There have been several studies suggesting that protein structures solved by NMR spectroscopy and x-ray crystallography show significant differences. To understand the origin of these differences, we assembled a datab...
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We perform computational studies of static packings of a variety of nonspherical particles including circulo-lines, circulo-polygons, ellipses, asymmetric dimers, dumbbells, and others to determine which shapes form p...
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We perform computational studies of static packings of a variety of nonspherical particles including circulo-lines, circulo-polygons, ellipses, asymmetric dimers, dumbbells, and others to determine which shapes form packings with fewer contacts than degrees of freedom (hypostatic packings) and which have equal numbers of contacts and degrees of freedom (isostatic packings), and to understand why hypostatic packings of nonspherical particles can be mechanically stable despite having fewer contacts than that predicted from naive constraint counting. To generate highly accurate force- and torque-balanced packings of circulo-lines and cir-polygons, we developed an interparticle potential that gives continuous forces and torques as a function of the particle coordinates. We show that the packing fraction and coordination number at jamming onset obey a masterlike form for all of the nonspherical particle packings we studied when plotted versus the particle asphericity A, which is proportional to the ratio of the squared perimeter to the area of the particle. Further, the eigenvalue spectra of the dynamical matrix for packings of different particle shapes collapse when plotted at the same A. For hypostatic packings of nonspherical particles, we verify that the number of “quartic” modes along which the potential energy increases as the fourth power of the perturbation amplitude matches the number of missing contacts relative to the isostatic value. We show that the fourth derivatives of the total potential energy in the directions of the quartic modes remain nonzero as the pressure of the packings is decreased to zero. In addition, we calculate the principal curvatures of the inequality constraints for each contact in circulo-line packings and identify specific types of contacts with inequality constraints that possess convex curvature. These contacts can constrain multiple degrees of freedom and allow hypostatic packings of nonspherical particles to be mechanically stable.
Short Abstract: Is it better to be left- or right-handed? The answer depends on whether the goal is making a handshake or winning a boxing match. The need for coordination favors the handedness of the majority, but be...
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Short Abstract: Is it better to be left- or right-handed? The answer depends on whether the goal is making a handshake or winning a boxing match. The need for coordination favors the handedness of the majority, but being different could also provide an advantage. The same rules could apply to microbial colonies and cancer tumors. Like humans, cells often have handedness (chirality) that reflects the lack of mirror symmetry in their shapes or movement patterns. We find that cells gain a substantial fitness advantage by either increasing the magnitude of their chirality or switching to the opposite handedness. Selection for specific chirality is mediated by the formation of bulges along the colony edge in regions where cells with different chiralities meet. Long Abstract: Chirality in shape and motility can evolve rapidly in microbes and cancer cells. To determine how chirality affects cell fitness, we developed a model of chiral growth in compact aggregates such as microbial colonies and solid tumors. Our model recapitulates previous experimental findings and shows that mutant cells can invade by increasing their chirality or switching their handedness. The invasion results either in a takeover or stable coexistence between the mutant and the ancestor depending on their relative chirality. For large chiralities, the coexistence is accompanied by strong intermixing between the cells, while spatial segregation occurs otherwise. We show that the competition within the aggregate is mediated by bulges in regions where the cells with different chiralities meet. The two-way coupling between aggregate shape and natural selection is described by the chiral Kardar-Parisi-Zhang equation coupled to the Burgers' equation with multiplicative noise. We solve for the key features of this theory to explain the origin of selection on chirality. Overall, our work suggests that chirality could be an important ecological trait that mediates competition, invasion, and spatial structure in
Dense packing of hydrophobic residues in the cores of globular proteins determines their stability. Recently, we have shown that protein cores possess packing fraction φ ≈ 0.56, which is the same as dense, random pa...
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Microbiota contribute to many dimensions of host phenotype, including disease. To link specific microbes to specific phenotypes, microbiome-wide association studies compare microbial abundances between two groups of s...
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Short Abstract: Traveling waves describe diverse natural phenomena from crystal growth in physics to range expansions in biology. Two classes of waves exist with very different properties: pulled and pushed. Pulled wa...
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Short Abstract: Traveling waves describe diverse natural phenomena from crystal growth in physics to range expansions in biology. Two classes of waves exist with very different properties: pulled and pushed. Pulled waves are driven by high growth rates at the expansion edge, where the number of organisms is small and fluctuations are large. In contrast, fluctuations are suppressed in pushed waves because the region of maximal growth is shifted towards the population bulk. Although it is commonly believed that expansions are either pulled or pushed, we found an intermediate class of waves with bulk-driven growth, but exceedingly large fluctuations. These waves are unusual because their properties are controlled by both the leading edge and the bulk of the front. Long Abstract: Epidemics, flame propagation, and cardiac rhythms are classic examples of reaction-diffusion waves that describe a switch from one alternative state to another. Only two types of waves are known: pulled, driven by the leading edge, and pushed, driven by the bulk of the wave. Here, we report a distinct class of semi-pushed waves for which both the bulk and the leading edge contribute to the dynamics. These hybrid waves have the kinetics of pushed waves, but exhibit giant fluctuations similar to pulled waves. The transitions between pulled, semi-pushed, and fully-pushed waves occur at universal ratios of the wave velocity to the Fisher velocity. We derive these results in the context of a species invading a new habitat by examining front diffusion, rate of diversity loss, and fluctuation-induced corrections to the expansion velocity. All three quantities decrease as a power law of the population density with the same exponent. We analytically calculate this exponent taking into account the fluctuations in the shape of the wave front. For fully-pushed waves, the exponent is -1 consistent with the central limit theorem. In semi-pushed waves, however, the fluctuations average out much more slowly, a
Genetic alterations initiate tumors and enable the evolution of drug resistance. The pro-cancer view of mutations is however incomplete, and several studies show that mutational load can reduce tumor fitness. Given it...
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The cover image, by Alexey Teplyakov et al., is based on the Short Communication Crystal structure of B‐cell co‐receptor CD19 in complex with antibody B43 reveals an unexpected fold, DOI: 10.1002/prot.25485.
The cover image, by Alexey Teplyakov et al., is based on the Short Communication Crystal structure of B‐cell co‐receptor CD19 in complex with antibody B43 reveals an unexpected fold, DOI: 10.1002/prot.25485.
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