scholarly journals Sliding Dynamics of Ring Chains on Two Asymmetric/Symmetric Chains in a Simple Slide-Ring Gel

Polymers ◽  
2021 ◽  
Vol 14 (1) ◽  
pp. 79
Author(s):  
Jiaxin Wu ◽  
Fuchen Guo ◽  
Ke Li ◽  
Linxi Zhang
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficient ◽  
Md Simulations ◽  
Time Range ◽  
Bending Energy ◽  
Diffusion Behavior ◽  
Symmetric Chains ◽  
Normal Diffusion ◽  
Intermediate Time ◽  
Sliding Dynamics

The sliding dynamics along two asymmetric/symmetric axial chains of ring chains linked by a linear chainis investigated using molecular dynamics (MD) simulations. A novel sub-diffusion behavior is observed for ring chains sliding along eithera fixed rod-like chain or fluctuating axial chain on asymmetric/symmetric axial chainsat the intermediate time range due to their strongly interplay between two ring chains. However, two ring chains slide in the normal diffusion at along time range because their sliding dynamics can be regarded as an overall motion of two ring chains. For ring chains sliding on two symmetric/asymmetricaxial chains, the diffusion coefficient D of ring chains relies on the bending energy of axial chains (Kb) as well as the distance of two axial chains (d). There exists a maximum diffusion coefficient Dmax at d = d* in which ring chains slide at the fastest velocity due to the maximum conformational entropy for the linking chain between two ring chainsat d = d*. Ring chain slide on fixed rod-like axial chainsfaster in the symmetric axial chain case than that in the asymmetric axial chain case. However, ring chains slide on fluctuatingaxial chainsslower in the symmetric axial chain case than that in the asymmetric axial chain case. This investigation can provide insights into the effects of the linked chain conformation on the sliding dynamics of ring chains in a slide-ring gel.

scholarly journals Diffusion of Water and Diatomic Oxygen in Poly(3-hexylthiophene) Melt: A Molecular Dynamics Simulation Study

2012 ◽  
Vol 11 (1 and 2) ◽  
Author(s):  
Julia Deitz ◽  
Yeneneh Yimer ◽  
Mesfin Tsige
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficient ◽  
Molecular Dynamics Simulation ◽  
Simulation Study ◽  
Dynamics Simulation ◽  
Fick’S Law ◽  
Fick's Law ◽  
Diffusion Behavior

Diffusion behavior of water, diatomic oxygen, and a mixture of both into a poly(3-hexylthiophene)[P3HT] melt were investigated using Molecular Dynamics Simulation. Once simulations were complete, the data was analyzed to determine the diffusion coefficient of those molecules in P3HT using Fick’s law. The diffusion coefficient values were then plotted as a function of concentration and temperature to determine if trends existed. For both water and oxygen, no dependence was observed of the diffusion coefficient on concentration and temperature for the ranges studied. However, a variation in the diffusion coefficient on concentration was observed due to the expected inhomogeneity of the P3HT melt. In the presence of O2, the diffusion of H2O decreased significantly by a factor between four and five, while in the presence of H2O, the diffusion of O2 slightly decreased.

scholarly journals A molecular dynamics study on the diffusion and imprint ability of spectinomycin under different sizes of aniline oligomers

2022 ◽  
Author(s):  
Chanadan Douykhumklaw ◽  
Thana Sutthibutpong
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficient ◽  
Mean Square Displacement ◽  
Md Simulations ◽  
Template Molecule ◽  
Aniline Oligomers ◽  
The Mean ◽  
The Stability ◽  
Further Development ◽  
Aniline Oligomer

