Exploring the visual styles of arcade game assets

This paper describes a method for evolving assets for video games based on their visuals properties. Focusing on assets for a space shooter game, a genotype consisting of turtle commands is transformed into a spaceship image composed of human-authored sprite components. Due to constraints on the final spaceships’ plausibility, the paper investigates two-population constrained optimization and constrained novelty search methods. A sample of visual styles is tested, each a combination of visual metrics which primarily evaluate balance and shape complexity. Experiments with constrained optimization of a visual style demonstrate that a visually consistent set of spaceships can be generated, while experiments with constrained novelty search demonstrate that several distinct visual styles can be discovered by exploring along select, or all, visual dimensions.peer-reviewe

Computational design of artificial organs

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Computational design of metal-supported molecular switches: Transient ion formation during light- and electron-induced isomerisation of azobenzene

In molecular nanotechnology, a single molecule is envisioned to act as the basic building block of electronic devices. Such devices may be of special interest for organic photovoltaics, data storage, and smart materials. However, more often than not the molecular function is quenched upon contact with a conducting support. Trial-and-error-based decoupling strategies via molecular functionalisation and change of substrate have in many instances proven to yield unpredictable results. The adsorbate-substrate interactions that govern the function can be understood with the help of first-principles simulation. Employing dispersion-corrected Density-Functional Theory (DFT) and linear expansion Delta-Self-Consistent-Field DFT, the electronic structure of a prototypical surface-adsorbed functional molecule, namely azobenzene adsorbed to (111) single crystal facets of copper, silver and gold, is investigated and the main reasons for the loss or survival of the switching function upon adsorption are identified. The light-induced switching ability of a functionalised derivative of azobenzene on Au(111) and azobenzene on Ag(111) and Au(111) is assessed based on the excited-state potential energy landscapes of their transient molecular ions, which are believed to be the main intermediates of the experimentally observed isomerisation reaction. We provide a rationalisation of the experimentally observed function or lack thereof that connects to the underlying chemistry of the metal-surface interaction and provides insights into general design strategies for complex light-driven reactions at metal surfaces.Comment: 14 pages, 5 figures, submitted to J. Phys. Condens. Matte

Iterative approach to computational enzyme design

A general approach for the computational design of enzymes to catalyze arbitrary reactions is a goal at the forefront of the field of protein design. Recently, computationally designed enzymes have been produced for three chemical reactions through the synthesis and screening of a large number of variants. Here, we present an iterative approach that has led to the development of the most catalytically efficient computationally designed enzyme for the Kemp elimination to date. Previously established computational techniques were used to generate an initial design, HG-1, which was catalytically inactive. Analysis of HG-1 with molecular dynamics simulations (MD) and X-ray crystallography indicated that the inactivity might be due to bound waters and high flexibility of residues within the active site. This analysis guided changes to our design procedure, moved the design deeper into the interior of the protein, and resulted in an active Kemp eliminase, HG-2. The cocrystal structure of this enzyme with a transition state analog (TSA) revealed that the TSA was bound in the active site, interacted with the intended catalytic base in a catalytically relevant manner, but was flipped relative to the design model. MD analysis of HG-2 led to an additional point mutation, HG-3, that produced a further threefold improvement in activity. This iterative approach to computational enzyme design, including detailed MD and structural analysis of both active and inactive designs, promises a more complete understanding of the underlying principles of enzymatic catalysis and furthers progress toward reliably producing active enzymes

Paradigms for computational nucleic acid design

The design of DNA and RNA sequences is critical for many endeavors, from DNA nanotechnology, to PCR‐based applications, to DNA hybridization arrays. Results in the literature rely on a wide variety of design criteria adapted to the particular requirements of each application. Using an extensively studied thermodynamic model, we perform a detailed study of several criteria for designing sequences intended to adopt a target secondary structure. We conclude that superior design methods should explicitly implement both a positive design paradigm (optimize affinity for the target structure) and a negative design paradigm (optimize specificity for the target structure). The commonly used approaches of sequence symmetry minimization and minimum free‐energy satisfaction primarily implement negative design and can be strengthened by introducing a positive design component. Surprisingly, our findings hold for a wide range of secondary structures and are robust to modest perturbation of the thermodynamic parameters used for evaluating sequence quality, suggesting the feasibility and ongoing utility of a unified approach to nucleic acid design as parameter sets are refined further. Finally, we observe that designing for thermodynamic stability does not determine folding kinetics, emphasizing the opportunity for extending design criteria to target kinetic features of the energy landscape