BIOVIA MATERIALS STUDIOMESOCITEDATASHEETBIOVIA Materials Studio Mesocite is a state-of-the-art coarsegrained simulation module for the study of materials atlength scales ranging from nanometers to micrometers andtime scale from nanoseconds to microseconds. Such materials
pervade industrial research in areas such as composites,
coatings, cosmetics and controlled release. BIOVIA Materials
Studio Mesocite can provide structural and dynamic propertiesof fluids in equilibrium, under shear or in confined geometries.

WHAT DOES BIOVIA MATERIALS STUDIOMESOCITE DO?
BIOVIA Materials Studio Mesocite is a method for studying
soft materials using either coarse-grained molecular dynamics(CGMD) or dissipative-particle dynamics1 (BIOVIA Materials
Studio DPD). The basic idea of BIOVIA Materials Studio Mesocite
is that it should be possible to replace groups of atoms withbeads which interact in such a way as to reproduce Newtonianmechanics of the system. The contributions of the atomistic
detail of the system, such as bond vibrations, are integrated

out, giving much larger time- and length-scales. Capturing theatomistic information in the interaction between the beads
means the underlying chemistry of the system is not lost in thecoarse-graining. Extending the length and time scales gives theability to study challenges such as micelle and vesicle formationor phase formation in block copolymers.
The elementary particle in BIOVIA Materials Studio Mesocite
is a bead which represents multiple atoms, or even multiple
molecules of a material. The beads can interact with each otherusing either CGMD or BIOVIA Materials Studio DPD. CGMD
uses Newtonian mechanics to represent the interactions inthe system and contains valence and non-bonded terms.
CGMD allows the simulation of charged systems and retains
much more control of the structure compared with BIOVIA
Materials Studio DPD models. However, this also means that
more parameters need to be generated to describe the system.
In BIOVIA Materials Studio Mesocite, BIOVIA Materials Studio
DPD is used to reproduce the hydrodynamics of the fluid asa whole. The BIOVIA Materials Studio DPD approach uses theFlory-Huggins interaction parameter to define how the beads
interact with each other and a soft potential is used to mimica fluid. This parameter can be measured experimentally or
obtained from modeling with atomistic detail.

KEY USES OF BIOVIA MATERIALSSTUDIO MESOCITEPolymers
The extended time and length scales accessible to BIOVIA
Materials Studio Mesocite allow simulation of polymer
mesophases. This enables researchers to study the affectof additives, solvents, and monomer ratios, on mesophaseformation for homopolymer, block copolymers, random
copolymers, and dendrimers. Soft BIOVIA Materials Studio DPD
potentials make the equilibration of large polymer systems far
faster than using classical techniques. The more detailed CGMDapproach enables time dependent properties such as viscosities
to be determined more accurately.
Figure 1: A phospholipid bilayer in apolar solvent such as water simulatedusing the CGMD method. CGMD is
ideally suited to studying such systems
as charges can be applied to model thecholine and phosphate groups in thehydrophilic head group.

Structured materials
Materials which have structure at the mesophase can bestudied to evaluate their dynamic properties. For example,
the ratio of tail to head or the effect of solvent on lipid bilayer
formation can be investigated. The influence of charges makes
the CGMD method particularly suited to these calculations.

Nanotechnology
Mesoscale methods offer insight into challenges innanotechnology where the alignment of carbon nanotubes ina polymer matrix influences electronic properties. Simulating
the motion of such nanotubes requires timescales that are
not accessible using fully atomistic representations, making
mesoscale methods ideal for such property prediction.

THE BIOVIA MATERIALS STUDIO ADVANTAGEBIOVIA Materials Studio Mesocite is operated from within
the BIOVIA Materials Studio® environment. BIOVIA Materials
Studio provides an integrated userinterface that is easy touse and quick to learn. BIOVIA Materials Studio Visualizer, thecore BIOVIA Materials Studio product, offers a wide range ofmodel building and visualization tools that allow you to rapidly
construct models of the system of interest, calculate thenecessary molecular level information that is required for theparameterization of mesoscale simulation, select the CGMD orBIOVIA Materials Studio DPD functionality, and run a dynamic
simulation of a complex fluid.

Figure 2: A diblock copolymer with blocks ofequal lengths forms a lamellar mesophasefrom a BIOVIA Materials Studio DPD
calculation. The soft potential model of
BIOVIA Materials Studio DPD enables fast
simulation of the mesophases of large
polymer systems.

The bead datamodel and hard-body potential functionality isalso exposed through the MaterialsScript API, giving the power
to automate workflows and further customize calculations.
A flexible client-server architecture means that calculations
can be run on servers located elsewhere on your network.
Results are returned to your PC, where they may be displayedand analyzed. You can easily produce high quality graphics
of molecular and mesoscopic material structures. Thesestructures, graphs, and other data such as video clips, produced
from BIOVIA Materials Studio Mesocite output, can be instantly
exchanged with other PC applications.

