57 research outputs found
Schwinger Boson Formulation and Solution of the Crow-Kimura and Eigen Models of Quasispecies Theory
We express the Crow-Kimura and Eigen models of quasispecies theory in a
functional integral representation. We formulate the spin coherent state
functional integrals using the Schwinger Boson method. In this formulation, we
are able to deduce the long-time behavior of these models for arbitrary
replication and degradation functions.
We discuss the phase transitions that occur in these models as a function of
mutation rate. We derive for these models the leading order corrections to the
infinite genome length limit.Comment: 37 pages; 4 figures; to appear in J. Stat. Phy
Neutrino oscillations: measuring including its sign
In neutrino phenomenology, terms in the oscillation probabilities linear in
lead naturally to the question ``How can one measure
including its sign?'' Here we demonstrate analytically and with a
simulation of neutrino data that and {\mathcal
{P}_{\mu\mu} at exhibit significant linear dependence
on in the limit of vacuum oscillations. Measurements at this
particular value of can thus determine not only but also
its sign, if CP violation is small.Comment: 5 pages, 5 figure
Lethal Mutants and Truncated Selection Together Solve a Paradox of the Origin of Life
BACKGROUND: Many attempts have been made to describe the origin of life, one of which is Eigen's cycle of autocatalytic reactions [Eigen M (1971) Naturwissenschaften 58, 465-523], in which primordial life molecules are replicated with limited accuracy through autocatalytic reactions. For successful evolution, the information carrier (either RNA or DNA or their precursor) must be transmitted to the next generation with a minimal number of misprints. In Eigen's theory, the maximum chain length that could be maintained is restricted to 100-1000 nucleotides, while for the most primitive genome the length is around 7000-20,000. This is the famous error catastrophe paradox. How to solve this puzzle is an interesting and important problem in the theory of the origin of life. METHODOLOGY/PRINCIPAL FINDINGS: We use methods of statistical physics to solve this paradox by carefully analyzing the implications of neutral and lethal mutants, and truncated selection (i.e., when fitness is zero after a certain Hamming distance from the master sequence) for the critical chain length. While neutral mutants play an important role in evolution, they do not provide a solution to the paradox. We have found that lethal mutants and truncated selection together can solve the error catastrophe paradox. There is a principal difference between prebiotic molecule self-replication and proto-cell self-replication stages in the origin of life. CONCLUSIONS/SIGNIFICANCE: We have applied methods of statistical physics to make an important breakthrough in the molecular theory of the origin of life. Our results will inspire further studies on the molecular theory of the origin of life and biological evolution
Complex temperatures zeroes of partition function in spin-glass models
An approximate method is proposed for investigating complex-temperature
properties of real-dimensional spin-glass models. The method uses the
complex-temperature data of the ferromagnetic model on the same lattice. The
universality line in the complex-temperature space is obtained.Comment: latex, corrected some misprint
Error threshold in optimal coding, numerical criteria and classes of universalities for complexity
The free energy of the Random Energy Model at the transition point between
ferromagnetic and spin glass phases is calculated. At this point, equivalent to
the decoding error threshold in optimal codes, free energy has finite size
corrections proportional to the square root of the number of degrees. The
response of the magnetization to the ferromagnetic couplings is maximal at the
values of magnetization equal to half. We give several criteria of complexity
and define different universality classes. According to our classification, at
the lowest class of complexity are random graph, Markov Models and Hidden
Markov Models. At the next level is Sherrington-Kirkpatrick spin glass,
connected with neuron-network models. On a higher level are critical theories,
spin glass phase of Random Energy Model, percolation, self organized
criticality (SOC). The top level class involves HOT design, error threshold in
optimal coding, language, and, maybe, financial market. Alive systems are also
related with the last class. A concept of anti-resonance is suggested for the
complex systems.Comment: 17 page
Error-correcting code on a cactus: a solvable model
An exact solution to a family of parity check error-correcting codes is
provided by mapping the problem onto a Husimi cactus. The solution obtained in
the thermodynamic limit recovers the replica symmetric theory results and
provides a very good approximation to finite systems of moderate size. The
probability propagation decoding algorithm emerges naturally from the analysis.
A phase transition between decoding success and failure phases is found to
coincide with an information-theoretic upper bound. The method is employed to
compare Gallager and MN codes.Comment: 7 pages, 3 figures, with minor correction
Exact scaling in the expansion-modification system
This work is devoted to the study of the scaling, and the consequent
power-law behavior, of the correlation function in a mutation-replication model
known as the expansion-modification system. The latter is a biology inspired
random substitution model for the genome evolution, which is defined on a
binary alphabet and depends on a parameter interpreted as a \emph{mutation
probability}. We prove that the time-evolution of this system is such that any
initial measure converges towards a unique stationary one exhibiting decay of
correlations not slower than a power-law. We then prove, for a significant
range of mutation probabilities, that the decay of correlations indeed follows
a power-law with scaling exponent smoothly depending on the mutation
probability. Finally we put forward an argument which allows us to give a
closed expression for the corresponding scaling exponent for all the values of
the mutation probability. Such a scaling exponent turns out to be a piecewise
smooth function of the parameter.Comment: 22 pages, 2 figure
Thermodynamics of adiabatic feedback control
We study adaptive control of classical ergodic Hamiltonian systems, where the
controlling parameter varies slowly in time and is influenced by system's state
(feedback). An effective adiabatic description is obtained for slow variables
of the system. A general limit on the feedback induced negative entropy
production is uncovered. It relates the quickest negentropy production to
fluctuations of the control Hamiltonian. The method deals efficiently with the
entropy-information trade off.Comment: 6 pages, 1 figur
Thermodynamic Basis for the Emergence of Genomes during Prebiotic Evolution
The RNA world hypothesis views modern organisms as descendants of RNA molecules. The earliest RNA molecules must have been random sequences, from which the first genomes that coded for polymerase ribozymes emerged. The quasispecies theory by Eigen predicts the existence of an error threshold limiting genomic stability during such transitions, but does not address the spontaneity of changes. Following a recent theoretical approach, we applied the quasispecies theory combined with kinetic/thermodynamic descriptions of RNA replication to analyze the collective behavior of RNA replicators based on known experimental kinetics data. We find that, with increasing fidelity (relative rate of base-extension for Watson-Crick versus mismatched base pairs), replications without enzymes, with ribozymes, and with protein-based polymerases are above, near, and below a critical point, respectively. The prebiotic evolution therefore must have crossed this critical region. Over large regions of the phase diagram, fitness increases with increasing fidelity, biasing random drifts in sequence space toward ‘crystallization.’ This region encloses the experimental nonenzymatic fidelity value, favoring evolutions toward polymerase sequences with ever higher fidelity, despite error rates above the error catastrophe threshold. Our work shows that experimentally characterized kinetics and thermodynamics of RNA replication allow us to determine the physicochemical conditions required for the spontaneous crystallization of biological information. Our findings also suggest that among many potential oligomers capable of templated replication, RNAs may have evolved to form prebiotic genomes due to the value of their nonenzymatic fidelity
- …