FLEXIBLE DISSIPATIVE PARTICLE DYNAMICS

2010 ◽  
Vol 21 (09) ◽  
pp. 1129-1148 ◽  
Author(s):  
Z. G. HUANG ◽  
T. M. YUE ◽  
K. C. CHAN ◽  
Z. N. GUO

Dissipative Particle Dynamics (DPD) has been recognized as a powerful tool for simulating the dynamics of complex fluids on a mesoscopic scale. However, owing to the rigid thermodynamic behavior of the standard model, it has limitations when applied to real systems. Although refined models have been developed to improve the thermodynamic consistency of DPD, they are not without limitations and deficiencies. In this paper, we extend the power of DPD beyond its traditional limits so that it can cope with systems where temperature and pressure changes occur. This is accomplished using a refined model termed Flexible DPD (FDPD), which allows the equation of state (EOS) to be given in priori. As a basis for the development of FDPD, the generalized expression for the thermodynamic variables is derived by solving the Langevin equation of a particle. It is found that the radial distribution function will be approximately invariant under variable transformation if the action range of potential is changed appropriately according to local density. With this invariant character of RDF, and by choosing the force functions to be variable separable, equations relating thermodynamic variables with the functions for DPD interactions are derived, and the weighting function for achieving thermodynamic is designed correspondingly. A case study on the validation of the FDPD method has been undertaken on the adiabatic compression of N2 gas. The simulation results were compared with the theoretical predictions as well as to the simulation results of the ordinary DPD method. The invariant of radial distribution function is justified by the results of the simulation.

2011 ◽  
Vol 10 (06) ◽  
pp. 731-745 ◽  
Author(s):  
HAINAN SUN ◽  
BAIQING LI ◽  
CHANGQIAO ZHANG ◽  
CHUNLING WANG ◽  
CHENGBU LIU

The self-assembly process of a symmetric diblock copolymer A5B5 in a selective solvent is studied using the dissipative particle dynamics method. Four types of morphologies can form, including lamellae, perforated lamellae, cylinders and spheres. Three phase diagrams are presented to demonstrate the effect of the concentration and interaction parameters on the ordered microstructures. Radial distribution function (RDF) characterizing the spatial correlations of the blocks is calculated. RDF not only confirms the morphological observations, but also provides more quantitative details. The evolution process of hexagonally packed cylinder and lamellae is also illustrated.


Author(s):  
Jurica Novak ◽  
Maria A. Grishina ◽  
Vladimir A. Potemkin

: In this letter the newly introduced approach based on the radial distribution function (RDF) weighted by the number of va-lence shell electrons is applied for a series of HIV-1 protease enzyme and its complexes with inhibitors to evaluate the influ-ence of hydrogen atoms on the performance of the model. The multiple linear regression method was used for the selection of the relevant descriptors. Two groups of residues having dominant contribution to the RDF descriptor are identified as relevant for the inhibition. In the first group are residues like Arg8, Asp25, Thr26, Gly27 and Asp29, which establish direct interaction with the inhibitor, while the second group consists of the amino acids at the interface of the two homodimer sub-units or with the solvent. The crucial motif pointed out by our approach as the most important for inhibition of the enzyme’s activity and present in all inhibitors is hydroxyl group that establish hydrogen bond with Asp25 side chain. Additionally, the comparison to the model without hydrogen showed that both models are of similar quality, but the downside of the current model is the need for the determination of residues’ protonation states.


2008 ◽  
Vol 47-50 ◽  
pp. 375-378 ◽  
Author(s):  
Zheng Han Hong ◽  
Shun Fa Hwang ◽  
Te Hua Fang

The mixing situation of Co atoms implanting onto Cu(001) substrate is investigated with regard to incident energy and substrate temperature by molecular dynamics. The results indicate that higher substrate temperature and/or incident energy will result in higher intermixing between the incident atoms and the substrate atoms. Furthermore, the value of the first peak of the radial distribution function (RDF) becomes lower and wider for the Co-Cu system as the substrate temperature and/or incident energy are increased.


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