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@INPROCEEDINGS{Tan:902786,
      author       = {Tan, Zihan and Calandrini, Vania and Dhont, Jan K.G. and
                      Winkler, Roland G. and Naegele, Gerhard},
      title        = {{Q}uasi-two-dimensional diffusion of interacting protein
                      monomers and dimers: {A} {MPC} simulation study},
      reportid     = {FZJ-2021-04557},
      year         = {2021},
      note         = {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, V. Calandrini, J.
                      K. G. Dhont, G. Nägele, and R. G. Winkler, arXiv:2105.01492
                      (2021).},
      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 the upper segment is
                      embedded in the neuronal cell membrane, and the lower one in
                      the cytosol. The protein is simply modelled 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
                      centres and the hydrodynamic centre of mobility of the
                      dumbbell, in dependence of the viscosity ratio sheet
                      thickness and interfacial bead distances.},
      month         = {Jul},
      date          = {2021-07-19},
      organization  = {11th LIQUID MATTER CONFERENCE
                       2020/2021, Prague/Online (Czech
                       Republic), 19 Jul 2021 - 23 Jul 2021},
      subtyp        = {After Call},
      cin          = {IBI-4 / IAS-5 / IBI-5 / INM-9},
      cid          = {I:(DE-Juel1)IBI-4-20200312 / I:(DE-Juel1)IAS-5-20120330 /
                      I:(DE-Juel1)IBI-5-20200312 / I:(DE-Juel1)INM-9-20140121},
      pnm          = {5244 - Information Processing in Neuronal Networks
                      (POF4-524)},
      pid          = {G:(DE-HGF)POF4-5244},
      typ          = {PUB:(DE-HGF)24},
      url          = {https://juser.fz-juelich.de/record/902786},
}