Potion Master @Potionmaster@qoto.org

The emergence of R, a freely available data analysis environment, brought to the researcher in any science field a set of well-concerted instruments of immense power and low cost. In botany and zoology, these instruments could be used, for example, to speed up work in two distant but related fields: analysis of DNA markers and preparation of natural history manuals. Both of these tasks require a significant amount of monotonous work, which could be automated with software. I developed "Ripeline and "Rmanual," two highly customizable R-based applications, designed with a goal of simplicity, reproducibility, and effectiveness. Ripeline is a pipeline that allows for a continuously updated analysis of multiple DNA markers. Rmanual is a "living book" which allows the creation and continuous update of manuals and checklists. Comparing with more traditional ways of DNA marker analysis and manual preparation, Ripeline and Rmanual allow for a significant reduction of time, which is usually spent doing repetitive tasks. They also provide tools which can be used in a broad spectrum of further applications.

Electronically-active organic molecules have demonstrated great promise as novel soft materials for energy harvesting and transport. Self-assembled nanoaggregates formed from $π$-conjugated oligopeptides composed of an aromatic core flanked by oligopeptide wings offer emergent optoelectronic properties within a water soluble and biocompatible substrate. Nanoaggregate properties can be controlled by tuning core chemistry and peptide composition, but the sequence-structure-function relations remain poorly characterized. In this work, we employ coarse-grained molecular dynamics simulations within an active learning protocol employing deep representational learning and Bayesian optimization to efficiently identify molecules capable of assembling pseudo-1D nanoaggregates with good stacking of the electronically-active $π$-cores. We consider the DXXX-OPV3-XXXD oligopeptide family, where D is an Asp residue and OPV3 is an oligophenylene vinylene oligomer (1,4-distyrylbenzene), to identify the top performing XXX tripeptides within all 20$^3$ = 8,000 possible sequences. By direct simulation of only 2.3% of this space, we identify molecules predicted to exhibit superior assembly relative to those reported in prior work. Spectral clustering of the top candidates reveals new design rules governing assembly. This work establishes new understanding of DXXX-OPV3-XXXD assembly, identifies promising new candidates for experimental testing, and presents a computational design platform that can be generically extended to other peptide-based and peptide-like systems.

Robustness and evolvability are essential properties to the evolution of biological networks. To determine if a biological network is robust and/or evolvable, the comparison of its functions before and after mutations is required. However, it has an increasing computational cost as network size grows. Here we aim to develop a predictor to estimate the robustness and evolvability of biological networks without an explicit comparison of functions. We measure antifragility in Boolean network models of biological systems and use this as the predictor. Antifragility is a property to improve the capability of a system through external perturbations. By means of the differences of antifragility between the original and mutated biological networks, we train a convolutional neural network (CNN) and test it to classify the properties of robustness and evolvability. We found that our CNN model successfully classified the properties. Thus, we conclude that our antifragility measure can be used as a significant predictor of the robustness and evolvability of biological networks.

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