THE "FOLDING" BEHAVIORS OF HOMOPOLYMERS WITH ONE END FIXED

2004 ◽  
Vol 18 (15) ◽  
pp. 2123-2139 ◽  
Author(s):  
BIN XUE ◽  
JUN WANG ◽  
WEI WANG
Keyword(s):  
Molecular Dynamics ◽  
Chain Length ◽  
Conformational Changes ◽  
Canonical Ensemble ◽  
Interaction Strength ◽  
Simulation Method ◽  
Dynamics Simulation ◽  
Radius Of Gyration ◽  
Native Conformation ◽  
Collapse Temperature

We study the "folding" behaviors of homopolymers with one end fixed. By using canonical ensemble molecular dynamics simulation method, we observe the conformational changes during folding processes. Long chains collapse to the helical nuclei, then regroup to helix from the free-end to form the compact conformations through the middle stages of helix-like coil and helix-like cone, while short chains do not apparently have the above mentioned middle stages. Through simulated annealing, the native conformation of homopolymer chain in our model is found to be helix. We show the relations between specific heat C v (T) and radius of gyration R g (T) as functions of temperature, chain length and the interaction strength, respectively. We find that these two quantities match well and can be combined to interpret the "folding" process of the homopolymer. It is found that the collapse temperature Tθ and the native-like folding temperature T f do not change with the chain length in our model, however the interaction strength affects the values of Tθ and T f .

Comparison of the effect of poly(N-vinyl caprolactam) and poly(N-isopropyl acrylamide) trimers on the stability of hydrated Na-montmorillonite: A molecular dynamics study

2020 ◽  
pp. 096739112093524
Author(s):  
Jiafang Xu ◽  
Moussa Camara ◽  
Hualin Liao ◽  
Hong Guo ◽  
Kouassi Louis Kra ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Conformational Changes ◽  
Stable State ◽  
Dynamics Simulation ◽  
Effect Of Temperature ◽  
Radius Of Gyration ◽  
Molecular Arrangement ◽  
Isopropyl Acrylamide ◽  
The Stability ◽  
The Impact

In the present study, we performed a molecular dynamics simulation of the intercalation of poly( N-isopropyl acrylamide) (NIPAM)3 and poly( N-vinyl caprolactam) (NVCL)3 trimers into Na-montmorillonite (Na-Mt) to evaluate their effects on the interlayer structure and the stability of hydrated Na-Mt. The impact of both trimers on the interlayer species and their dynamics properties at different temperatures in a canonical ensemble (NVT) were investigated. The results showed that the electrostatic forces exerted by Na cations on H2O molecules and the interlayer H2O molecular arrangement are not affected by the rise in temperature after adding both trimers. Trimer addition reinforced the structure of interlayer H2O molecules so that the effect of temperature increase on them became negligible. The structural dynamics evolution of the radius of gyration of both trimers showed the existence of conformation changes when temperature increased. These conformational changes are more complex in the case of (NVCL)3 than (NIPAM)3 due to its large monomers. Both trimers reduced the mobility of interlayer particles with a better inhibition effect obtained for (NVCL)3 compared to (NIPAM)3. The concentration profile of interlayers’ species showed the affinity of Na cations for clay mineral surfaces while H2O molecules moved away. Compared these two trimers, the most stable state of Na-Mt is achieved with (NVCL)3. These results could help highlight the inhibition properties of (NIPAM)3 and (NVCL)3 on hydrated Na-Mt and to predict its stability against changes in environmental conditions.

Molecular Dynamics Simulation on Dynamic Properties of Bubble

2013 ◽  
Vol 705 ◽  
pp. 150-156
Author(s):  
Chao Qiu ◽  
Hui Сhen Zhang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Potential Energy ◽  
Canonical Ensemble ◽  
Dynamic Properties ◽  
Simulation Method ◽  
Dynamics Simulation ◽  
Final State ◽  
Balance State ◽  
Three Stages

Development of a single bubble in free space under the canonical ensemble was studied by using molecular dynamics simulation method. The detailed dynamic characteristics in the evolution process were analyzed by calculating the displacement of molecules, density, diffusion coefficient, pressure and potential energy of bubble. The results indicate that the evolution is divided into three stages according to the change of bubble potential energy, which are expansion, compression and balance state respectively. The temperature and density have significant influences on the final state of bubbles. The bubble in the liquid with larger density has a higher transition rate. The collapsing speed of bubble becomes faster with temperature increasing.

scholarly journals Influence of lactide vs glycolide composition of poly (lactic-co-glycolic acid) polymers on encapsulation of hydrophobic molecules: molecular dynamics and formulation studies

2021 ◽  
Vol 32 (10) ◽  
Author(s):  
Anurag Dobhal ◽  
Ashu Srivastav ◽  
Prajakta Dandekar ◽  
Ratnesh Jain
Keyword(s):  
Molecular Dynamics ◽  
Chain Length ◽  
Polymer Chain ◽  
Continuous Process ◽  
Spatial Arrangement ◽  
Binding Energies ◽  
Polymer Chains ◽  
Dynamics Simulation ◽  
Radius Of Gyration ◽  
Coumarin 6

