Open PhD position
 

Mutual adaptation of the structure in molecular motors and impact of structural changes in the thermodynamic efficiency of the molecular motor.

Open PhD position
 

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Cell membranes represent a serious protective barrier for external molecules, proteins, nanoparticles and drugs. This barrier is quite efficient in protecting the interior of the cells. However, large nanoscale objects, single-walled carbon nanotubes (SWNTs) have been found inside the cells both in direct and indirect biological experiments. Such experiments suggest that carbon nanotubes can efficiently […]

Thomas Heimburg

Biophys. J., 103 (5), 918–929 (2012)

Biomembranes are thin capacitors with the unique feature of displaying phase transitions in a physiologically relevant regime. We investigate the voltage and lateral pressure dependence of their capacitance close to their chain melting transition. Because the gel and the fluid membrane have different area and thickness, the capacitance of […]

Sabyasachi Dasgupta, Thorsten Autha, Gerhard Gompper

Soft Matter, 9, 5473-5482 (2013)

Membrane budding and wrapping of particles, such as viruses and nano-particles, play a key role in intracellular transport and have been studied for a variety of biological and soft matter systems. We study nano-particle wrapping by numerical minimization of bending, surface tension, and adhesion energies. We […]

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 on the bilayer in a […]

Thibault Tabarin, Aaron Martin, Robert J. Forster and Tia E. Keyes

Soft Matter, 8, 8743-8751 (2012)

Fluorescence lifetime correlation spectroscopy (FLCS) has been used to probe the influence of PEG-8000 on the fluidity of fluorescently labeled planar supported lipid bilayers on ozone plasma treated glass. The lipid membrane compositions examined were; DOPC, DOPC/DOPS (80/20 mol/mol) […]

Marcus Müller, Yuliya G. Smirnova, Giovanni Marelli, Marc Fuhrmans, and An-Chang Shi

Phys. Rev. Lett. 108, 228103 (2012)

The formation of an hourglass-shaped passage (stalk) connecting two apposed membranes is an essential initial step in membrane fusion. The most probable transition path from two separate membranes to a stalk, i.e., the minimum free-energy path (MFEP), is […]

Herre Jelger Risselada, Giovanni Marelli, Marc Fuhrmans, Yuliya G. Smirnova, Helmut Grubmüller, Siewert Jan Marrink, Marcus Müller

PLoS ONE 7(6): e38302 (2012)

Our molecular simulations reveal that wild-type influenza fusion peptides are able to stabilize a highly fusogenic pre-fusion structure, i.e. a peptide bundle formed by four or more trans-membrane arranged fusion peptides. We rationalize that the […]

Marco Werner, Jens-Uwe Sommer and Vladimir A. Baulin

Soft Matter, 8, 11708-11716 (2012)

Recent experimental studies indicate that polymeric structures with a well-adjusted balance of amphiphilic parts may translocate through self-assembled phospholipid bilayers and enhance the passive trans-membrane transport of smaller molecules. Using a coarse grained lattice Monte Carlo model with explicit solvent we investigate self-assembled lipid […]

Matthew R. Cheetham, Jonathan P. Bramble, Duncan G. G. McMillan, Richard J. Bushby, Peter D. Olmsted, Lars J. C. Jeuken and Stephen D. Evans

Soft Matter, 2012,8, 5459-5465

We present ratchets capable of directing the movement of charged components within supported bilayer lipid membranes. These ratchets make use of asymmetrically patterned features […]

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 model the resulting α-helical structures […]

Cell membranes represent a serious protective barrier for external molecules, proteins, nanoparticles and drugs. This barrier is quite efficient in protecting the interior of the cells. However, large nanoscale objects, single-walled carbon nanotubes (SWNTs) have been found inside the cells both in direct and indirect biological experiments. Such experiments suggest that carbon nanotubes can efficiently […]

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 rods into the 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 nanotube. Single-chain mean field (SCMF) […]

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 model and the minimal 3-beads […]

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 exact microscopic mechanism of their […]