Exploiting sparsity in free energy basin-hopping

GOCIA: a grand canonical global optimizer for clusters, interfaces, and adsorbates

Restructuring of surfaces and interfaces plays a key role in the activation and/or deactivation of a wide spectrum of heterogeneous catalysts and functional materials. The statistical ensemble representation can provide unique atomistic insights into this fluxional and metastable realm, but constructing the ensemble is very challenging, especially for the systems with off-stoichiometric reconstruction and varying coverage of mixed adsorbates. Here, we report GOCIA, a versatile global optimizer for exploring the chemical space of these systems. It features the grand canonical genetic algorithm (GCGA), which bases the target function on the grand potential and evolves across the compositional space, as well as many useful functionalities, with implementation details explained. GOCIA has been applied to various systems in catalysis, from clusters to surfaces and from thermal to electrocatalysis.

Energy landscapes for clusters of hexapeptides

We present the results for energy landscapes of hexapeptides obtained using interfaces to the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) program. We have used basin-hopping global optimization and discrete path sampling to explore the landscapes of hexapeptide monomers, dimers, and oligomers containing 10, 100, and 200 monomers modeled using a residue-level coarse-grained potential, Mpipi, implemented in LAMMPS. We find that the dimers of peptides containing amino acid residues that are better at promoting phase separation, such as tyrosine and arginine, have melting peaks at higher temperature in their heat capacity compared to phenylalanine and lysine, respectively. This observation correlates with previous work on the same uncapped hexapeptide monomers modeled using atomistic potential. For oligomers, we compare the variation in monomer conformations with radial distance and observe trends for selected angles calculated for each monomer. The LAMMPS interfaces to the GMIN and OPTIM programs for landscape exploration offer new opportunities to investigate larger systems and provide access to the coarse-grained potentials implemented within LAMMPS.

100 Years of the Lennard-Jones Potential

It is now 100 years since Lennard-Jones published his first paper introducing the now famous potential that bears his name. It is therefore timely to reflect on the many achievements, as well as the limitations, of this potential in the theory of atomic and molecular interactions, where applications range from descriptions of intermolecular forces to molecules, clusters, and condensed matter.