scholarly journals ddcMD: A fully GPU-accelerated molecular dynamics program for the Martini force field

2020 ◽  
Vol 153 (4) ◽  
pp. 045103 ◽  
Author(s):  
Xiaohua Zhang ◽  
Shiv Sundram ◽  
Tomas Oppelstrup ◽  
Sara I. L. Kokkila-Schumacher ◽  
Timothy S. Carpenter ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Accelerated Molecular Dynamics ◽  
Martini Force Field

scholarly journals Nanocomposite of Fullerenes and Natural Rubbers: MARTINI Force Field Molecular Dynamics Simulations

Polymers ◽  
2021 ◽  
Vol 13 (22) ◽  
pp. 4044
Author(s):  
Jiramate Kitjanon ◽  
Wasinee Khuntawee ◽  
Saree Phongphanphanee ◽  
Thana Sutthibutpong ◽  
Nattaporn Chattham ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Quantitative Agreement ◽  
Filler Loading ◽  
Coarse Grained ◽  
Experimental Result ◽  
High Wear Resistance ◽  
Mechanical And Thermal Properties ◽  
Interfacial Interactions ◽  
Martini Force Field

The mechanical properties of natural rubber (NR) composites depend on many factors, including the filler loading, filler size, filler dispersion, and filler-rubber interfacial interactions. Thus, NR composites with nano-sized fillers have attracted a great deal of attention for improving properties such as stiffness, chemical resistance, and high wear resistance. Here, a coarse-grained (CG) model based on the MARTINI force field version 2.1 has been developed and deployed for simulations of cis-1,4-polyisoprene (cis-PI). The model shows qualitative and quantitative agreement with the experiments and atomistic simulations. Interestingly, only a 0.5% difference with respect to the experimental result of the glass transition temperature (Tg) of the cis-PI in the melts was observed. In addition, the mechanical and thermodynamical properties of the cis-PI-fullerene(C60) composites were investigated. Coarse-grained molecular dynamics (MD) simulations of cis-PI-C60 composites with varying fullerene concentrations (0–32 parts per hundred of rubber; phr) were performed over 200 microseconds. The structural, mechanical, and thermal properties of the composites were determined. The density, bulk modulus, thermal expansion, heat capacity, and Tg of the NR composites were found to increase with increasing C60 concentration. The presence of C60 resulted in a slight increasing of the end-to-end distance and radius of the gyration of the cis-PI chains. The contribution of C60 and cis-PI interfacial interactions led to an enhancement of the bulk moduli of the composites. This model should be helpful in the investigations and design of effective fillers of NR-C60 composites for improving their properties.

scholarly journals In silico modelling of drug–polymer interactions for pharmaceutical formulations

2010 ◽  
Vol 7 (suppl_4) ◽  
Author(s):  
Samina Ahmad ◽  
Blair F. Johnston ◽  
Simon P. Mackay ◽  
Andreas G. Schatzlein ◽  
Paul Gellert ◽  
...  
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Force Field ◽  
Drug Level ◽  
Pharmaceutical Formulations ◽  
Coarse Grained ◽  
Glycol Chitosan ◽  
Heterogeneous Distribution ◽  
Martini Force Field ◽  
Initial Drug

Selecting polymers for drug encapsulation in pharmaceutical formulations is usually made after extensive trial and error experiments. To speed up excipient choice procedures, we have explored coarse-grained computer simulations (dissipative particle dynamics (DPD) and coarse-grained molecular dynamics using the MARTINI force field) of polymer–drug interactions to study the encapsulation of prednisolone (log p = 1.6), paracetamol (log p = 0.3) and isoniazid (log p = −1.1) in poly( l -lactic acid) (PLA) controlled release microspheres, as well as the encapsulation of propofol (log p = 4.1) in bioavailability enhancing quaternary ammonium palmitoyl glycol chitosan (GCPQ) micelles. Simulations have been compared with experimental data. DPD simulations, in good correlation with experimental data, correctly revealed that hydrophobic drugs (prednisolone and paracetamol) could be encapsulated within PLA microspheres and predicted the experimentally observed paracetamol encapsulation levels (5–8% of the initial drug level) in 50 mg ml −1 PLA microspheres, but only when initial paracetamol levels exceeded 5 mg ml −1 . However, the mesoscale technique was unable to model the hydrophilic drug (isoniazid) encapsulation (4–9% of the initial drug level) which was observed in experiments. Molecular dynamics simulations using the MARTINI force field indicated that the self-assembly of GCPQ is rapid, with propofol residing at the interface between micellar hydrophobic and hydrophilic groups, and that there is a heterogeneous distribution of propofol within the GCPQ micelle population. GCPQ–propofol experiments also revealed a population of relatively empty and drug-filled GCPQ particles.

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