Downward transference of mice and universality of local core models

If M is a proper class inner model of ZFC and omega_2^M=omega_2, then every sound mouse projecting to omega and not past 0-pistol belongs to M. In fact, under the assumption that 0-pistol does not belong to M, K^M \| omega_2 is universal for all countable mice in V. Similarly, if M is a proper class inner model of ZFC, delta>omega_1 is regular, (delta^+)^M = delta^+, and in V there is no proper class inner model with a Woodin cardinal, then K^M \| delta is universal for all mice in V of cardinality less than delta.Comment: Revised version, incorporating the referee's suggestion

On sets of numbers rationally represented in a rational base number system

In this work, it is proved that a set of numbers closed under addition and whose representations in a rational base numeration system is a rational language is not a finitely generated additive monoid. A key to the proof is the definition of a strong combinatorial property on languages : the bounded left iteration property. It is both an unnatural property in usual formal language theory (as it contradicts any kind of pumping lemma) and an ideal fit to the languages defined through rational base number systems

An Introduction to Programming for Bioscientists: A Python-based Primer

Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in the biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by fundamental developments in hardware, software, and algorithms. These advances have influenced, and even engendered, a phenomenal array of bioscience fields, including molecular evolution and bioinformatics; genome-, proteome-, transcriptome- and metabolome-wide experimental studies; structural genomics; and atomistic simulations of cellular-scale molecular assemblies as large as ribosomes and intact viruses. In short, much of post-genomic biology is increasingly becoming a form of computational biology. The ability to design and write computer programs is among the most indispensable skills that a modern researcher can cultivate. Python has become a popular programming language in the biosciences, largely because (i) its straightforward semantics and clean syntax make it a readily accessible first language; (ii) it is expressive and well-suited to object-oriented programming, as well as other modern paradigms; and (iii) the many available libraries and third-party toolkits extend the functionality of the core language into virtually every biological domain (sequence and structure analyses, phylogenomics, workflow management systems, etc.). This primer offers a basic introduction to coding, via Python, and it includes concrete examples and exercises to illustrate the language's usage and capabilities; the main text culminates with a final project in structural bioinformatics. A suite of Supplemental Chapters is also provided. Starting with basic concepts, such as that of a 'variable', the Chapters methodically advance the reader to the point of writing a graphical user interface to compute the Hamming distance between two DNA sequences.Comment: 65 pages total, including 45 pages text, 3 figures, 4 tables, numerous exercises, and 19 pages of Supporting Information; currently in press at PLOS Computational Biolog

Local Definability of HOD\mathsf{HOD} in L(R)L(\mathbb{R})

We show that in $L(\mathbb{R})$, assuming large cardinals, $\mathsf{HOD} {\parallel}\eta^{+\mathsf{HOD}}$ is locally definable from $\mathsf{HOD} {\parallel}\eta$ for all $\mathsf{HOD}$-cardinals $\eta\in [\boldsymbol{\delta}^2_1,\Theta)$. This is a further elaboration of the statement "$\mathsf{HOD}^{L(\mathbb{R})}$ is a core model below $\Theta$" made by John Steel