Armen H. Poghosyan

Molecular Dynamics Study of Poly(diallyldimethylammonium chloride) (PDADMAC)/ Sodium Dodecyl Sulfate (SDS)/Decanol/Water Systems

We have performed a 50 ns of molecular dynamics study of poly(diallyldimethylammonium chloride) (PDADMAC)/sodium dodecyl sulfate (SDS)/decanol/water systems. The influence of the cationic polyelectrolyte on the anionic SDS-based lamellar liquid crystalline system was investigated. The main structural parameters have been calculated and compared with experimental data. We obtain two types of PDADMAC conformation, a more folded structure A and a structure B where the PDADMAC molecule is adsorbed at the anionic head groups of the surfactant molecules. The polyelectrolyte-induced coexistence of two lamellar phases at a concentration of 2-3% of PDADMAC is observed, which is in agreement with experimental findings.

Molecular dynamics simulations of inverse sodium dodecyl sulfate (SDS) micelles in a mixed toluene/pentanol solvent in the absence and presence of poly(diallyldimethylammonium chloride) (PDADMAC).

We have performed a 15 ns molecular dynamics simulation of inverse sodium dodecyl sulfate (SDS) micelles in a mixed toluene/pentanol solvent in the absence and presence of a cationic polyelectrolyte, i.e. poly(diallyldimethylammonium chloride) (PDADMAC). The NAMD code and CHARMM force field were used. During the simulation time, the radii of SDS inverse micelles changed and the radii of the water droplets have been calculated. The behavior of SDS hydrocarbon chains has been characterized by calculating the orientation order parameter and the chain average length. The water droplet properties (water flow, water molecules displacement) have been examined. In summary the MD simulations indicate a more rigid and ordered surfactant film due to the formation of a polyelectrolyte palisade layer in full agreement with the experimental findings, e.g. the viscosity increase and shift of the percolation boundary.

A molecular dynamics study of Na–dodecylsulfate/water liquid crystalline phase

We have performed a Series of long (about 130 ns) molecular dynamics simulations of a sodium dodecylsulfate/water liquid crystalline (LC) phase, consisting of 512 sodium dodecylsulfate and 15,000 water molecules, where the initial starting configuration is varied. In addition, the all atom and the united atom model were compared using NAMD and GROMACS codes with CHARMM27 and modified GROMOS87 force fields, respectively. Characteristic parameters, such as area per molecule, bilayer thickness, roughening, and orientation of the hydrocarbon chains in the hydrophobic core of the bilayer have been calculated. In general, the data obtained by means of molecular dynamics simulation are in agreement with the experimental X-ray diffraction data. However, only for the all-atom model, we found an excellent agreement with the experimental values of area per molecule and hydrocarbon chain packing parameters. Therefore, one can conclude that the use of a CHARMM27 all-atom force field, implemented in NAMD code, is the best approach for simulations of a SDS LC-phase.

Molecular Dynamics Study of Intermediate Phase of Long Chain Alkyl Sulfonate/Water Systems

Using atomic level simulation we aimed to investigate various intermediate phases of the long chain alkyl sulfonate/water system. Overall, about 800 ns parallel molecular dynamics simulation study was conducted for a surfactant/water system consisting of 128 sodium pentadecyl sulfonate and 2251 water molecules. The GROMACS software code with united atom force field was applied. Despite some differences, the analysis of main structural parameters is in agreement with X-ray experimental findings. The mechanism of self-assembly of SPDS molecules was also examined. At T = 323 K we obtained both tilted fully interdigitated and liquid crystalline-like disordered hydrocarbon chains; hence, the presence of either gel phase that coexists with a lamellar phase or metastable gel phase with fraction of gauche configuration can be assumed. Further increase of temperature revealed that the system underwent a transition to a lamellar phase, which was clearly identified by the presence of fully disordered hydrocarbon chains. The transition from gel-to-fluid phase was implemented by simulated annealing treatment, and the phase transition point at T = 335 K was identified. The surfactant force field in its presented set is surely enabled to fully demonstrate the mechanism of self-assembly and the behavior of phase transition making it possible to get important information around the phase transition point.

