◽  
Author(s):  
B Mao
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Ligand Binding ◽  
Molecular Dynamics Simulations ◽  
Computational Method ◽  
Conformational Space ◽  
Dynamics Simulation ◽  
General Notion ◽  
Molecular Flexibility ◽  
Dynamics Simulations

The molecular flexibility of an inhibitor in ligand-binding process has been investigated by the mass-weighted molecular-dynamics simulation, a computational method adopted from the standard molecular-dynamics simulation and one by which the conformational space of a biomolecular system over potential energy barriers can be sampled effectively. The bimolecular complex of the aspartyl proteinase from Rhizopus chinensis, rhizopuspepsin, and an octapeptide inhibitor was previously studied in a mass-weighted molecular-dynamics simulation; the study has been extended for investigating the molecular flexibility in ligand binding. A series of mass-weighted molecular-dynamics simulations was carried out in which libration of the inhibitor dihedral angles was parametrically controlled, and threshold values of dihedral angle libration amplitudes were observed from monitoring the sampling of the enzyme binding pocket by the inhibitor in the simulations. The computational results are consistent with the general notion of molecular-flexibility requirement for ligand binding; the freedom of dihedral rotations of side-chain groups was found to be particularly important for ligand binding. Thus the critical degree of molecular flexibility which would contribute to effective enzyme inhibition can be obtained precisely from the modified molecular-dynamics simulations; the procedure described herein represents a first step toward providing quantitative measures of such a molecular-flexibility index for inhibitor molecules that have been otherwise targeted for optimal protein-ligand interactions.

scholarly journals Ab initio molecular dynamics simulation of methanol and acetonitrile: The effect of van der Waals interactions

2019 ◽  
Vol 714 ◽  
pp. 172-177 ◽  
Author(s):  
Rafael F. Dias ◽  
Cleidineia C. da Costa ◽  
Taise M. Manhabosco ◽  
Alan B. de Oliveira ◽  
Matheus J.S. Matos ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Ab Initio ◽  
Van Der Waals ◽  
Van Der Waals Interactions ◽  
Dynamics Simulation ◽  
Ab Initio Molecular Dynamics
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