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@INPROCEEDINGS{Tan:885564,
      author       = {Tan, Zihan and Dhont, Jan K.G. and Calandrini, Vania and
                      Naegele, Gerhard},
      title        = {{Q}uasi-two-dimensional diffusion of interacting protein
                      monomers and dimers: a {MPC} simulation study},
      reportid     = {FZJ-2020-03935},
      year         = {2020},
      abstract     = {Understanding lateral diffusion of proteins along a
                      membrane is of importance in biological soft matter science.
                      An example in case is postsynaptic neuronal signal
                      transduction where specific proteins diffuse alongside a
                      postsynaptic membrane, triggering a cascade of biochemical
                      processes. There are challenging questions to answer such as
                      how the collective and self-diffusion of the proteins are
                      affected by their direct and hydrodynamic interactions for
                      larger areal protein concentrations.Using the multi-particle
                      collision dynamics (MPC) simulation methods [1], we explore
                      protein diffusion under quasi-two-dimensional (Q2D)
                      confinement, for two different model systems of proteins. In
                      the first system, the proteins are modeled as Brownian
                      spheres interacting, respectively, by a hard-sphere
                      potential serving as a reference potential, and by a soft
                      potential with competing short-range attractive and
                      long-range repulsive parts. For a minimalistic description
                      of proteins diffusing along a cytosol-membrane interface,
                      the Brownian spheres are confined to lateral motion in a
                      planar monolayer embedded in an unbound three-dimensional
                      Newtonian fluid. The time scales in the dynamic simulations
                      extend from very short times where inertial effects are
                      resolved, up to long times where the solvent-mediated
                      hydrodynamic interactions between the proteins are fully
                      developed and non-retarded [2]. By computing velocity
                      autocorrelation functions, mean-square displacements and
                      Fourier-space current auto-correlation functions, we
                      quantify how concentration-induced correlations affect,
                      e.g., the anomalous enhancement of large-scale collective
                      diffusion under Q2D confinement [3], and the development of
                      inter-protein hydrodynamic interactions by multiple
                      scattering of sound and by vorticity diffusion [2]. The
                      second model system relates to the diffusion of a human
                      dumbbell-shaped M2 muscarinic acetylcholine receptor protein
                      where one segment is embedded in the neuronal cell membrane,
                      and the other one in the cytosol. The protein is simply
                      modeled by a two-beads dimer with the upper bead immersed in
                      a high-viscosity fluid sheet (fluid A) mimicking the
                      membrane, and the lower one in a lower-viscosity fluid B
                      mimicking the intra- and also extracellular environment. We
                      use a recently developed MPC scheme for generating a fluid
                      sheet A inside another fluid B [4]. Using this mesoscale
                      method, diffusion can be probed over time spans not
                      accessible in atomistic MD simulations of proteins. We study
                      the mean squared displacement and velocity autocorrelation
                      function of the individual bead centers, as well as of the
                      hydrodynamic center of mobility of the dumbbell, in
                      dependence of the viscosity ratio, sheet thickness, and
                      interfacial bead distances.References:[1] G. Gompper, T.
                      Ihle, D. M. Kroll, R. G. Winkler, Adv. Polym. Sci, 221, 1-87
                      (2008). [2] Z. Tan, J. K. G. Dhont, V. Calandrini, and G.
                      Nägele, paper in preparation.[3] S. Panzuela and R.
                      Delgado-Buscalioni, Phys. Rev. Lett., 121, 048101 (2018).[4]
                      Z. Tan, J. K. G. Dhont, R. G. Winkler, and G. Nägele, paper
                      in preparation.},
      month         = {Feb},
      date          = {2020-02-27},
      organization  = {NIC Symposium 2020, Jülich (Germany),
                       27 Feb 2020 - 28 Feb 2020},
      subtyp        = {Invited},
      cin          = {IBI-4},
      cid          = {I:(DE-Juel1)IBI-4-20200312},
      pnm          = {551 - Functional Macromolecules and Complexes (POF3-551)},
      pid          = {G:(DE-HGF)POF3-551},
      typ          = {PUB:(DE-HGF)24},
      url          = {https://juser.fz-juelich.de/record/885564},
}