:orphan:

.. status publishable
.. product Mesoscale Builder
.. sectionauthor Jörg
.. SME Jörg
.. PR Marianna
.. TW Kathy
.. date 2020

.. _mesoscalebuilderDTS:

|medea|  |mesoscalebuilder| -  Going Beyond Atomistic Simulations
-----------------------------------------------------------------------

.. admonition:: **At-a-Glance**

   The  |medea|\ :sup:`®`\ [#TM]_ |mesoscalebuilder| creates models
   for simulations on the time and length scale of microseconds and
   tens of nanometers. The models created can be used with other
   |medea| tools to build more complex systems, such
   as polymers or thermosets. Mesoscale bead definitions and parameters
   are provided for the MARTINI\ [#martini]_ and SPICA\ [#spica]_ forcefields.

   **Key Benefits**

   * *Quickly build mesoscale models with beads from the scientific literature*
   * *Utilize the MARTINI and SPICA forcefields*
   * *Define your own beads*
   * *Use mesoscale models with Polymer, Amorphous, and Thermoset builders*
   * *Use mesoscale models to run* |medea|  |lammps|
     *simulations on time and lengths scales which exceed atomistic modeling*

Think Big
^^^^^^^^^

The |medea|  |mesoscalebuilder| creates mesoscale models using bead definitions
from the scientific literature. Use the mesoscale models to build polymers,
amorphous systems, or thermosets for modeling on time and lengths scales which
are outside the reach of atomistic simulations. Study the phase behavior,
mechanical properties, or any other property which can be modeled by forcefields
of systems representing millions of atoms.

Mesoscale simulations make it possible to study effects that cannot be observed
in atomistic simulations. Self-assembly of molecules, the effect of detergents,
explicit solvation, or fluid dynamics become accessible to modeling.

.. figure:: /Datasheets/images/MesoscaleBuilder.png
   :align: center

   A lipid bilayer has formed in a mesoscale simulation of
   dipalmitoylphosphatidylcholine molecules (green and purple) in water (blue)

Key Features
^^^^^^^^^^^^

* Integrated extensible library with bead definitions and forcefield parameters for

  * MARTINI forcefield\ [#martini]_
  * SPICA forcefield\ [#spica]_

* Sketching of mesoscale models using

  * predefined beads, or
  * user-defined beads

* Built systems can be used in mesoscale simulations performed with
  |medea|  |mlammps| and gain access to all properties available
  via |medea|  |mlammps|


Characteristics & Uses
^^^^^^^^^^^^^^^^^^^^^^

* Create any desired mesoscale model with the |medea|  |mesoscalebuilder|
* Use the models that |medea|  |mesoscalebuilder| creates to prepare
  bulk models for mesoscale simulations of physical properties including:

  * Density and PVT Properties
  * Surface and Interfacial tension
  * Thermal Conductivity
  * Diffusivity

.. * Gas and Moisture Sorption


Required Modules
^^^^^^^^^^^^^^^^

* |medea| |menvironment|
* |medea| |mesoscalebuilder|

Related Modules
^^^^^^^^^^^^^^^

* |medea|  |amorphousbuilder|
* |medea|  |forcefields|
* |medea|  |diffusion|
* |medea|  |surfacetension|
* |medea|  |thermalconductivity|
* |medea|  |mtfull|
* |medea|  |thermosetbuilder|
* |medea|  |mlammps| |mstdenv|

.. add for a column break, adjust where needed
.. raw:: latex

   \newpage


Find Out More
^^^^^^^^^^^^^

To learn more about mesoscale simulations see the following papers on the following topics:

* Development of the MARTINI coarse-grained forcefield for lipid and biomolecular
  simulations [#Marrink2004]_\ :sup:`,`\ [#Marrink2007]_

* Application of the MARTINI forcefield to model a thermoset polyester coating [#Rossi2011]_

* Parameterization of coarse-grained forcefields for aqueous surfactants and
  lipid assemblies [#Shinoda2007]_\ :sup:`,`\ [#Shinoda2010]_

* Coarse-grained modeling of entangled polyethylene melts and polyethylene
  crystallization [#Hall2019]_\ :sup:`,`\ [#Hall2019b]_


.. [#TM] |regTMinfo|

.. [#martini] http://cgmartini.nl/

.. [#spica] https://www.spica-ff.org/

.. [#Marrink2004] S. J. Marrink *et al.*,
   *J. Phys. Chem. B* **108**, 750 (2004)
   (`DOI <https://doi.org/10.1021/jp036508g>`__)

.. [#Marrink2007] S. J. Marrink *et al.*,
   *J. Phys. Chem. B* **111**, 7812 (2007)
   (`DOI <https://doi.org/10.1021/jp071097f>`__)

.. [#Rossi2011] G. Rossi *et al.*,
   *Macromolecules* **44**, 6198 (2011)
   (`DOI <https://doi.org/10.1021/ma200788a>`__)

.. [#Shinoda2007] W. Shinoda *et al.*,
   *Molecular Simulation* **33**, 27 (2007)
   (`DOI <https://doi.org/10.1080/08927020601054050>`__)

.. [#Shinoda2010] W. Shinoda *et al.*,
   *J. Phys. Chem. B* **114**, 6836 (2010)
   (`DOI <https://doi.org/10.1021/jp9107206>`__)

.. [#Hall2019] K. Hall *et al.*,
   *J. Chem. Phys.* **150**, 244901 (2019)
   (`DOI <https://doi.org/10.1063/1.5092229>`__)

.. [#Hall2019b] K. W. Hall *et al.*,
   *J. Chem. Phys.* **151**, 144901 (2019)
   (`DOI <https://doi.org/10.1063/1.5123983>`__)


.. only:: html

   :download: :download:`pdf </Datasheets/Datasheet-MesoscaleBuilder.pdf>`