Computer Simulation of Nanoparticles Translocation through Phospholipid Membranes within Single Chain Mean Field Approach

  • Currently: postdoc in ICIQ
  • PhD thesis defended: April 2012, Nomination best PhD thesis
  • Education: Moscow State University (2008 with honors)
  • Supervisor: Vladimir Baulin
Sergey Pogodin
Work is devoted to development and usage in practical applications of the Single Chain Mean Field (SCMF) method of computer simulation of molecular systems. It covers the theoretical bases of the approach in general and special cases, as well as peculiarities of efficient numerical implementation of the method. Few coarse-grained models of DMPC lipid membrane, reproducing within the SCMF method essential characteristics of the lipid bilayer, such as its thickness, density and elasticity, are proposed. One of these models is used to study features of interac- tion between the membrane and different homogeneous and patterned nano-objects, such as carbon nanotubes with different coverings and LEA-protein-like objects.

 

Related publications

  • Can a carbon nanotube pierce through a phospholipid bilayer?

    S. Pogodin and V.A. Baulin
    ACS Nano, 4 (9), 5293–5300 (2010)
    Great efficiency to penetrate into living cells is attributed to carbon nanotubes due to a number of direct and indirect observations of carbon nanotubes inside the cells. However, a direct evidence of physical translocation of nanotubes through phospholipid bilayers and the …

  • Coarse-grained models of phospholipid membranes within the single chain mean field theory

    S. Pogodin and V.A. Baulin
    Soft Matter, 6, 2216 – 2226 (2010)
    The single chain mean field theory is used to simulate the equilibrium structure of phospholipid membranes at the molecular level. Three levels of coarse-graining of DMPC phospholipid surfactants are present: the detailed 44-beads double tails model, the 10-beads double tails …

  • Surface patterning of carbon nanotubes can enhance their penetration through a phospholipid bilayer

    S. Pogodin, N.K.H. Slater and V.A. Baulin
    ACS Nano, 5 (2), 1141–1146 (2011)

    Nanotube patterning may occur naturally upon the spontaneous self-assembly of biomolecules onto the surface of single-walled carbon nanotubes (SWNTs). It results in periodically alternating bands of surface properties, ranging from relatively hydrophilic to hydrophobic, along the axis of the …

  • Equilibrium insertion of nanoscale objects into phospholipid bilayers

    S. Pogodin and V.A. Baulin
    Current Nanoscience, 7 (5), 721-726 (2011)

    Certain membrane proteins, peptides, nanoparticles and nanotubes have rigid structure and fixed shape. They are often viewed as spheres and cylinders with certain surface properties. Single Chain Mean Field theory is used to model the equilibrium insertion of nanoscale spheres and …

  • Coupled concentration polarization and electroosmotic circulation near micro/nanointerfaces: Taylor–Aris model of hydrodynamic dispersion and limits of its applicability

    A. Yaroshchuk, E. Zholkovskiy, S. Pogodin and V.A. Baulin
    Langmuir, 27(18), 11710-11721 (2011)

    Mismatches in electrokinetic properties between micro- and nanochannels give rise to superposition of electroosmotic and pressure-driven flows in the microchannels. Parabolic or similar flow profiles are known to cause the so-called hydrodynamic dispersion, which under certain conditions can …

  • Biomolecule Surface Patterning May Enhance Membrane Association

    S. Pogodin, N. K. H. Slater and V. A. Baulin

    ACS Nano, 6(2), 1308-1313 (2012)

    Under dehydration conditions, amphipathic late embryogenesis abundant proteins fold spontaneously from a random conformation into α-helical structures, and this transition is promoted by the presence of membranes. To gain insight into the thermodynamics of membrane association, we …

  • Natural Bactericidal Surfaces: Mechanical Rupture of Pseudomonas aeruginosa Cells by Cicada Wings

    Elena P. Ivanova, Jafar Hasan, Hayden K. Webb, Vi Khanh Truong, Gregory S. Watson, Jolanta A. Watson, Vladimir A. Baulin, Sergey Pogodin, James Y. Wang, Mark J. Tobin, Christian Löbbe, Russell J. Crawford

    Small, 8 (16), 2489 – 2494 (2012)

    Natural superhydrophobic surfaces are often thought to have antibiofouling potential due to …

  • Nanoparticle-Induced Permeability of Lipid Membranes

    Sergey Pogodin, Marco Werner, Jens-Uwe Sommer, Vladimir A. Baulin

    ACS Nano, DOI: 10.1021/nn3028858 (2012)

    Monte Carlo simulations using the bond fluctuation method with explicit solvent reveal the mechanism of enhanced permeability of lipid bilayers induced by the adsorption of nanoparticles with controlled hydrophobicity. Simulation results indicate an adsorption transition of nanoparticles …

  • Biophysical Model of Bacterial Cell Interactions with Nanopatterned Cicada Wing Surfaces

    S. Pogodin, J. Hasan, V.A. Baulin, H.K. Webb, V.K. Truong, T.H.P. Nguyen, V. Boshkovikj, C.J. Fluke, G.S. Watson, J.A. Watson, R.J. Crawford and E.P. Ivanova

    Biophys. J., 104 (4), 835-840 (2013)

    The nanopattern on the surface of Clanger cicada (Psaltoda claripennis) wings represents the first example of a new class of …

  • Selective bactericidal activity of nanopatterned superhydrophobic cicada Psaltoda claripennis wing surfaces

    Appl Microbiol Biotechnol., 97 (20), 9257-9262 (2013)
    Jafar Hasan, Hayden K. Webb, Vi Khanh Truong, Sergey Pogodin, Vladimir A. Baulin, Gregory S. Watson, Jolanta A. Watson, Russell J. Crawford, Elena P. Ivanova
    The nanopattern on the surface of Clanger cicada (Psaltoda claripennis) wings represents the first example of a new class of biomaterials that …

  • General model of phospholipid bilayers in fluid phase within the single chain mean field theory

    J. Chem. Phys. 140, 174903 (2014)
    Yachong Guo, Sergey Pogodin and Vladimir A. Baulin

    Coarse-grained model for saturated phospholipids: 1,2-didecanoyl-sn-glycero-3-phosphocholine (DCPC), 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC), 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC) and unsaturated phospholipids: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), 1,2- dioleoyl-sn-glycero-3-phosphocholine (DOPC) is introduced within the single chain mean field theory. A single set of parameters adjusted for DMPC …