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Scientific Report 2007-2009
Condensed matter physics and biophysics
C20. Coarse Grained Molecular Dynamics Simulations: application to
proteins and colloids
All atoms Molecular dynamics (MD) or Monte Carlo
(MC) simulations of large systems, evolving on very long
timescales, are very demanding in terms of computer resources.
In these cases, it becomes important to develop
coarse-grained (CG) models, i.e. a reduced representations
of the interparticle interaction potential. Several
systems in condensed matter physics and biophysics
have been successfully modeled in this way. Protein folding
and protein aggregation are often studied employing
simplified CG. We have recently developed one of
these models for the protein lysozime, to describe the
clustering phenomenon which takes place in the absence
of salt, as a result of a competition between hydrophobic
attraction and screened electrostatic repulsion. CG
models are also very relevant for testing state-of-the-art
theoretical modeling, since they often allow for a oneto-one
correspondence between the theoretical assumptions
and the numerical realization. For example, the
glass transition of rigid molecules where excluded volume
interactions play a relevant role (e.g. lyotropic liquid
crystals), can be conveniently modeled approximating
their constituent particles as hard ellipsoids. We
have investigate [1] the dynamic phase diagram of hard
ellipsoids, employing event-driven MD, discovering, close
to the isotropic-nematic transition clear indications of a
new kind of glass transition, in agreement with recent
theoretical predictions.
CG models are also relevant in the investigation of
soft-matter systems. Often, the interactions between
colloidal particles can be modeled via an effective potential,
by integrating out all solvent and internal degrees
of freedom of the particles. One example is offered
by star-polymers (SP), i.e. macromolecules containing a
single branch point from which linear chains (arms) emanate.
In [2], we reported the observation of several glass
states in mixtures of SPs, modeled as simple spheres interacting
with a suitable soft potential (see Fig.1 (a)).
Another interesting example is offered by the chemical
gelation of epoxy resins, which we have modeled as a
mixture of two rigid ellipsoids forming permanent bonds
through localized interaction sites[3]. MD allows us to
follow the bonding process and study the structure and
connectivity of the system in time (details in Fig. 2).
More recently, we have studied the phase diagram of the
recently synthesized Janus particles[4], i.e. spherical particles
characterized by a surface divided into two areas
of different chemical composition. The calculated phase
diagram is very peculiar, showing competition between
critical fluctuations and micelle formation.
Figure 2: (a) Coarse-grained model of resins DGEBA and
DETA. (b) Snapshot of sol phase (c) Cluster size distributions
at various bond probability p (symbols) and corresponding
theoretical predictions (continous lines).
Figure 1: (a) Coarse-grained model of a star polymer mixture,
constituted by large and small particles. The kinetic
phase diagram (in the plane density-asymmetry) obtained by
experiments (b) is qualitatively reproduced with simulations
(c). (d) Snapshots of typical cages around a fixed large star
(along the line in panel (c)).
References
1. C. De Michele et al., Phys. Rev. Lett. 98, 265702 (2007).
2. C. Mayer et al., Nature Materials 7, 780-784 (2008).
3. S. Corezzi et al., Soft Matter 4, 1173-1177 (2008).
4. F. Sciortino et al., Phys. Rev. Lett. 103, 237801 (2009).
Authors
C. De Michele 1 , C. Mayer 1 , F. Romano 1 , J. Russo 1 , F.
Sciortino, P. Tartaglia, E. Zaccarelli 1,2
http://soft.phys.uniroma1.it/
Sapienza Università di Roma 73 Dipartimento di Fisica