AbstractThe work demonstrates the preparation of PLGA (PLGA 50:50, PLGA 75:25) nanoparticles, to encapsulate a hydrophobic molecule (coumarin-6), using the microreactor-based continuous process. The formulations were characterized using dynamic light scattering and transmission electron microscopy to determine their size, homogeneity, zeta potential, and surface morphology. The resulting nanoparticles were safe to the CHO cells (≈80% cell survival), at the concentration of ≤600 µg/mL and were successfully taken up by the cells, as demonstrated using confocal microscopy. Moreover, imaging flow cytometry confirmed that the nanoparticles were internalized in 73.96% of the cells. Furthermore, molecular dynamics simulation and docking studies were carried out to explore the effect of polymer chain length of PLGA and lactide vs glycolide (LA:GA) ratio on their compatibility with the coumarin-6 molecules and to study the coiling and flexibility of PLGA in the presence of coumarin-6 molecules. Flory–Huggins interaction parameter (χ) was calculated for polymer chains of varying lengths and LA:GA ratio, with respect to coumarin-6. χ parameter increased with increase in polymer chain length, which indicated superior interaction of coumarin-6 with the smaller chains. Amongst all the polymeric systems, PLGA55 exhibited the strongest interaction with coumarin-6, for all the chain lengths, possibly because of their homogeneous spatial arrangements and superior binding energy. PLGA27 showed better compatibility compared to PLGA72 and PGA, whereas PLA-based polymers exhibited the least compatibility. Analysis of the radius of gyration of the polymer chains in the polymer–coumarin-6 complexes, at the end of molecular dynamics run, exhibited that the polymer chains displayed varying coiling behavior and flexibility, depending upon the relative concentrations of the polymer and coumarin-6. Factors like intra-chain interactions, spatial arrangement, inter-chain binding energies, and polymer–coumarin-6 compatibility also influenced the coiling and flexibility of polymer chains.

Femtosecond photoelectron spectroscopy of the I2− anion: A semiclassical molecular dynamics simulation method

1999 ◽  
Vol 110 (8) ◽  
pp. 3736-3747 ◽  
Author(s):  
Victor S. Batista ◽  
Martin T. Zanni ◽  
B. Jefferys Greenblatt ◽  
Daniel M. Neumark ◽  
William H. Miller
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Photoelectron Spectroscopy ◽  
Simulation Method ◽  
Dynamics Simulation

Self-diffusion of lignite/water under different temperatures and pressure: A molecular dynamics study

2016 ◽  
Vol 30 (01) ◽  
pp. 1550253 ◽  
Author(s):  
Xinjian Liu ◽  
Yu Jin ◽  
Congliang Huang ◽  
Jingfeng He ◽  
Zhonghao Rao ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Water System ◽  
Simulation Method ◽  
The Self ◽  
Dynamics Simulation ◽  
Low Rank ◽  
Self Diffusion ◽  
Change Mechanism ◽  
Different Temperatures ◽  
Temperature And Pressure

Temperature and pressure have direct and remarkable implications for drying and dewatering effect of low rank coals such as lignite. To understand the microenergy change mechanism of lignite, the molecular dynamics simulation method was performed to study the self-diffusion of lignite/water under different temperatures and pressure. The results showed that high temperature and high pressure can promote the diffusion of lignite/water system, which facilitates the drying and dewatering of lignite. The volume and density of lignite/water system will increase and decrease with temperature increasing, respectively. Though the pressure within simulation range can make lignite density increase, the increasing pressure showed a weak impact on variation of density.

scholarly journals Molecular Dynamics Study on the Mechanism of Nanoscale Jet Instability Reaching Supercritical Conditions

2018 ◽  
Vol 8 (10) ◽  
pp. 1714 ◽  
Author(s):  
Qingfei Fu ◽  
Yunxiao Zhang ◽  
Chaojie Mo ◽  
Lijun Yang
Keyword(s):  
Molecular Dynamics ◽  
Growth Rate ◽  
Theoretical Result ◽  
Molecular Model ◽  
Simulation Method ◽  
Dynamics Simulation ◽  
Jet Instability ◽  
Subcritical Region ◽  
Thermodynamic Conditions ◽  
Spatio Temporal

This paper investigates the characteristics of a nitrogen jet (the thermodynamic conditions ranging from subcritical to supercritical) ejected into a supercritical nitrogen environment using the molecular dynamics (MD) simulation method. The thermodynamic properties of nitrogen obtained by molecular dynamics show good agreement with the Soave-Redlich-Kwong (SRK) equation of state (EOS). The agreement provides validation for this nitrogen molecular model. The molecular dynamics simulation of homogeneous nitrogen spray is carried out in different thermodynamic conditions from subcritical to supercritical, and a spatio-temporal evolution of the nitrogen spray is obtained. The interface of the nitrogen spray is determined at the point where the concentration of ejected fluid component reaches 50%, since the supercritical jet has no obvious vapor-liquid interface. A stability analysis of the transcritical jets shows that the disturbance growth rate of the shear layer coincides very well with the classical theoretical result at subcritical region. In the supercritical region, however, the growth rate obtained by molecular dynamics deviates from the theoretical result.

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