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Register a new userNon-Equilibrium Thermodynamics of Self-Replicating Protocells
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Bernat Corominas-Murtra BCM
Publication date
2015
fields
Physics
and research's language is
English
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We provide a non-equilibrium thermodynamic description of the life-cycle of a droplet based, chemically feasible, system of protocells. By coupling the protocells metabolic kinetics with its thermodynamics, we demonstrate how the system can be driven out of equilibrium to ensure protocell growth and replication. This coupling allows us to derive the equations of evolution and to rigorously demonstrate how growth and replication life-cycle can be understood as a non-equilibrium thermodynamic cycle. The process does not appeal to genetic information or inheritance, and is based only on non-equilibrium physics considerations. Our non-equilibrium thermodynamic description of simple, yet realistic, processes of protocell growth and replication, represents an advance in our physical understanding of a central biological phenomenon both in connection to the origin of life and for modern biology.
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Self-assembling, semi-flexible polymers are ubiquitous in biology and technology. However, there remain conflicting accounts of the equilibrium kinetics for such an important system. Here, by focusing on a dynamical description of a minimal model in an overdamped environment, I identify the correct kinetic scheme that describes the system at equilibrium in the limits of high bonding energy and dilute concentration.
Colonies of bacterial cells endowed with a pili-based self-propulsion machinery represent an ideal model system for studying how active adhesion forces affect structure and dynamics of many-particle systems. As a novel computational tool, we describe here a highly parallel molecular dynamics simulation package for modeling of textit{Neisseria gonorrhoeae} colonies. Simulations are employed to investigate growth of bacterial colonies and the dependence of the colony structure on cell-cell interactions. In agreement with experimental data, active pilus retraction is found to enhance local ordering. For mixed colonies consisting of different types of cell types, the simulations show a segregation of cell types depending on the pili-mediated interactions, as seen in experiments. Using a simulated experimental setup, we study the power-spectral density of colony-shape fluctuations and the associated fluctuation-response relation. The simulations predict a strong violation of the equilibrium fluctuation-response relation across the measurable frequency range. Lastly, we illustrate the essential role of active force generation for colony dynamics by showing that pilus-mediated activity drives the spreading of colonies on surfaces and the invasion of narrow channels.
We study the conformational dynamics within homo-polymer globules by solvent-implicit Brownian dynamics simulations. A strong dependence of the internal chain dynamics on the Lennard-Jones cohesion strength {epsilon} and the globule size NG is observed. We find two distinct dynamical regimes: a liquid- like regime (for {epsilon} < {epsilon}s) with fast internal dynamics and a solid-like regime (for {epsilon} > {epsilon}s) with slow internal dynamics. The cohesion strength {epsilon}s of this freezing transition depends on NG. Equilibrium simulations, where we investigate the diffusional chain dynamics within the globule, are compared with non-equilibrium simulations, where we unfold the globule by pulling the chain ends with prescribed velocity (encompassing low enough velocities so that the linear-response, viscous regime is reached). From both simulation protocols we derive the internal viscosity within the globule. In the liquid-like regime the internal friction increases continuously with {epsilon} and scales extensive in NG. This suggests an internal friction scenario where the entire chain (or an extensive fraction thereof) takes part in conformational reorganization of the globular structure.
We demonstrate that the clustering statistics and the corresponding phase transition to non-equilibrium clustering found in many experiments and simulation studies with self-propelled particles (SPPs) with alignment can be obtained from a simple kinetic model. The key elements of this approach are the scaling of the cluster cross-section with the cluster mass -- characterized by an exponent $alpha$ -- and the scaling of the cluster perimeter with the cluster mass -- described by an exponent $beta$. The analysis of the kinetic approach reveals that the SPPs exhibit two phases: i) an individual phase, where the cluster size distribution (CSD) is dominated by an exponential tail that defines a characteristic cluster size, and ii) a collective phase characterized by the presence of non-monotonic CSD with a local maximum at large cluster sizes. At the transition between these two phases the CSD is well described by a power-law with a critical exponent $gamma$, which is a function of $alpha$ and $beta$ only. The critical exponent is found to be in the range $0.8 < gamma < 1.5$ in line with observations in experiments and simulations.
In this paper we explore the topological properties of self-replicating, 3-dimensional manifolds, which are modeled by idempotents in the (2+1)-cobordism category. We give a classification theorem for all such idempotents. Additionally, we characterize biologically interesting ways in which self-replicating 3-manifolds can embed in $mathbb{R}^3$.
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