HOW DOES BIOVIA MATERIALSSTUDIO MESOCITE WORK?
BIOVIA Materials Studio Mesocite offers two complementary
approaches for coarse grained simulations: CGMD and BIOVIA
Materials Studio DPD.

The CGMD approach uses a classical molecular mechanics
algorithm with hard particles that cannot penetrate each other.
The interactions between each bead are defined by a forcefield
which contains parameters for all the different combination ofinteractions. The interactions are defined by different functional
forms which describe valence interactions, such as bondstretches and angle terms, and non-bonded interactions suchas van der Waals and electrostatic interactions. The forcefield
can contain as many, or few, of the different functional
forms as is required to accurately describe the system ofinterest. As the complexity of the forcefield increases, thenumber of parameters required also increases. Generating goodparameters for the forcefield is key in using the CGMD modelof BIOVIA Materials Studio Mesocite to simulate a material. Aversion of the MARTINI2 forcefield, developed by Marrink et al3
for biomolecular systems, is provided. MARTINI has four main
forcefield types; apolar, nonpolar, polar, and charged. Eachof these types has several subtypes allowing MARTINI to be
applied to many different organic molecules.
The BIOVIA Materials Studio DPD approach is based on theconcept of fluid droplets that can penetrate each other. Inthe method this is reflected by soft potentials as well as athermostat which is related to Brownian motion. BIOVIA
Materials Studio DPD simulates fluid phases which arehomogeneous in density, but show compositional fluctuations.
The composition dependence stems from pair-wise repulsions
between the constituent beads. The repulsive force depends
upon the nature of the colliding beads. Unlike beads frequently
have a stronger repulsion for one another than like beads.
This small difference in the bead-bead forces can lead toremarkably complex systems with exotic morphologies. Thesystem reaches equilibrium very rapidly due to the inclusion ofthermal noise. Polymeric species are viewed as chains of beads,
with harmonic springs connecting successive beads. Chains
may contain more than one bead type, e.g. a block copolymer,
and chain architecture may comprise branches and complex
connectivities. All forces are short-ranged and so the algorithm
is rapid allowing calculations on realistic system sizes.

FEATURES AND CAPABILITIESSpecifying input structures• Build molecule topologies using the Mesoscale Moleculebuilding tools• Build molecule topologies by coarse graining from anatomistic representation• Use the Mesotructure templating tools to create initialstructures such as micelles, slab, rods, etc• Use random starting conditions• Fix the Cartesian positions of beads• Define charges on beads• Define rigid walls with different interactions

Calculation Tasks• Single point energies• Geometry optimization• Dynamics• Dissipative particle dynamics• Restart all tasks, including optional append to trajectory• All tasks in BIOVIA Materials Studio Mesocite support MPI
parallel execution• All tasks in BIOVIA Materials Studio Mesocite are exposed
through MaterialsScript for automation• Shearing (Legacy BIOVIA Materials Studio DPD only)• Nose• Velocity Scale• Andersen• Berendsen• BIOVIA Materials Studio DPD thermostat (accessible throughthe BIOVIA Materials Studio DPD task)

Ensembles• Radial distribution function and structure factor• Radius of gyration• Rotational time correlation• Space-time correlation function• Spatial orientation correlation function• Stress autocorrelation function and shear viscosity• Stress tensor (available through MaterialsScript)• Velocity autocorrelation function• View trajectory data in a study table

• NVE
• NVT
• NPT

To learn more about BIOVIA Materials Studio, go toaccelrys.com/materials-studio

Forcefields

REFERENCES:• MS-MARTINI• Shinoda2007

Analysis• Animate trajectories• Visualize density fields (Legacy BIOVIA Materials Studio DPD
only)• Concentration profiles• Density profiles• Dipole autocorrelation function and power spectrum• Distance, angle, and torsion distributions• Mean squared displacement of beads• Pressure profiles

1. Hoogerbrugge, P. J.; Koelman, J. M. V. A. ‘Simulating microscopic hydrodynamic phenomena with
dissipative particle dynamics’, Europhys. Lett., 1992, 19, 155-160. Groot R.D.;Warren, P. B.‘Dissipativeparticle dynamics: bridging the gap between atomistic and mesoscopic simulation’, J.
Chem. Phys., 1997, 107, 4423-4435.
2. http://md.chem.rug.nl/~marrink/coarsegrain.html
3. S.J. Marrink, H.J. Risselada, S. Yefimov, D.P. Tieleman, A.H. de Vries. “The MARTINI forcefield: coarse
grained model for biomolecular simulations.” J. Phys. Chem. B, 111:7812-7824, 2007.

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