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Question 8: Bridging the Gap Between In Silico and In Vitro Approaches to Minimal Cells
No full textIn this short paper we argue for the relevance and value of theoretical models in the field of origins of life, but also claim that both theoreticians and experimentalists should make an effort to come together and interact more closely to obtain more fruitful and significant results. As an example, we present our own modeling approach to protocell dynamics, including some simulation results, to show that it is possible to develop computational tools that start bridging that traditional gap between theory and experiments
Stationary self-reproduction and osmotic regulation in model proto-cells: an extended stochastic kinetics approach
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Theoretical conditions for the stationary reproduction of model protocells
No full textIn previous works we have explored the dynamics of chemically reacting proto-cellular systems, under different experimental conditions and kinetic parameters, by means of our stochastic simulation platform ‘ENVIRONMENT’. In this paper we, somehow, turn the question around: accepting some broad modeling assumptions, we investigate the conditions under which simple protocells will spontaneously settle into a stationary reproducing regime, characterized by a regular growth/division cycle and the maintenance of a certain standard size and chemical composition across generations. In the first part, starting from purely geometric considerations, the condition for stationary reproduction of a protocell will be expressed in terms of a growth control coefficient (). Then, an explicit relationship, the osmotic synchronization condition, will be analytically derived under a set of kinetic simplifications and taking into account the osmotic pressure balance operating across the protocell membrane. In the second part of the paper, this general condition that constrains different molecular/kinetic parameters and features of the system (reaction rates, permeability coefficients, metabolite concentrations, system volume) will be applied to different cases of self-producing vesicles, predicting the stationary protocell size or lifetime. Finally, in order to test the validity of our analytic results and predictions, the case study is contrasted with data obtained through both stochastic and deterministic computational algorithms
On the way towards basic autonomous systems: stochastic simulations of minimal lipid-peptide cells
No full textIn this paper, we apply a recently developed stochastic simulation platform to investigate the dynamic behaviour of minimal
‘self-(re-)producing’ cellular systems. In particular, we study a set of preliminary conditions for appearance of the simplest forms of autonomy in the context of lipid vesicles (more specifically, lipid–peptide vesicles) that enclose an autocatalytic/proto-metabolic
reaction network. The problem is approached from a ‘bottom-up’ perspective, in the sense that we try to show how relatively simple
cell components/processes could engage in a far-from-equilibrium dynamics, staying in those conditions thanks to a rudimentary but
effective control of the matter-energy flow through it. In this general scenario, basic autonomy and, together with it, minimal agent
systems would appear when (hypothetically pre-biological) cellular systems establish molecular trans-membrane mechanisms that
allow them to couple internal chemical reactions with transport processes, in a way that they channel/transform external materialenergetic
resources into their own means and actively regulate boundary conditions (e.g., osmotic gradients, inflow/outflow of
different compounds, . . .) that are critical for their constitution and persistence as proto-metabolic cells. The results of our simulations
indicate that, before that stage is reached, there are a number of relevant issues that have to be carefully analysed and clarified:
especially the immediate effects that the insertion of peptide chains (channel precursors) in the lipid bilayer may have in the structural properties of the membrane (elasticity, permeability, . . .) and in the overall dynamic behaviour of the cell
Stochastic simulations of minimal self-reproducing cellular systems
No full textThis paper is a theoretical attempt to gain insight into the problemof howself-assembling vesicles (closed
bilayer structures) could progressively turn into minimal self-producing and self-reproducing cells, i.e.
into interesting candidates for (proto)biological systems. With this aim, we make use of a recently
developed object-oriented platform to carry out stochastic simulations of chemical reaction networks
that take place in dynamic cellular compartments. We apply this new tool to study the behaviour of
different minimal cell models, making realistic assumptions about the physico-chemical processes and
conditions involved (e.g. thermodynamic equilibrium/non-equilibrium, variable volume-to-surface
relationship, osmotic pressure, solute diffusion across the membrane due to concentration gradients,
buffering effect). The new programming platform has been designed to analyse not only how a single protometabolic cell could maintain itself, grow or divide, but also how a collection of these cells could ‘evolve’ as a result of their mutual interactions in a common environment
Working towards ‘basic autonomy’ a simulation model to study minimal self-producing cells
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Modelling minimal ‘lipid-peptide’ cells
No full textThis contribution is aimed to give support to 'bottom-up' approaches to the minimal or early cell research project. Even if, from this perspective, the most simple living cell still seems very far away, the analysis of less complex, infrabiological cellular systems (some of which could be relatively soon implemented in the lab) probably holds the key, or one of the fundamental keys, to the problem of origins of life. On these lines, we propose a simulation model to study the transition from proto-metabolic 'lipid' cells to 'lipid-peptide' cells, as a critical step in which self-reproducing vesicles could develop into more functionalized supramolecular system
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