Recent Publications

Ikeda, H, Brito C, Wyart M.  2020.  Infinitesimal asphericity changes the universality of the jamming transition, 2020. Journal of Statistical Mechanics: Theory and Experiment. 2020(3):033302.: IOP Publishing AbstractWebsite

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The jamming transition of non-spherical particles is fundamentally different from the spherical case. Non-spherical particles are hypostatic at their jamming points, while isostaticity is ensured in the case of the jamming of spherical particles. This structural difference implies that the presence of asphericity affects the critical exponents related to the contact number and the vibrational density of states. Moreover, while the force and gap distributions of isostatic jamming present power-law behaviors, even an infinitesimal asphericity is enough to smooth out these singularities. In a recent work (Brito et al 2018 Proc. Natl Acad. Sci. 115 11736–41), we have used a combination of marginal stability arguments and the replica method to explain these observations. We argued that systems with internal degrees of freedom, like the rotations in ellipsoids, or the variation of the radii in the case of the breathing particles fall in the same universality class. In this paper, we review comprehensively the results about the jamming with internal degrees of freedom in addition to the translational degrees of freedom. We use a variational argument to derive the critical exponents of the contact number, shear modulus, and the characteristic frequencies of the density of states. Moreover, we present additional numerical data supporting the theoretical results, which were not shown in the previous work.

Bravi, B, Ravasio R, Brito C, Wyart M.  2020.  Direct coupling analysis of epistasis in allosteric materials, 2020/03/02. PLOS Computational Biology. 16(3):e1007630-.: Public Library of Science AbstractWebsite

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Author summary Allostery in proteins is the property of highly specific responses to ligand binding at a distant site. To inform protocols of de novo drug design, it is fundamental to understand the impact of mutations on allosteric regulation and whether it can be predicted from evolutionary correlations. In this work we consider allosteric architectures artificially evolved to optimize the cooperativity of binding at allosteric and active site. We first characterize the emergent pattern of epistasis as well as the underlying mechanical phenomena, finding the four types of epistasis (Synergistic, Sign, Antagonistic, Saturation), which can be both short or long-range. The numerical evolution of these allosteric architectures allows us to benchmark Direct Coupling Analysis, a method which relies on co-evolution in sequence data to infer direct evolutionary couplings, in connection to allostery. We show that Direct Coupling Analysis predicts quantitatively point mutation costs but underestimates strong long-range epistasis. We provide an argument, based on a simplified model, illustrating the reasons for this discrepancy. Our analysis suggests neural networks as more promising tool to measure epistasis.