Conformation and dynamic properties of a saturated hydrocarbon chain confined in a model membrane: a Brownian dynamics simulation

Abstract

A Brownian dynamics simulation of a saturated hydrocarbon chain with simple mean-field potentials, namely anchorage, orientation and enclosing, reproducing a biological membrane environment is presented. The simulation was performed for a time equivalent to 1.4 micros thanks to the simplicity of our model. The results are compared with those obtained for a hydrocarbon chain simulated in the absence of the membrane potentials but with confinement. With the appropriate choice of parameters, equilibrium properties, such as deuterium order parameter, chain length, tilt angle and geometry, and dynamic properties, such as dihedral angle transition rate, rotational and translational diffusion, recovered from our simulations, correctly reproduced, are consistent with hydrocarbon-derived molecule experimental results and simulation results obtained from other more complex studies.

Monte Carlo Simulation of Partially Confined Flexible Polymers

“…Aoyagi et al performed molecular simulations on melts of coarse-grained chains and found that polymers near the walls are deformed by attraction and the presence of other molecules and studied also the relaxation times of the chains in confinements for strong attractive segment−wall interactions. Brownian dynamics simulations of hydrocarbons in (biological) membranes were carried out to cover greater time intervals . These studies were all for fully confined polymers.…”

“…Brownian dynamics simulations of hydrocarbons in (biological) membranes were carried out to cover greater time intervals. 13 These studies were all for fully confined polymers.…”

Orientational Order of the Polyene Fatty Acid Membrane Probe trans-Parinaric Acid in Langmuir−Blodgett Multilayer Films

“…BD simulations provide an easy way to analyze a large number of systems subject to various conditions such as molecular composition, bilayer thickness, temperature, and many more. ,, Detailed and reliable information about conformational and dynamical properties of acyl-like chains is provided by BD simulations. , The mean field potentials used in our simulations have thoroughly proved their suitability 14,28 and can be used to provide very important information.…”

“…The anchorage potential constant, K anch , used was 9.7 × 10 -2 kJ/mol; the enclosing potential constant, K z , takes the value of 19.38 kJ/(mol Å 2 ), and the orientational potential constant, K q ( z ) , was set to 6.2 × 10 -2 kJ/mol at z = z 0 and 5.2 × 10 -2 kJ/mol at z = 0. The potentials were set to these particular values in order to recover the characteristic deuterium order parameter profile and magnitude of a phospholipid and other derived hydrocarbon molecules in a membrane …”

Influences of streaming potential on cross stream migration of flexible polymer molecules in nanochannel flows

“…Here f ij S represents the spring force exerted on the bead i by the bead j, b k is the Kuhn length of the polymer chain, q 0 is the maximum extension of the molecule ͑expressed as q 0 = N k,S b k , with N k,S being the number of Kuhn segments per spring͒. The finite rigidity of the chain may be accounted by appealing to the harmonic bending potential between the adjacent beads 40 U i,i+1…”