Abstract Molecularly imprinted polymers (MIP) are the polymers created by molecular imprinting techniques that leave cavities for the specific interactions with a template molecule, and have been applied in molecular selectivity tasks. In this study, the molecular dynamics (MD) simulation technique was used to demonstrate that aniline oligomer could be developed as a potential MIP for detection and separation of the spectinomycin drug molecule for gonorrhoea treatment. MD simulations were performed for the systems of a spectinomycin within aniline oligomers of different sizes. The mean square displacement (MSD) and the diffusivity calculated from MD simulations showed that the diffusion coefficient was significantly dropped when the length of aniline oligomer was greater than two. The diffusion coefficient of spectinomycin became the lowest within aniline trimers, corresponded to the highest atomic distribution of MIP around the template. Then, the specific cavity in MIP systems with and without spectinomycin were calculated to assess the stability of the cavity created by the template. The volume of a cavity created within the trimer system was closest to the spectinomycin volume, and therefore became the optimal oligomer size for further development of MIP.

New View of Low-Temperature Sintering Phenomenon of Nanometer-Size Particles Based on Molecular Dynamics Study

MRS Advances ◽  
2016 ◽  
Vol 1 (30) ◽  
pp. 2167-2172
Author(s):  
Norie Matsubara ◽  
Shinji Munetoh ◽  
Osamu Furukimi
Keyword(s):  
Molecular Dynamics ◽  
Surface Layer ◽  
Diffusion Coefficient ◽  
Heating Temperature ◽  
Md Simulations ◽  
Atomic Scale ◽  
Self Diffusion ◽  
The Mean ◽  
The Relationship ◽  
Self Diffusion Coefficient

ABSTRACTIn this study, we have investigated a behavior of particle with diameter several ten nanometers size at the time of heating on an atomic scale by numerical analysis using the molecular dynamics (MD) simulation. On solving the equation of motion, the Langevin equation was adopted. The Finnis-Sinclair potential, which can well reproduce the mechanical properties of a BCC-metal, was used as the interatomic force. We determined the relationship between the melting point (Tm) of the nano-sized particles and its diameter by MD simulations. We have also investigated the self-diffusion coefficient of each atom-forming at a temperature larger or less than Tm of the submicron-size metal particles . As a result, even in case of heating at a temperature larger than Tm, the mean self-diffusion coefficient at the center of a particle was 10-7–10-6 cm2/sec. On the other hand, at the surface layer of the particle was two to three orders of magnitude larger than that at the center. Those particles were in a quasi-molten state. It is conceivable that the thickness of the surface layer can explain a phenomenon that sintering progresses as the heating temperature increases.

scholarly journals Molecular Dynamics Simulation on the Effect of Bonding Pressure on Thermal Bonding of Polymer Microfluidic Chip

Polymers ◽  
2019 ◽  
Vol 11 (3) ◽  
pp. 557 ◽  
Author(s):  
Mingyong Zhou ◽  
Xiang Xiong ◽  
Dietmar Drummer ◽  
Bingyan Jiang
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficient ◽  
Md Simulations ◽  
Equivalent Strain ◽  
Bonding Process ◽  
Tensile Failure ◽  
Dynamics Simulation ◽  
Thermal Bonding ◽  
Yield Strain ◽  
Bonding Pressure

Thermal bonding technology is the most commonly used approach in bonding injection-molded microfluidic chips. Although the bonding mechanism is still under debate, the molecular dynamics (MD) method can provide insight into the bonding process on a macromolecular level. In this study, MD simulations for thermal bonding of PMMA substrate and cover sheet were performed. The molecule configuration and density distribution during the thermal bonding process were studied. The effects of bonding pressure on the equivalent strain, joining energy and diffusion coefficient were investigated. The debonding process was simulated to analyze the bonding strength and failure mechanism. Simulation results show that penetration mainly takes place near the interface area. Although the final density increases slightly with increasing pressure, the bonding interface is still insufficiently filled. The equivalent strain grows faster than that in the later stage because of the gap at the interface. The bonding pressure shows clear effects on the joining energy, diffusion coefficient and stress–strain behavior. Tensile failure occurs at the interface, with PMMA chains stretched between two layers. The majority of the change in potential energy is correlated with the change in non-bonded energy. At yield strain, the low-density defect at the interface weakens the tensile strength of bonded chip.

