Biology subjects

Curatolo, A. I.

Publications and source records attributed to Curatolo, A. I..

3 recordsLinked to original sources

bioRxiv2022

The assembly yield of complex, heterogeneous structures: A computational toolbox

The self-assembly of complex structures from a set of non-identical building blocks is a hallmark of soft matter and biological systems, including protein complexes, colloidal clusters, and DNA-based assemblies. Predicting the dependence of the equilibrium assembly yield on the concentrations and interaction energies of building blocks is highly challenging, owing to the difficulty of computing the entropic contributions to the free energy of the many structures that compete with the ground state configuration. While these calculations yield well known results for spherically symmetric building blocks, we discovered that they do not hold when the building blocks have internal rotational degrees of freedom. Here we present an approach for solving this problem that works with arbitrary building blocks, including proteins with known structure and complex colloidal building blocks. Our algorithm combines classical statistical mechanics with recently developed computational tools for automatic differentiation. Automatic differentiation allows efficient evaluation of equilibrium averages over configurations that would otherwise be intractable. We demonstrate the validity of our framework by comparison to molecular dynamics simulations of simple examples, and apply it to calculate the yield curves for known protein complexes and for the assembly of colloidal shells.

biophysics↗

bioRxiv2020

Self-assembly based post-translational protein oscillators

Recent advances in synthetic post-translational protein circuits are significantly impacting the landscape of biomimicry engineering. However, designing sustained dynamic phenomena in these circuits remains an outstanding challenge. Inspired by the KaiABC system regulating the circadian clock in cyanobacteria, we develop two experimentally realizable post-translational oscillators. The oscillators rely on a small number of components interacting only through reversible binding and phosphorylation/dephosphorylation reactions.

systems biology↗

bioRxiv2019

Cooperative pattern formation in multi-species bacterial colonies

Self-organization is a hallmark of all living systems [1]. In particular, coordinated cellular behavior, commonly orchestrated at the population level through reciprocal interactions among different cell species [2-4], regulates the spatial arrangement of specialized cell types to generate tissue patterning and form complex body layouts [5, 6]. The overwhelming complexity of living systems, however, makes deciphering the underlying mechanisms difficult and limits our knowledge of basic pattern-forming mechanism in vivo [7, 8]. A successful strategy is then to work with synthetic, engineered systems, in which cellular interactions can be more easily tailored and studied [9-13]. Here, we demonstrate a simple mechanism through which different populations of cells can self-organize in periodic patterns. Programmed population interactions are shown to lead to coordinated out-ofphase spatial oscillations of two engineered populations of Escherichia coli. Using a combination of experimental and theoretical approaches, we show how such patterns arise autonomously from reciprocal density-dependent activation of cellular motility between the two species, without the need of any preexisting positional or orientational cues. Moreover, by re-designing the interaction, the original out-of-phase spatial oscillation rhythm of the two populations can be accordingly turned into in-phase oscillations. The robustness and versatility of the underlying pattern-formation process suggest that it could both be generically encountered in nature, for instance in the complex bacterial ecosystems found in biofilms [14-16], and used to promote the mixing or demixing of active particles in a controlled way.

biophysics↗