Funded by



Event date:  April 26, 2018 4:00 PM



Prof. Gerhard Hummer, Max Planck Institute of Biophysics Frankfurt/Main


Dealing with Divergent Diffusion Coefficients in Large-Scale Lipid Membrane Simulations


We used molecular dynamics simulations to study the diffusive motions of lipids, membrane-spanning nanopores, and integral membrane proteins within lipid membranes. We found that their apparent diffusion coefficients diverge logarithmically as the width of the simulation box is increased, seemingly without bound. This divergence would appear to preclude the calculation of proper size-independent diffusion coefficients that can be compared to experiment. However, in simulations with systems of more than 100 million particles, we show that a hydrodynamic model not only explains the divergence, but can also be used to obtain both proper diffusion coefficients and difficult-to-calculate membrane properties.

Hydrodynamics also accounts for the box-size dependence of the rotational diffusion of macromolecules. We show that the rotational diffusion tensors of proteins and nucleic acids can be determined directly from the time-dependent covariances of the quaternion describing their orientations in space. However, in molecular dynamics simulations the rotational dynamics is slowed as a result of the imposition of periodic boundary conditions. A simple hydrodynamic correction accounts quantitatively for this finite-size effect and makes it possible to estimate proper infinite-system rotational diffusion coefficients from simulations using small boxes.

Overall, the analysis of long simulation trajectories of large membrane, protein, and nucleic acid systems demonstrates that both translational and rotational diffusion coefficients suffer from significant finite-size effects. Hydrodynamics allows us to correct for the system-size dependences, giving us diffusion coefficients that can be compared to experiment.




Speaker Stephen Copplestone, 
Institut für Aerodynamik und Gasdynamik
(IAG), Subproject B.8

Coupling MD Simulations of Laser Ablation with PIC-DSMC Simulations of Plasma Plume Expansions and subsequent Laser-Plasma Interacitons


Plasmas created by laser light interacting with metals are of great interest regarding numerous
fields, e.g., medical laser applications, spacecraft propulsion or material processing. The process of
laser-solid interaction is examined by atomistic Molecular Dynamics (MD) simulations for a
detailed description of the creation of lattice ions and their removal from the target surface 1. In
order to investigate the expansion of the plasma plume for larger spatial and temporal dimensions,
the MD results are used as initial conditions for Particle-In-Cell (PIC) simulations, where particle
collisions are incorporated using the Direct Simulation Monte Carlo (DSMC) method, which
considers chemical reactions, e.g., impact ionization and recombination processes.

These combined methods 2 offer an elaborate simulation of the expansion characteristics, which are
crucial for subsequent laser pulses interacting with the expanding plasma plume. The simulations
are performed using PICLas 3, a parallel high-order three-dimensional PIC-DSMC solver developed
cooperatively by the Institute of Space Systems and Institute of Aerodynamics and Gas Dynamics
at the University of Stuttgart.

1. J. Roth, C. Trichet, H.-R. Trebin, and S. Sonntag. “Laser Ablation of Metals”, pages 159–168.
Springer Berlin Heidelberg, Berlin, Heidelberg, 2011.

2. V. V. Serikov, S. Kawamoto and K. Nanbu, "Particle-in-cell plus direct simulation Monte Carlo
(PIC-DSMC) approach for self-consistent plasma-gas simulations," in IEEE Transactions on
Plasma Science, vol. 27, no. 5, pp. 1389-1398, Oct 1999.

3. C.-D. Munz, M. Auweter-Kurtz, S. Fasoulas, A. Mirza, P. Ortwein, M. Pfeiffer, and T. Stindl.
”Coupled Particle-In-Cell and Direct Simulation Monte Carlo method for simulating reactive
plasma flows”. Comptes Rendus Mécanique 342.10-11 (2014), 662−670


Event location:  Universität Stuttgart, Campus Vaihingen, Institut für Computerphysik (ICP)
Seminarraum 1.079
Allmandring 3
70569  Stuttgart