MOLECULAR DYNAMICS STUDY OF THE DISRUPTION OF H-BONDS BY WATER MOLECULES AND ITS DIFFUSION BEHAVIOR IN AMORPHOUS CELLULOSE

2012 ◽  
Vol 26 (14) ◽  
pp. 1250088 ◽  
Author(s):  
RUIJIN LIAO ◽  
MENGZHAO ZHU ◽  
XIN ZHOU ◽  
FUZHOU ZHANG ◽  
JIAMING YAN ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Diffusion Coefficient ◽  
Hydrogen Bonds ◽  
Water Molecule ◽  
Free Volume ◽  
Water Molecules ◽  
Amorphous Cellulose ◽  
Diffusion Behavior ◽  
Bonding Structure

Hydrolysis is an important component of the aging of cellulose, and it severely affects the insulating performance of cellulosic materials. The diffusion behavior of water molecules in amorphous cellulose and their destructive effect on the hydrogen bonding structure of cellulose were investigated by molecular dynamics. The change in the hydrogen bonding structure indicates that water molecules have a considerable effect on the hydrogen bonding structure within cellulose: both intermolecular and intramolecular hydrogen bonds decreased with an increase in ingressive water molecules. Moreover, the stabilities of the cellulose molecules were disrupted when the number of intermolecular hydrogen bonds declined to a certain degree. Both the free volumes of amorphous cells and water molecule-cellulose interaction affect the diffusion of water molecules. The latter, especially the hydrogen bonding interaction between water molecules and cellulose, plays a predominant role in the diffusion behavior of water molecules in the models of which the free volume rarely varies. The diffusion coefficient of water molecules has an excellent correlation with water molecule-cellulose interaction and the average hydrogen bonds between each water molecule and cellulose; however, this relationship was not apparent between the diffusion coefficient and free volume.

scholarly journals Molecular Dynamics Investigation of Graphene Nanoplate Diffusion Behavior in Poly-α-Olefin Lubricating Oil

Crystals ◽  
2018 ◽  
Vol 8 (9) ◽  
pp. 361 ◽  
Author(s):  
Lupeng Wu ◽  
Baoyu Song ◽  
Leon Keer ◽  
Le Gu
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficient ◽  
Functional Groups ◽  
Lubricating Oil ◽  
Diffusion Behavior ◽  
Long Term Stability ◽  
Temperature And Pressure ◽  
First Time ◽  
Graphene Nanoplates

Graphene as a type of novel additive significantly enhanced the tribological performance of blended lubricating oil. However, the dispersibility of graphene with long-term stability in lubricating oil is still a challenge. Chemical modification for graphene, rather than using surfactants, provided a better method to improve the dispersibility of graphene in lubricants. In this study, the equilibrium molecular dynamics (EMD) simulations were carried out to investigate the diffusion behavior of graphene nanoplates in poly-α-olefin (PAO) lubricating oil. The effects of graphene-size, edge-functionalization, temperature, and pressure on the diffusion coefficient were studied. In order to understand the influence of edge-functionalization, three different functional groups were grafted to the edge of graphene nanoplates: COOH, COON(CH3)2, CONH(CH2)8CH3 (termed GO, MG, and AG, respectively). The EMD simulations results demonstrated that the relationships between diffusion coefficient and graphene-size and number of functional groups were linear while the temperature and pressure had a nonlinear influence on the diffusion coefficient. It was found that the larger dimension and more functional groups provided the lower diffusion coefficient. AG with eight CONH(CH2)8CH3 groups exhibited the lowest diffusion coefficient. Furthermore, the experimental results and radial distribution function for graphene-PAO illustrated that the diffusion coefficient reflected the dispersibility of nanoparticles in nanofluids to some degree. To our best knowledge, this study is the first time the diffusion behavior of graphene in PAO lubricating oil was investigated using EMD simulations.

