Trajectories and renders from my simulations: gold cores, DNA ligand shells, crowded solutions and polymers on patterned surfaces. Click any frame to enlarge it.
Polymer meets patterned surfaceA coarse-grained copolymer exploring a chemically heterogeneous surface. Red sites attract strongly, white sites weakly. Hundreds of thousands of runs like this one trained the adhesion model.DNA-grafted gold in waterA T10 ss-DNA-functionalised Au201 nanoparticle, with the solvent rendered as a translucent volume.The full simulation cellThe same nanoparticle seen in its periodic box, tumbling as the ligand shell breathes.Facets of a polarizable nanoparticleA truncated-octahedral gold core with Drude-style polarizable sites. {111} and {100} facets are coloured differently, which is the distinction that decides where citrate binds.A bare gold coreThe atomistic truncated-octahedral gold core before ligands or solvent are added.ss-DNA dodecamer5′-CGCGAATTCGCG-3′, the single strand used in the crowding study.DNA in a dense crowdss-DNA surrounded by amino acid crowders at molar concentration.Crowded, but extendedDepending on the crowder, the strand extends or folds back into native-like hairpins.Hairpin in a mixed crowdIn binary crowder mixtures the response is non-additive, so a mixture can do what neither crowder does alone.Two models, two coronasCitrate-coated gold nanoparticles with a non-polarizable (left) and polarizable (right) gold model.A crowded simulation cellFour ss-DNA strands anchored to a gold core, in a periodic box filled with amino acid crowders and water.Into the crowdA DNA-grafted nanoparticle in a glycine + serine solution. Crowders are drawn as a molecular surface.Ligand shell, close upCartoon rendering of ss-DNA chains anchored to the gold core through alkyl linkers.
