HYPERBIO · Hybrid Particle-Field Approach Including Electrostatics for Large-Scale Simulations of Biological Systems

Hybrid Particle-Field Approach Including Electrostatics for Large-Scale Simulations of Biological Systems

Biochemical/biophysical processes are very diverse, and they may occur at different time scales (from femtoseconds to seconds) and may require propagation over different sizes (from few Angstroms over nano- or micro- metres). Such broad extension of both the time- and size- scales poses a unique set of problems to the computational scientists in building models of the biological matter on physical principles. In recent years, Milano and Kawakatsu [J. Chem. Phys. 2009, 130, 214106; 2010, 133, 214102] reformulated the hybrid particle-field (hPF) method within molecular dynamics (hPF-MD) framework. The hPF-MD was validated for different molecular models including molecular surfactants, atomistic models of polymers, and bio membranes. This project was aimed at implementation of electrostatics into hPF-MD where the field explicitly takes into account both particle and charge densities. The overall objectives of the project are listed below. Each objective is considered as a separate work package (WP). 1.The first objective of the proposal was to implement electrostatics into OCCAM software (WP1). The new code would be tested for its efficiency and performance in both serial and parallel implementations. 2.The second objective was the application of hPF-MD to realistic soft matter models (WP2). We aimed to validate the models for charged amphiphile systems and investigate the ability of hPF-MD in describing both the structural and dynamic properties of those charged systems. Our goal was to address the structure and assembly of complex ipopolysaccharide (LPS) membranes. In fact, we started our study with coarse grained models for simple charged amphiphile systems such as palmitoyloleoylphosphatidylglycerol (POPG) lipid bilayer and sodium dodecyl sulfate (SDS) surfactant in aqueous environment. 3.Our original plan for WP3 was to extend the charge-field formalism to incorporate dipole-field and dipole-dipole interactions for the description of proteins in a field approach compatible with CG method proposed by Michele Cascella and coworkers. On the contrary, we preferred to concentrate our efforts to introduce spatially resolved dielectric which depends on the local density of the different molecular species. This step is crucial for the better treatment of electrostatics in complex phase separated systems like biological membranes comprised of complex polyelectrolytes. In WP3, we also aimed at the introduction of protocols to perform simulations of tensionless bio membranes by considering an interaction energy due to surface tension in particle-field formalism. Conclusion: We introduced a series of methods in particle-field formalism to compute the electrostatic energy and forces for a mesoscopic system in the condensed phase, described with molecular resolution. The methods are inexpensive, robust and are able to reproduce the correct electrostatic features for dipolar/charged lipid membranes. A pressure tensor is derived in particle field formalism to perform simulations on tensionless bio membranes to study major conformational changes like membrane curvature, disruption and pore formation.

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