Molecular dynamics simulation of the diffusion behavior of water in poly(vinylidene fluoride)/silica hybrid membranes

RSC Advances ◽  
2015 ◽  
Vol 5 (70) ◽  
pp. 57147-57154 ◽  
Author(s):  
Ruibing Bai ◽  
Huixia Wang ◽  
Pan Zhang ◽  
Bo Xiao ◽  
Bo Jiang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Vinylidene Fluoride ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Hybrid Membranes ◽  
Diffusion Behavior ◽  
Poly Vinylidene Fluoride ◽  
Silica Hybrid ◽  
Diffusion Properties

The effects of inorganic SiO2 particles on the diffusion properties of small penetrant molecules in PVDF/SiO2 hybrid membranes are investigated using MD simulations.

Molecular Dynamics Study of H2O Molecular Diffusion Behavior in PAM/PVA Polymer Blends

2015 ◽  
Vol 1119 ◽  
pp. 268-272
Author(s):  
Qing Hua Wei ◽  
Ya Nen Wang ◽  
Ming Ming Yang ◽  
Wei Hong Chai ◽  
Ying Feng Zhang
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficient ◽  
Polymer Blends ◽  
Molecular Diffusion ◽  
Theoretical Method ◽  
Component Ratio ◽  
Diffusion Behavior ◽  
Method Of Molecular Dynamics ◽  
Influence Of Temperature On ◽  
Water Contents

The theoretical method of molecular dynamics was applied to study H2O molecular diffusion behavior in PAM/PVA Polymer blends, investigated the effects of component ratios, temperatures and water contents on diffusion coefficient. Results show that with the increase of PVA content in blend systems, the H2O molecule diffusion coefficient first increased and then decreased. This indicates there is an optimum component ratio to make the H2O molecule diffusion coefficient maximum. There is a certain influence of temperature on H2O molecular diffusion in PAM/PVA blend system, the higher the temperature, the bigger the H2O molecular diffusion coefficient. When the less H2O molecules contained in system, there is a less impact on the diffusion coefficient. As the number of H2O molecules reaches a certain amount, the effect on the diffusion coefficient is more obvious.

Efficient Treatment of Fixed and Induced Dipolar Interactions

2000 ◽  
Vol 653 ◽  
Author(s):  
Celeste Sagui ◽  
Thoma Darden
Keyword(s):  
Molecular Dynamics ◽  
Md Simulations ◽  
Lagrangian Formalism ◽  
Dipolar Interactions ◽  
Time Step ◽  
Efficient Treatment ◽  
Particle Mesh Ewald ◽  
Fixed Charges ◽  
Self Consistency ◽  
Induced Dipoles

AbstractFixed and induced point dipoles have been implemented in the Ewald and Particle-Mesh Ewald (PME) formalisms. During molecular dynamics (MD) the induced dipoles can be propagated along with the atomic positions either by interation to self-consistency at each time step, or by a Car-Parrinello (CP) technique using an extended Lagrangian formalism. The use of PME for electrostatics of fixed charges and induced dipoles together with a CP treatment of dipole propagation in MD simulations leads to a cost overhead of only 33% above that of MD simulations using standard PME with fixed charges, allowing the study of polarizability in largemacromolecular systems.

Split the Charge Difference in Two! a Rule of Thumb for Adding Proper Amounts of Ions in MD Simulations

2020 ◽  
Author(s):  
Matías R. Machado ◽  
Sergio Pantano
Keyword(s):  
Molecular Dynamics ◽  
Ionic Strength ◽  
Molecular Simulations ◽  
Md Simulations ◽  
Good Practices ◽  
Rule Of Thumb ◽  
Ionic Concentrations

<p> Despite the relevance of properly setting ionic concentrations in Molecular Dynamics (MD) simulations, methods or practical rules to set ionic strength are scarce and rarely documented. Based on a recently proposed thermodynamics method we provide an accurate rule of thumb to define the electrolytic content in simulation boxes. Extending the use of good practices in setting up MD systems is promptly needed to ensure reproducibility and consistency in molecular simulations.</p>

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