Literature DB >> 15945771

Artifacts in dynamical simulations of coarse-grained model lipid bilayers.

Ask F Jakobsen1, Ole G Mouritsen, Gerhard Besold.   

Abstract

With special focus on dissipative particle dynamics simulations of anisotropic and complex soft matter, such as lipid bilayers in water, we have investigated the occurrence of artifacts in the results obtained from dynamical simulations of coarse-grained particle-based models. The particles are modeled by beads that interact via soft repulsive conservative forces (as defined in dissipative particle dynamics simulations), harmonic bond potentials, as well as bending potentials imparting stiffness to the lipid tails. Two different update schemes are investigated: dissipative particle dynamics with a velocity-Verlet-like integration scheme [G. Besold, I. Vattulainen, M. Karttunen, and J. M. Polson, Phys. Rev. E 63, R7611 (2000)] and Lowe-Andersen thermostatting [C. P. Lowe, Europhys. Lett. 47, 145 (1999)] with the standard velocity-Verlet integration algorithm. By varying the integration time step, we examine various physical quantities, in particular pressure profiles and kinetic bead temperatures, for their sensitivity to artifacts caused by the specific combination of integration technique and the thermostat. We then propose a simple fingerprint method that allows monitoring the presence of simulation artifacts.

Entities:  

Mesh:

Substances:

Year:  2005        PMID: 15945771     DOI: 10.1063/1.1900725

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  5 in total

1.  An implicit solvent coarse-grained lipid model with correct stress profile.

Authors:  Alex J Sodt; Teresa Head-Gordon
Journal:  J Chem Phys       Date:  2010-05-28       Impact factor: 3.488

2.  A mesoscopic bridging scale method for fluids and coupling dissipative particle dynamics with continuum finite element method.

Authors:  Milos Kojic; Nenad Filipovic; Akira Tsuda
Journal:  Comput Methods Appl Mech Eng       Date:  2013-01-15       Impact factor: 6.756

3.  Mesoscale computational studies of membrane bilayer remodeling by curvature-inducing proteins.

Authors:  N Ramakrishnan; P B Sunil Kumar; Ravi Radhakrishnan
Journal:  Phys Rep       Date:  2014-10-01       Impact factor: 25.600

4.  Determining the Gaussian curvature modulus of lipid membranes in simulations.

Authors:  Mingyang Hu; John J Briguglio; Markus Deserno
Journal:  Biophys J       Date:  2012-03-20       Impact factor: 4.033

5.  Changes in Ion Concentrations upon the Binding of Short Polyelectrolytes on Phospholipid Bilayers: Computer Study Addressing Interesting Physiological Consequences.

Authors:  Tomáš Blovský; Karel Šindelka; Zuzana Limpouchová; Karel Procházka
Journal:  Polymers (Basel)       Date:  2022-09-02       Impact factor: 4.967

  5 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.