Modeling biomembranes.

Abstract

Understanding the properties and behavior of biomembranes is fundamental to many biological processes and technologies. Microdomains in biomembranes or 'lipid rafts' are now known to be an integral part of cell signaling, vesicle formation, fusion processes, protein trafficking, and viral and toxin infection processes. Understanding how microdomains form, how they depend on membrane constituents, and how they act not only has biological implications, but also will impact Sandia's effort in development of membranes that structurally adapt to their environment in a controlled manner. To provide such understanding, we created physically-based models of biomembranes. Molecular dynamics (MD) simulations and classical density functional theory (DFT) calculations using these models were applied to phenomena such as microdomain formation, membrane fusion, pattern formation, and protein insertion. Because lipid dynamics and self-organization in membranes occur on length and time scales beyond atomistic MD, we used coarse-grained models of double tail lipid molecules that spontaneously self-assemble into bilayers. DFT provided equilibrium information on membrane structure. Experimental work was performed to further help elucidate the fundamental membrane organization principles.3 4

Sodium Diffusion through Aluminum-Doped Zeolite BEA System: Effect of Water Solvation

“…All molecular dynamics (MD) simulations were performed using the LAMMPS (large-scale atomic/molecular massively parallel simulator) MD code developed by Plimpton at Sandia. 28, 29 The velocity Verlet algorithm 30 was used to solve the equations of motion with a time step of 1.0 fs. The isobaric-isothermal ensembles (NPT) were generated using Nose-Hoover thermostat with a temperature damping relaxation time of 0.1 ps and the Andersen-Hoover barostat with a dimensionless cell mass factor of 1.0.…”

“…[7][8][9][10][11][12][13][14][15][16][17][18] In aluminosilicate zeolites the aluminum is generally incorporated in the three-dimensional framework in the form of AlO 4 -surrounded by neighboring SiO 4 while alkali metals such as Na + or K + are in the pores, interacting electrostatically with the zeolite framework. These positively charged and Movable cations in various zeolite systems have been studied intensively 7,8,[19][20][21][22][23][24][25][26][27][28][29] since they impart many interesting properties to the zeolite systems. In particular, the ionic conductivity of zeolites can be controlled by the level of nonframework ions and their hydration (undoped zeolites are insulators with an electronic band gap of ∼7 eV).…”

Modified Poisson–Boltzmann theory for polyelectrolytes in monovalent salt solutions with finite-size ions

“…The CG-MD simulations are performed using the LAMMPS simulation package 57,58 . The long-range electrostatic interactions are calculated using the particle-particle particle-mesh method (PPPM) 59 . A real space cutoff of 1.5 nm is used, beyond which the contributions are obtained in reciprocal space.…”

Effect of perfluorosulfonic acid side chains on oxygen permeation in hydrated ionomers of PEMFCs: Molecular dynamics simulation approach

“…where vdW , Q , bond , angle , torsion , inversion , and EAM are the van der Waals, electrostatic, bond-stretching, angle-bending, torsion, inversion, and the EAM energies, respectively. For calculating entire MD simulations for PEMFC systems, the large-scale atomic/molecular massively parallel simulator (LAMMPS) code 32,33 from Plimpton at Sandia was used. All MD simulations were carried out using the velocity Ve rlet algorithm 34 to integrate equations of atomic motion, with a time steps of 1 fs.…”