59 research outputs found
Prebiotic Homochirality as a Critical Phenomenon
The development of prebiotic homochirality on early-Earth or another
planetary platform may be viewed as a critical phenomenon. It is shown, in the
context of spatio-temporal polymerization reaction networks, that environmental
effects -- be them temperature surges or other external disruptions -- may
destroy any net chirality previously produced. In order to understand the
emergence of prebiotic homochirality it is important to model the coupling of
polymerization reaction networks to different planetary environments.Comment: 6 Pages, 1 Figure, In Press: Origins of Life and Evolution of
Biosphere
Homochirality and the need of energy
The mechanisms for explaining how a stable asymmetric chemical system can be
formed from a symmetric chemical system, in the absence of any asymmetric
influence other than statistical fluctuations, have been developed during the
last decades, focusing on the non-linear kinetic aspects. Besides the absolute
necessity of self-amplification processes, the importance of energetic aspects
is often underestimated. Going down to the most fundamental aspects, the
distinction between a single object -- that can be intrinsically asymmetric --
and a collection of objects -- whose racemic state is the more stable one --
must be emphasized. A system of strongly interacting objects can be described
as one single object retaining its individuality and a single asymmetry; weakly
or non-interacting objects keep their own individuality, and are prone to
racemize towards the equilibrium state. In the presence of energy fluxes,
systems can be maintained in an asymmetric non-equilibrium steady-state. Such
dynamical systems can retain their asymmetry for times longer than their
racemization time.Comment: 8 pages, 7 figures, submitted to Origins of Life and Evolution of
Biosphere
An Extended Model for the Evolution of Prebiotic Homochirality: A Bottom-Up Approach to the Origin of Life
A generalized autocatalytic model for chiral polymerization is investigated
in detail. Apart from enantiomeric cross-inhibition, the model allows for the
autogenic (non-catalytic) formation of left and right-handed monomers from a
substrate with reaction rates and , respectively. The
spatiotemporal evolution of the net chiral asymmetry is studied for models with
several values of the maximum polymer length, N. For N=2, we study the validity
of the adiabatic approximation often cited in the literature. We show that the
approximation obtains the correct equilibrium values of the net chirality, but
fails to reproduce the short time behavior. We show also that the autogenic
term in the full N=2 model behaves as a control parameter in a chiral symmetry-
breaking phase transition leading to full homochirality from racemic initial
conditions. We study the dynamics of the N -> infinity model with symmetric
() autogenic formation, showing that it only achieves
homochirality for , where is an N-dependent
critical value. For we investigate the behavior of
models with several values of N, showing that the net chiral asymmetry grows as
tanh(N). We show that for a given symmetric autogenic reaction rate, the net
chirality and the concentrations of chirally pure polymers increase with the
maximum polymer length in the model. We briefly discuss the consequences of our
results for the development of homochirality in prebiotic Earth and possible
experimental verification of our findings
Punctuated Chirality
Most biomolecules occur in mirror, or chiral, images of each other. However,
life is homochiral: proteins contain almost exclusively levorotatory (L) amino
acids, while only dextrorotatory (R) sugars appear in RNA and DNA. The
mechanism behind this fundamental asymmetry of life remains an open problem.
