Chemically Active Nanodroplets in a Multi-Component Fluid

We introduce a model of chemically active particles of a multi-component fluid that can change their interactions with other particles depending on their state. Since such switching of interactions can only be maintained by the input of chemical energy, the system is inherently non-equilibrium. Focusing on a scenario where the equilibrium interactions would lead to condensation into a liquid droplet, and despite the relative simplicity of the interaction rules, these systems display a wealth of interesting and novel behaviors such as oscillations of droplet size and molecular sorting, and raise the possibility of spatio-temporal control of chemical reactions on the nanoscal

On the microscopic response of equilibrium systems to dissipative perturbations

The standard relationships of statistical mechanics are upended my the presence of active forces. In particular, it is no longer possible to simply write down what the stationary probability of a state of such a system will be, as can be done in ordinary statistical mechanics. Moreover, it is not immediately apparent how qualitatively different notions of dissipative processes would manifest themselves in the probability of a microscopic state, including forces with curls or coupling of interacting particles to different temperature baths. In this manuscript, we demonstrate that a single microscopic response function governs the response of the stationary probability to non-equilibrium perturbations for two qualitatively different notions of non-equilibrium in an overdamped system (differential heat bath and deterministic non-conservative forces). This response function can be computed as a path integral in the unperturbed system. An analytic expression can be computed in harmonic systems, and by analogy with quantum theory, it can be shown that the microscopic probability associated with a state is related to the total dissipation along all paths starting from that state. Simple analytic expressions can be obtained for harmonic systems, where we show that two different notions of non-equilibrium show different behavior when considered in the mode space of the original system. Finally, we discuss the extension of this work to anharmonic systems. From this, it appears a generic relationship exists where the presence of dissipative processes has its largest effects on the soft modes of the equilibrium system. We verify our theoretical predictions against simulations of active polymers.Comment: 17 pages, 3 figure

Chemically active nanodroplets in a multi-component fluid

We introduce a model of chemically active particles of a multi-component fluid that can change their interactions with other particles depending on their state. Since such switching of interactions can only be maintained by the input of chemical energy, the system is inherently non-equilibrium. Focusing on a scenario where the equilibrium interactions would lead to condensation into a liquid droplet, and despite the relative simplicity of the interaction rules, these systems display a wealth of interesting and novel behaviors such as oscillations of droplet size and molecular sorting, and raise the possibility of spatio-temporal control of chemical reactions on the nanoscale. ©201

Darwinian selection of host and bacteria supports emergence of Lamarckian-like adaptation of the system as a whole

Background The relatively fast selection of symbiotic bacteria within hosts and the potential transmission of these bacteria across generations of hosts raise the question of whether interactions between host and bacteria support emergent adaptive capabilities beyond those of germ-free hosts. Results To investigate possibilities for emergent adaptations that may distinguish composite host-microbiome systems from germ-free hosts, we introduce a population genetics model of a host-microbiome system with vertical transmission of bacteria. The host and its bacteria are jointly exposed to a toxic agent, creating a toxic stress that can be alleviated by selection of resistant individuals and by secretion of a detoxification agent (“detox”). We show that toxic exposure in one generation of hosts leads to selection of resistant bacteria, which in turn, increases the toxic tolerance of the host’s offspring. Prolonged exposure to toxin over many host generations promotes anadditional form of emergent adaptation due to selection of hosts based on detox produced by their bacterial community as a whole (as opposed to properties of individual bacteria). Conclusions These findings show that interactions between pure Darwinian selections of host and its bacteria can give rise to emergent adaptive capabilities, including Lamarckian-like adaptation of the host-microbiome system. Reviewers This article was reviewed by Eugene Koonin, Yuri Wolf and Philippe Huneman

Dynamic control of DNA condensation.

Artificial biomolecular condensates are emerging as a versatile approach to organize molecular targets and reactions without the need for lipid membranes. Here we ask whether the temporal response of artificial condensates can be controlled via designed chemical reactions. We address this general question by considering a model problem in which a phase separating component participates in reactions that dynamically activate or deactivate its ability to self-attract. Through a theoretical model we illustrate the transient and equilibrium effects of reactions, linking condensate response and reaction parameters. We experimentally realize our model problem using star-shaped DNA motifs known as nanostars to generate condensates, and we take advantage of strand invasion and displacement reactions to kinetically control the capacity of nanostars to interact. We demonstrate reversible dissolution and growth of DNA condensates in the presence of specific DNA inputs, and we characterize the role of toehold domains, nanostar size, and nanostar valency. Our results will support the development of artificial biomolecular condensates that can adapt to environmental changes with prescribed temporal dynamics

Dynamic control of DNA condensation

Abstract Artificial biomolecular condensates are emerging as a versatile approach to organize molecular targets and reactions without the need for lipid membranes. Here we ask whether the temporal response of artificial condensates can be controlled via designed chemical reactions. We address this general question by considering a model problem in which a phase separating component participates in reactions that dynamically activate or deactivate its ability to self-attract. Through a theoretical model we illustrate the transient and equilibrium effects of reactions, linking condensate response and reaction parameters. We experimentally realize our model problem using star-shaped DNA motifs known as nanostars to generate condensates, and we take advantage of strand invasion and displacement reactions to kinetically control the capacity of nanostars to interact. We demonstrate reversible dissolution and growth of DNA condensates in the presence of specific DNA inputs, and we characterize the role of toehold domains, nanostar size, and nanostar valency. Our results will support the development of artificial biomolecular condensates that can adapt to environmental changes with prescribed temporal dynamics