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Updated: Jun 11, 2025

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides
Published on: November 21, 2013
Fingerprints of ordered self-assembled structures in the liquid phase of a hard-core, square-shoulder system
Michael Wassermair1,2,3, Gerhard Kahl1, Roland Roth4
1Institut für Theoretische Physik, TU Wien, Wiedner Hauptstraße 8-10, A-1040 Vienna, Austria.
Abstract:
We investigate the phase ordering (pattern formation) of systems of two-dimensional core-shell particles using Monte Carlo (MC) computer simulations and classical density functional theory (DFT). The particles interact via a pair potential having a hard core and a repulsive square shoulder. Our simulations show that on cooling, the liquid state structure becomes increasingly characterized by long wavelength density modulations and on further cooling forms a variety of other phases, including clustered, striped, and other patterned phases. In DFT, the hard core part of the potential is treated using either fundamental measure theory or a simple local density approximation, whereas the soft shoulder is treated using the random phase approximation. The different DFTs are benchmarked using large-scale grand-canonical-MC and Gibbs-ensemble-MC simulations, demonstrating their predictive capabilities and shortcomings. We find that having the liquid state static structure factor S(k) for wavenumber k is sufficient to identify the Fourier modes governing both the liquid and solid phases. This allows us to identify from easier-to-obtain liquid state data the wavenumbers relevant to the periodic phases and to predict roughly where in the phase diagram these patterned phases arise.
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