English (United Kingdom)

https://curated-unify.zendy.io/wp-json/zendy-region/v1/featured_content/oa?rat=en

https://curated-unify.zendy.io/wp-json/zendy-region/v1/highlighted_journal/

Global: Zendy Plus annual

Presents the access of premium content as premium feature

Premium Content

Presents the keyphrase highlighting as premium feature

Keyphrase Highlighting

Presents the summarisation as premium feature

Summarisation

Insights

Presents the pdf analysis as premium feature

PDF Analysis

Presents the zaia usage as premium feature

ZAIA

Global: Zendy Tools annual

Global: Zendy Free Plan

Global: Zendy Tools monthly

Global: Zendy Plus monthly

The increasing number of protein-based metamaterials demands reliable andefficient theoretical and computational methods to study the physicochemicalproperties they may display. In this regard, we develop a simulation strategybased on Molecular Dynamics (MD) that addresses the geometric degrees offreedom of an auxetic two-dimensional protein crystal. This model consists of anetwork of impenetrable rigid squares linked through massless rigid rods. OurMD methodology extends the well-known protocols SHAKE and RATTLE to includehighly non-linear holonomic and non-holonomic constraints, with emphasis oncollision detection and response between anisotropic rigid bodies. Thepresented method enables the simulation of long-time dynamics with reasonablylarge time-steps. The data extracted from the simulations allow thecharacterization of the dynamical correlations featured by the proteinsubunits, which show a persistent motional interdependence across the array. Onthe other hand, non-holonomic constraints (collisions between subunits)increase the number of inhomogeneous deformations of the network, thus drivingit away from an isotropic response. Our work provides the first long-timescalesimulation of the dynamics of protein crystals and offers insights intopromising mechanical properties afforded by these materials.

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