MOLECULAR DYNAMICS SIMULATIONS OF DMPC/DPPC MIXED BILAYERS

We have performed the atomistic MD simulation of dimyristoylphosphatidylcholine(DMPC)/dipalmitoylphosphatidylcholine(DPPC) mixed bilayers, consisting of various fraction of lipids, i.e., with fraction 0.25, 0.5 and 0.75 and hydration level 33 water molecules per lipid. The simulations were performed using NAMD code. The area per lipid, densities, orientational order parameters and tilt angle of hydrocarbon chain and also the interdigitation of chains were calculated. It has been established that the interdigitation degree of hydrocarbon chains is increased as the DPPC fraction is decreased. It has been also stated that the area per lipid value in case of racemic mixtures is about 0.72 nm2, which is in good agreement with experimental estimations. The hydrocarbon thickness is increased as the DPPC fraction increased. The DMPC/DPPC mixtures behave as almost ideally mixtures. The diffusion coefficients were also calculated and the results are in agreement with experimental findings. All the calculated parameters were compared with values obtained either from experimental data of DPPC or DMPC depending on the fraction of compound. The reason is that there are no experimental findings on DMPC/DPPC mixtures.

Long-chain alkyl sulfonate micelle fission: a molecular dynamics study

In this study, we investigate micelle fission of long-chain alkyl sulfonate molecules using atomistic scale simulation. GROMACS software code with the united atom force field was applied. 0.5-μs parallel molecular dynamics simulation study was conducted for a surfactant/water system consisting of 192 sodium pentadecyl sulfonate and 40,553 water molecules. The large preassembled micelle was ruptured at Krafft above T = 323-K temperature, and we track two ellipsoid-like micelles over the course of the production run. To estimate the micelle shape, we determined the principal moments of inertia and the eccentricity, which proved that the micelles have a pronounced prolate spheroid shape, which agrees well with our previous experimental data. The mechanism of micelle fission was explored in detail. The aggregation number, ionization degree, and other parameters obtained from simulation were consistent with existing experimental finding. The determined parameters in addition to simple visual inspection of trajectories revealed monomer-micelle exchange—with the estimated relaxation time τ1 = 10− 9s. We assume that the exchange process is conditioned by the unequal size of micelles leading to adjustment of aggregation number.

Dynamic Features of Complex Systems: A Molecular Simulation Study

The main aim of the article is the molecular simulation study and detailed analysis of surfactant molecules of complex micellar systems [1-2] consist of long hydrocarbon chain surfactant. The GROMACS software package [3] designed for high-performance simulations of large complex systems is used for the simulations. The IBM BlueGene/P supercomputer [4] at Bulgarian National Centre for Supercomputing Applications, with 8,192 processor cores connected by multiple high-performance networks, enables to investigate a completely new class of problems. The initially random distributed surfactant molecules in aqueous solute hydration have been simulated using GROMOS united atom force field [5]. An extensive series of short benchmarks run for timing purposes with different number of cores show that the studied system achieves good scalability (0.5ns per day) in case of using up to 512 processor cores. Further increasing the numbers of cores (for instance, 1024 cores) does not lead any significant increase. In spite of the limitation of number of simulations, the qualitative statistical data gave some interesting results, which indicates that long hydrocarbon chain surfactant self-assemble into small oligomers since 50ns of simulations, meanwhile in our previous study with surfactant rich content shows that 43ns is enough for self-assembling of spherical micelle.

A new parameter for validation molecular dynamics simulation (MD) data

We have obtained the new parameters coming from the simulated wide angle X-ray scattering (WAXS) (halo shapes, peak maximum (PM) and full width half maximum (FWHM)) for the validation of molecular dynamics (MD) simulation data.

Catanionic AOT/BDAC micelles on gold {111} surfaces

A sodium dioctyl sulfosuccinate (AOT)/benzyl hexadecyl dimethyl ammonium chloride (BDAC) mixed micelle self-organization and adsorption on gold Au(111) surfaces have been investigated using a molecular dynamics approach. The spherical AOT/BDAC mixed micelle is strongly adsorbed on the gold surface and is disoriented to a cylinder-like shape.

On the Performance and Energy Consumption of Molecular Dynamics Applications for Heterogeneous CPU-GPU Platforms Based on Gromacs

Abstract High Performance Computing (HPC) accelerates life science discoveries by enabling scientists to analyze large data sets, to develop detailed models of entire biological systems and to simulate complex biological processes. As computational experiments, molecular dynamics simulations are widely used in life sciences to evaluate the equilibrium nature of classical many-body systems The modelling and molecular dynamics study of surfactant, polymer solutions and the stability of proteins and nucleic acids under different conditions, as well as deoxyribonucleic acid proteins are studied. The study aims to understand the scaling behavior of Gromacs (Groningen machine for chemical simulations) on various platforms, and the maximum performance in the prospect of energy consumption that can be accomplished by tuning the hardware and software parameters. Different system sizes (48K, 64K, and 272K) from scientific investigations have been studied show that the GPU (Graphics Processing Unit) scales rather beneficial than other resources, i.e., with GPU support. We track 2-3 times speedup compared to the latest multi-core CPUs. However, the so-called “threading effect” leads to the better results.