Bendability parameter for twisted ribbons to describe longitudinal wrinkling and delineate the near-threshold regime.

We propose a dimensionless bendability parameter, ε^{-1}=[(h/W)^{2}T^{-1}]^{-1}, for wrinkling of thin, twisted ribbons with thickness h, width W, and tensional strain T. Bendability permits efficient collapse of data for wrinkle onset, wavelength, critical stress, and residual stress, demonstrating longitudinal wrinkling's primary dependence on this parameter. This parameter also allows us to distinguish the highly bendable range (ε^{-1}>20) from moderately bendable samples (ε^{-1}∈(0,20]). We identify scaling relations to describe longitudinal wrinkles that are valid across our entire set of simulated ribbons. When restricted to the highly bendable regime, simulations confirm theoretical near-threshold (NT) predictions for wrinkle onset and wavelength.

How microscopic epistasis and clonal interference shape the fitness trajectory in a spin glass model of microbial long-term evolution.

The adaptive dynamics of evolving microbial populations takes place on a complex fitness landscape generated by epistatic interactions. The population generically consists of multiple competing strains, a phenomenon known as clonal interference. Microscopic epistasis and clonal interference are central aspects of evolution in microbes, but their combined effects on the functional form of the population's mean fitness are poorly understood. Here, we develop a computational method that resolves the full microscopic complexity of a simulated evolving population subject to a standard serial dilution protocol. Through extensive numerical experimentation, we find that stronger microscopic epistasis gives rise to fitness trajectories with slower growth independent of the number of competing strains, which we quantify with power-law fits and understand mechanistically via a random walk model that neglects dynamical correlations between genes. We show that increasing the level of clonal interference leads to fitness trajectories with faster growth (in functional form) without microscopic epistasis, but leaves the rate of growth invariant when epistasis is sufficiently strong, indicating that the role of clonal interference depends intimately on the underlying fitness landscape. The simulation package for this work may be found at https://github.com/nmboffi/spin_glass_evodyn.

Computational model of twisted elastic ribbons.

We develop an irregular lattice mass-spring model to simulate and study the deformation modes of a thin elastic ribbon as a function of applied end-to-end twist and tension. Our simulations reproduce all reported experimentally observed modes, including transitions from helicoids to longitudinal wrinkles, creased helicoids and loops with self-contact, and transverse wrinkles to accordion self-folds. Our simulations also show that the twist angles at which the primary longitudinal and transverse wrinkles appear are well described by various analyses of the Föppl-von Kármán equations, but the characteristic wavelength of the longitudinal wrinkles has a more complex relationship to applied tension than previously estimated. The clamped edges are shown to suppress longitudinal wrinkling over a distance set by the applied tension and the ribbon width, but otherwise have no apparent effect on measured wavelength. Further, by analyzing the stress profile, we find that longitudinal wrinkling does not completely alleviate compression, but caps the magnitude of the compression. Nonetheless, the width over which wrinkles form is observed to be wider than the near-threshold analysis predictions: the width is more consistent with the predictions of far-from-threshold analysis. However, the end-to-end contraction of the ribbon as a function of twist is found to more closely follow the corresponding near-threshold prediction as tension in the ribbon is increased, in contrast to the expectations of far-from-threshold analysis. These results point to the need for further theoretical analysis of this rich thin elastic system, guided by our physically robust and intuitive simulation model.

A subcellular biochemical model for T6SS dynamics reveals winning competitive strategies.

The type VI secretion system (T6SS) is a broadly distributed interbacterial weapon that can be used to eliminate competing bacterial populations. Although unarmed target populations are typically used to study T6SS function in vitro, bacteria most likely encounter other T6SS-armed competitors in nature. However, the connection between subcellular details of the T6SS and the outcomes of such mutually lethal battles is not well understood. Here, we incorporate biological data derived from natural competitors of Vibrio fischeri light organ symbionts to build a biochemical model for T6SS at the single-cell level, which we then integrate into an agent-based model (ABM). Using the ABM, we isolate and experiment with strain-specific physiological differences between competitors in ways not possible with biological samples to identify winning strategies for T6SS-armed populations. Through in vitro experiments, we discover that strain-specific differences exist in T6SS activation speed. ABM simulations corroborate that faster activation is dominant in determining survival during competition. Once competitors are fully activated, the energy required for T6SS creates a tipping point where increased weapon building and firing becomes too costly to be advantageous. Through ABM simulations, we identify the threshold where this transition occurs in the T6SS parameter space. We also find that competitive outcomes depend on the geometry of the battlefield: unarmed target cells survive at the edges of a range expansion where unlimited territory can be claimed. Alternatively, competitions within a confined space, much like the light organ crypts where natural V. fischeri compete, result in the rapid elimination of the unarmed population.

Cut site preference allows influenza A virus PA-X to discriminate between host and viral mRNAs.

