Computational method for highly constrained molecular dynamics of rigid bodies: Coarse-grained simulation of auxetic two-dimensional protein crystals

The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on Molecular Dynamics (MD) that addresses the geometric degrees o...

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Bibliographic Details
Published in:The Journal of chemical physics 2020-06, Vol.152 (24), p.244102-244102
Main Authors: Campos-Gonzalez-Angulo, Jorge A., Wiesehan, Garret, Ribeiro, Raphael F., Yuen-Zhou, Joel
Format: Article
Language:English
Subjects:
Computer simulation
Constraints
Crystals
Mechanical properties
Metamaterials
Molecular dynamics
Molecular Dynamics Simulation
Physics
Proteins
Proteins - chemistry
Protocol (computers)
Rigid structures
Rigid-body dynamics
Simulation
Two dimensional models
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Summary:The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on Molecular Dynamics (MD) that addresses the geometric degrees of freedom of an auxetic two-dimensional protein crystal. This model consists of a network of impenetrable rigid squares linked through massless rigid rods. Our MD methodology extends the well-known protocols SHAKE and RATTLE to include highly non-linear holonomic and non-holonomic constraints, with an emphasis on collision detection and response between anisotropic rigid bodies. The presented method enables the simulation of long-time dynamics with reasonably large time steps. The data extracted from the simulations allow the characterization of the dynamical correlations featured by the protein subunits, which show a persistent motional interdependence across the array. On the other hand, non-holonomic constraints (collisions between subunits) increase the number of inhomogeneous deformations of the network, thus driving it away from an isotropic response. Our work provides the first long-timescale simulation of the dynamics of protein crystals and offers insights into promising mechanical properties afforded by these materials.
ISSN:0021-9606
1089-7690
DOI:10.1063/5.0004518