diff --git a/docs/source/userGuide/models/cell/cell.rst b/docs/source/userGuide/models/cell/cell.rst index f21d307a..1b57ed26 100644 --- a/docs/source/userGuide/models/cell/cell.rst +++ b/docs/source/userGuide/models/cell/cell.rst @@ -2,8 +2,10 @@ Cell model ============================================= -LBPM includes a whole-cell simulator based on a coupled solution of the Nernst-Planck equations with Gauss's law. -The lattice Boltzmann formulation is described below. +LBPM includes a whole-cell simulator based on a coupled solution of the Nernst-Planck equations with Gauss's law. +The resulting model is fully non-equilibrium, and can resolve the dynamics of how ions diffuse through the cellular +environment when subjected to complex membrane responses. +The lattice Boltzmann formulation is described below. ********************* Nernst-Planck model @@ -209,13 +211,13 @@ interior and exterior. See the script ``NaCl-cell.py`` and input file ``NaCl.db` Example input files for both cases are stored within the LBPM repository, located at ``example/SingleCell/`` -The membrane simply prevents the diffusion of ions. All lattice links crossing the membrane are stored in a dedicated data structure so that transport is decoupled from the bulk regions. Suppose that site :math:`\mathbf{x}_{q\ell}` is inside the membrane and :math:`\mathbf{x}_{p\ell}` is outside the membrane. For each species :math:`k`, transport across each link :math:`\ell` is controlled by a pair of coefficients, :math:`\alpha^k_{\ell p}` and :math:`\alpha^k_{\ell q}`. Ions transported from the outside to the inside is +The membrane simply prevents the diffusion of ions. All lattice links crossing the membrane are stored in a dedicated data structure so that transport is decoupled from the bulk regions. Suppose that site :math:`\mathbf{x}_{q\ell}` is inside the membrane and :math:`\mathbf{x}_{p\ell}` is outside the membrane, with :math:`\mathbf{x}_{p \ell } = \mathbf{x}_{q\ell} + \bm{\xi}_q \Delta t`. For each species :math:`k`, transport across each link :math:`\ell` is controlled by a pair of coefficients, :math:`\alpha^k_{\ell p}` and :math:`\alpha^k_{\ell q}`. Ions transported from the outside to the inside is .. math:: :nowrap: $$ - { f_{q}^{k \prime} (\mathbf{x}_{q\ell}) \gets (1-\alpha^k_{\ell q}) f_{q}^{k} (\mathbf{x}_{q\ell}) + \alpha^k_{\ell p } f_{ p}^{k} (\mathbf{x}_{p\ell})} + { f_{q}^{k \prime} (\mathbf{x}_{q \ell}) \gets (1-\alpha^k_{\ell q}) f_{q}^{k} (\mathbf{x}_{q\ell}) + \alpha^k_{\ell p } f_{ p}^{k} (\mathbf{x}_{p\ell})} $$ Similarly, for ions transported from the inside to the outside