J Phys Chem B, 2010, 114: 11207
We presented an implicit solvent coarse-grained (CG) model for quantitative simulations of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayers. The use of implicit solvent enables membrane simulations on large length- and time-scales at moderate computational expense. Despite an improved computational efficiency, the model preserves chemical specificity and quantitative accuracy. The bonded and nonbonded interactions together with the effective cohesion mimicking the hydrophobic effect were systematically tuned by matching structural and mechanical properties from experiments and all-atom bilayer simulations, such as saturated area per lipid, radial distribution functions, density and pressure profiles across the bilayer, P2 order, etc. The CG lipid model is shown to self-assemble into a bilayer starting from a random dispersion. Its elastic properties, such as bending and stretching modulus, are semi-quantitatively consistent with experiments. The effects of reduced molecular friction and more efficient integration combine to an overall speedup of three to four orders of magnitude compared to all-atom bilayer simulations. Our CG lipid model is especially useful for studies of large-scale phenomena in membranes which nevertheless require a fair description of chemical specificity, e.g. membrane patches interacting with movable and transformable membrane proteins and peptides.
New J Phys, 2010, 12: 095004
We study lipid and phase transferability of our recently developed
systematically coarse-grained solvent-free membrane model. The
force field was explicitly parametrized to describe a fluid
POPC bilayer at 310 K with correct structure and area per lipid,
while gaining at least three orders of magnitude in computational
efficiency ( J Phys Chem
B, 2010, 114: 11207 ). Here we show that exchanging CG tails,
without any subsequent re-parameterization, creates reliable models of
DOPC and DPPC lipids in terms of structure and
area per lipid. Furthermore, all CG lipids undergo a liquid-gel transition
upon cooling, with characteristics as observed in experiments and
all-atom simulations during phase transformation. These studies
suggest a promising transferability of our force field parameters to
different lipid species and thermodynamic state-points, properties
that are prerequisite for even more complex systems, such as
J Phys Chem B, 2009, 113: 3776
We report a Molecular Dynamics study of homogenous bubble
nucleation in a Lennard-Jones fluid. The rate of bubble nucleation
is estimated using forward-flux sampling (FFS). FFS is well suited
to simulate nucleation processes because it does not assume that
the nucleation process is slow compared to the time it takes all
other degrees of freedom to equilibrate. The latter assumption is
implicit in the Umbrella Sampling scheme.
We find that cavitation starts with compact bubbles rather than with ramified
structures as had been suggested by Shen and Debenedetti
(J Chem Phys, 111:3581, 1999). Our estimate of the
bubble-nucleation rate is higher than predicted on the basis of
Classical Nucleation Theory (CNT). Our simulations show that local
temperature fluctuations correlate strongly with subsequent bubble
formation - this mechanism is not taken into account in CNT.
J Chem Phys, 2005, 123: 154701
We report a computer-simulation study of the free-energy barrier for the nucleation of pores in the
bilayer membrane under constant stretching lateral pressure. We find that incipient pores are
hydrophobic but as the lateral size of the pore nucleus becomes comparable with the molecular
length, the pore becomes hydrophilic. In agreement with previous investigations, we find that the
dynamical process of growth and closure of hydrophilic pores is controlled by the competition
between the surface tension of the membrane and the line tension associated with the rim of the
pore. We estimate the line tension of a hydrophilic pore from the shape of the computed free-energy
barriers. The line tension thus computed is in a good agreement with available experimental data.
We also estimate the line tension of hydrophobic pores at both macroscopic and microscopic levels.
The comparison of line tensions at these two different levels indicates that the "microscopic" line
tension should be carefully distinguished from the "macroscopic" effiective line tension used in the
theoretical analysis of pore nucleation. The overall shape of the free-energy barrier for pore
nucleation shows no indication for the existence of a metastable intermediate during pore
J Chem Phys, 2005, 122: 234711
We present a simple, implicit-solvent model for fluid bilayer membranes. The model was designed
to reproduce the elastic properties of real bilayer membranes. For this model, we observed the
solid-fluid transition and studied the in-plane diffusivity of the fluid phase. As a test, we compute the elastic-bending and area-compressing moduli of fluid bilayer membranes.We find that the computed
elastic properties are consistent with the available experimental data.
Molecular Simulation, 2007, 33: 1023.
The most naive perturbation method to estimate interfacial free energies is based on the assumption that the interface between coexisting phases is infinitely sharp. Although this approximation does not yield particularly accurate estimates for the liquid-vapor surface tension, we find that it works surprisingly well for the interface between a dense liquid and a solid. As an illustration we estimate the liquid-solid interfacial free energy of a Lennard-Jones (LJ) system with truncated and shifted interactions and compare the results with numerical data that have been reported in the literature.
We find that the agreement between theory and simulation is excellent. In contrast, if we apply the same procedure to estimate the variation of the liquid-vapor surface tension, for different variants of the LJ potential (truncated/shifted/force-shifted), we find that the agreement with the available simulation data is, at best, fair. The present method makes it possible to obtain quick and easy estimate of the effect on the surface free energy of different potential-truncation schemes used in computer simulations.
Microscale Thermophysical Engineering, 2003, 7: 275
The evaporation and condensation processes of argon at the liquid-vapor interface are
investigated with molecular dynamics simulations. By introducing a novel statistical
method, namely, the characteristic time method, the condensed then re-evaporated
molecules are successfully distinguished from the reflected molecules according to their
different characteristic times, which are estimated based on the statistic during simulation.
The kinetic characteristics of the condensed, reflected, and evaporated molecules are separately
studied and compared. The results show that the high kinetic energy component
normal to the interface is an important character of the interphase transport process.
Fluid Phase Equilibria, 2001, 183-184: 321
Molecular dynamics simulations are carried out to study the thermodynamic properties in the liquid-vapo coexistent systems with liquid-vapor interfaces. The interactions between the particles are modeled with a truncated Lennard-Jones pair potential. The density profile, the temperature profile and the pressure tensor are obtained at two different bulk temperatures. There exist a sharp peak and a small valley at the thin region outside the liquid-vapor interface in the local kinetic energy distribution across the interface. When the system temperature increases, the magnitude of the peak and the valley decreases. The non-equilibrium molecular kinetic energy distribution located at the thin region outside the liquid-vapor interface confirms that though the liquid and vapor phases are in thermodynamic equilibrium, the interface may not be in thermostatic equilibrium. This kind of molecular kinetic energy distribution may embody the behavior of energy transport between the liquid and the vapor phases.