Coupling the spatiotemporal evolution of a general autocatalytic polymerization
reaction network to external environmental effects, we show through a detailed
statistical analysis that high intensity and long duration events may drive
achiral initial conditions towards chirality. We argue that life's
homochirality resulted from sequential chiral symmetry breaking triggered by
environmental events, thus extending the theory of punctuated equilibrium to
the prebiotic realm. Applying our arguments to other potentially life-bearing
planetary platforms, we predict that a statistically representative sampling
will be racemic on average.Comment: 13 pages, 4 color figures. Final version published in Origins of Life
and Evolution of Biospheres. Typos corrected, figures improved, and a few
definitions and word usage clarifie
Chiral Polymerization in Open Systems From Chiral-Selective Reaction Rates
We investigate the possibility that prebiotic homochirality can be achieved
exclusively through chiral-selective reaction rate parameters without any other
explicit mechanism for chiral bias. Specifically, we examine an open network of
polymerization reactions, where the reaction rates can have chiral-selective
values. The reactions are neither autocatalytic nor do they contain explicit
enantiomeric cross-inhibition terms. We are thus investigating how rare a set
of chiral-selective reaction rates needs to be in order to generate a
reasonable amount of chiral bias. We quantify our results adopting a
statistical approach: varying both the mean value and the rms dispersion of the
relevant reaction rates, we show that moderate to high levels of chiral excess
can be achieved with fairly small chiral bias, below 10%. Considering the
various unknowns related to prebiotic chemical networks in early Earth and the
dependence of reaction rates to environmental properties such as temperature
and pressure variations, we argue that homochirality could have been achieved
from moderate amounts of chiral selectivity in the reaction rates.Comment: 15 pages, 6 figures, accepted for publication in Origins of Life and
Evolution of Biosphere
Speed-Dependent Cellular Decision Making in Nonequilibrium Genetic Circuits
Despite being governed by the principles of nonequilibrium transitions, gene expression dynamics underlying cell fate decision is poorly understood. In particular, the effect of signaling speed on cellular decision making is still unclear. Here we show that the decision between alternative cell fates, in a structurally symmetric circuit, can be biased depending on the speed at which the system is forced to go through the decision point. The circuit consists of two mutually inhibiting and self-activating genes, forced by two external signals with identical stationary values but different transient times. Under these conditions, slow passage through the decision point leads to a consistently biased decision due to the transient signaling asymmetry, whereas fast passage reduces and eventually eliminates the switch imbalance. The effect is robust to noise and shows that dynamic bifurcations, well known in nonequilibrium physics, are important for the control of genetic circuits
Calculation of the relative metastabilities of proteins in subcellular compartments of Saccharomyces cerevisiae
[abridged] Background: The distribution of chemical species in an open system
at metastable equilibrium can be expressed as a function of environmental
variables which can include temperature, oxidation-reduction potential and
others. Calculations of metastable equilibrium for various model systems were
used to characterize chemical transformations among proteins and groups of
proteins found in different compartments of yeast cells.
Results: With increasing oxygen fugacity, the relative metastability fields
of model proteins for major subcellular compartments go as mitochondrion,
endoplasmic reticulum, cytoplasm, nucleus. In a metastable equilibrium setting
at relatively high oxygen fugacity, proteins making up actin are predominant,
but those constituting the microtubule occur with a low chemical activity. A
reaction sequence involving the microtubule and spindle pole proteins was
predicted by combining the known intercompartmental interactions with a
hypothetical program of oxygen fugacity changes in the local environment. In
further calculations, the most-abundant proteins within compartments generally
occur in relative abundances that only weakly correspond to a metastable
equilibrium distribution. However, physiological populations of proteins that
form complexes often show an overall positive or negative correlation with the
relative abundances of proteins in metastable assemblages.
Conclusions: This study explored the outlines of a thermodynamic description
of chemical transformations among interacting proteins in yeast cells. The
results suggest that these methods can be used to measure the degree of
departure of a natural biochemical process or population from a local minimum
in Gibbs energy.Comment: 32 pages, 7 figures; supporting information is available at
http://www.chnosz.net/yeas
Nonequilibrium thermodynamics and energy efficiency in weight loss diets
Carbohydrate restriction as a strategy for control of obesity is based on two effects: a behavioral effect, spontaneous reduction in caloric intake and a metabolic effect, an apparent reduction in energy efficiency, greater weight loss per calorie consumed. Variable energy efficiency is established in many contexts (hormonal imbalance, weight regain and knock-out experiments in animal models), but in the area of the effect of macronutrient composition on weight loss, controversy remains. Resistance to the idea comes from a perception that variable weight loss on isocaloric diets would somehow violate the laws of thermodynamics, that is, only caloric intake is important ("a calorie is a calorie"). Previous explanations of how the phenomenon occurs, based on equilibrium thermodynamics, emphasized the inefficiencies introduced by substrate cycling and requirements for increased gluconeogenesis. Living systems, however, are maintained far from equilibrium, and metabolism is controlled by the regulation of the rates of enzymatic reactions. The principles of nonequilibrium thermodynamics which emphasize kinetic fluxes as well as thermodynamic forces should therefore also be considered
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