A touch of awe: crafting meaning from the wonder of the cosmos
Annals of the New York Academy of Sciences Wiley 1432:1 (2018) 46-62
Abstract:
From the birth of galaxies to the self-organizing dynamics of our planet to the ongoing expansion of the universe, the more we discover about the evolution of the cosmos, the more acutely we realize the enormity of what remains to be known. Just this year astrophysicists at the University of Nottingham confirmed that there are at least two trillion galaxies in the cosmos, 10 times more than had been previously thought. What guidance or wisdom can the study of cosmology and astrophysics offer us in our search for meaning and purpose? In conversation with Steve Paulson, executive producer and host of To the Best of Our Knowledge, theoretical physicists Paul Davies and Ard Louis, and astrophysicist Lucianne Walkowicz share their perceptions based on years of gazing upward and beyond our own intimate planet.Force-induced unravelling of DNA origami
ACS Nano American Chemical Society 12:7 (2018) 6734-6747
Abstract:
The mechanical properties of DNA nanostructures are of widespread interest as applications that exploit their stability under constant or intermittent external forces become increasingly common. We explore the force response of DNA origami in comprehensive detail by combining AFM single molecule force spectroscopy experiments with simulations using oxDNA, a coarse-grained model of DNA at the nucleotide level, to study the unravelling of an iconic origami system: the Rothemund tile. We contrast the force-induced melting of the tile with simulations of an origami 10-helix bundle. Finally, we simulate a recently proposed origami biosensor, whose function takes advantage of origami behavior under tension. We observe characteristic stick–slip unfolding dynamics in our force–extension curves for both the Rothemund tile and the helix bundle and reasonable agreement with experimentally observed rupture forces for these systems. Our results highlight the effect of design on force response: we observe regular, modular unfolding for the Rothemund tile that contrasts with strain-softening of the 10-helix bundle which leads to catastropic failure under monotonically increasing force. Further, unravelling occurs straightforwardly from the scaffold ends inward for the Rothemund tile, while the helix bundle unfolds more nonlinearly. The detailed visualization of the yielding events provided by simulation allows preferred pathways through the complex unfolding free-energy landscape to be mapped, as a key factor in determining relative barrier heights is the extensional release per base pair broken. We shed light on two important questions: how stable DNA nanostructures are under external forces and what design principles can be applied to enhance stability.Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly
Journal of Chemical Physics AIP Publishing 148:13 (2018) 134910
Abstract:
Inspired by recent successes using single-stranded DNA tiles to produce complex structures, we develop a two-step coarse-graining approach that uses detailed thermodynamic calculations with oxDNA, a nucleotide-based model of DNA, to parametrize a coarser kinetic model that can reach the time and length scales needed to study the assembly mechanisms of these structures. We test the model by performing a detailed study of the assembly pathways for a two-dimensional target structure made up of 334 unique strands each of which are 42 nucleotides long. Without adjustable parameters, the model reproduces a critical temperature for the formation of the assembly that is close to the temperature at which assembly first occurs in experiments. Furthermore, the model allows us to investigate in detail the nucleation barriers and the distribution of critical nucleus shapes for the assembly of a single target structure. The assembly intermediates are compact and highly connected (although not maximally so), and classical nucleation theory provides a good fit to the height and shape of the nucleation barrier at temperatures close to where assembly first occurs.Input-output maps are strongly biased towards simple outputs
Nature Communications Springer Nature 9 (2018) 761
Abstract:
Many systems in nature can be described using discrete input–output maps. Without knowing details about a map, there may seem to be no a priori reason to expect that a randomly chosen input would be more likely to generate one output over another. Here, by extending fundamental results from algorithmic information theory, we show instead that for many real-world maps, the a priori probability P(x) that randomly sampled inputs generate a particular output x decays exponentially with the approximate Kolmogorov complexity K˜(x) of that output. These input–output maps are biased towards simplicity. We derive an upper bound P(x) ≲ 2−aK˜(x)−b, which is tight for most inputs. The constants a and b, as well as many properties of P(x), can be predicted with minimal knowledge of the map. We explore this strong bias towards simple outputs in systems ranging from the folding of RNA secondary structures to systems of coupled ordinary differential equations to a stochastic financial trading model.How do I obtain reliable knowledge about the world? *
Chapter in A Teacher’s Guide to Science and Religion in the Classroom, Taylor & Francis (2018) 146-151