Many viruses block host gene expression to take over the infected cell. This process, termed host shutoff, is thought to promote viral replication by preventing antiviral responses and redirecting cellular resources to viral processes. Several viruses from divergent families accomplish host shutoff through RNA degradation by endoribonucleases. However, viruses also need to ensure expression of their own genes. The influenza A virus endoribonuclease PA-X solves this problem by sparing viral mRNAs and some host RNAs necessary for viral replication. To understand how PA-X distinguishes between RNAs, we characterized PA-X cut sites transcriptome-wide using 5' rapid amplification of complementary DNA ends coupled to high-throughput sequencing. This analysis, along with RNA structure predictions and validation experiments using reporters, shows that PA-Xs from multiple influenza strains preferentially cleave RNAs at GCUG tetramers in hairpin loops. Importantly, GCUG tetramers are enriched in the human but not the influenza transcriptome. Moreover, optimal PA-X cut sites inserted in the influenza A virus genome are quickly selected against during viral replication in cells. This finding suggests that PA-X evolved these cleavage characteristics to preferentially target host over viral mRNAs in a manner reminiscent of cellular self versus non-self discrimination.

Machine-Learning Spectral Indicators of Topology.

Topological materials discovery has emerged as an important frontier in condensed matter physics. While theoretical classification frameworks have been used to identify thousands of candidate topological materials, experimental determination of materials' topology often poses significant technical challenges. X-ray absorption spectroscopy (XAS) is a widely used materials characterization technique sensitive to atoms' local symmetry and chemical bonding, which are intimately linked to band topology by the theory of topological quantum chemistry (TQC). Moreover, as a local structural probe, XAS is known to have high quantitative agreement between experiment and calculation, suggesting that insights from computational spectra can effectively inform experiments. In this work, computed X-ray absorption near-edge structure (XANES) spectra of more than 10 000 inorganic materials to train a neural network (NN) classifier that predicts topological class directly from XANES signatures, achieving F1 scores of 89% and 93% for topological and trivial classes, respectively is leveraged. Given the simplicity of the XAS setup and its compatibility with multimodal sample environments, the proposed machine-learning-augmented XAS topological indicator has the potential to discover broader categories of topological materials, such as non-cleavable compounds and amorphous materials, and may further inform field-driven phenomena in situ, such as magnetic field-driven topological phase transitions.

Inverse Design of Mechanical Metamaterials with Target Nonlinear Response via a Neural Accelerated Evolution Strategy.

Materials with target nonlinear mechanical response can support the design of innovative soft robots, wearable devices, footwear, and energy-absorbing systems, yet it is challenging to realize them. Here, mechanical metamaterials based on hinged quadrilaterals are used as a platform to realize target nonlinear mechanical responses. It is first shown that by changing the shape of the quadrilaterals, the amount of internal rotations induced by the applied compression can be tuned, and a wide range of mechanical responses is achieved. Next, a neural network is introduced that provides a computationally inexpensive relationship between the parameters describing the geometry and the corresponding stress-strain response. Finally, it is shown that by combining the neural network with an evolution strategy, one can efficiently identify geometries resulting in a wide range of target nonlinear mechanical responses and design optimized energy-absorbing systems, soft robots, and morphing structures.

Nuclear speed and cycle length co-vary with local density during syncytial blastoderm formation in a cricket.

The blastoderm is a broadly conserved stage of early animal development, wherein cells form a layer at the embryo's periphery. The cellular behaviors underlying blastoderm formation are varied and poorly understood. In most insects, the pre-blastoderm embryo is a syncytium: nuclei divide and move throughout the shared cytoplasm, ultimately reaching the cortex. In Drosophila melanogaster, some early nuclear movements result from pulsed cytoplasmic flows that are coupled to synchronous divisions. Here, we show that the cricket Gryllus bimaculatus has a different solution to the problem of creating a blastoderm. We quantified nuclear dynamics during blastoderm formation in G. bimaculatus embryos, finding that: (1) cytoplasmic flows are unimportant for nuclear movement, and (2) division cycles, nuclear speeds, and the directions of nuclear movement are not synchronized, instead being heterogeneous in space and time. Moreover, nuclear divisions and movements co-vary with local nuclear density. We show that several previously proposed models for nuclear movements in D. melanogaster cannot explain the dynamics of G. bimaculatus nuclei. We introduce a geometric model based on asymmetric pulling forces on nuclei, which recapitulates the patterns of nuclear speeds and orientations of both unperturbed G. bimaculatus embryos, and of embryos physically manipulated to have atypical nuclear densities.

Eulerian simulation of complex suspensions and biolocomotion in three dimensions.

We present a numerical method specifically designed for simulating three-dimensional fluid-structure interaction (FSI) problems based on the reference map technique (RMT). The RMT is a fully Eulerian FSI numerical method that allows fluids and large-deformation elastic solids to be represented on a single fixed computational grid. This eliminates the need for meshing complex geometries typical in other FSI approaches and greatly simplifies the coupling between fluid and solids. We develop a three-dimensional implementation of the RMT, parallelized using the distributed memory paradigm, to simulate incompressible FSI with neo-Hookean solids. As part of our method, we develop a field extrapolation scheme that works efficiently in parallel. Through representative examples, we demonstrate the method's suitability in investigating many-body and active systems, as well as its accuracy and convergence. The examples include settling of a mixture of heavy and buoyant soft ellipsoids, lid-driven cavity flow containing a soft sphere, and swimmers actuated via active stress.