Graphs obtained from a binary leaf labeled ("phylogenetic") tree by adding an edge so as to introduce a cycle provide a useful representation of hybrid evolution in molecular evolutionary biology. This class of graphs (which we call "unicyclic networks") also has some attractive combinatorial properties, which we present. We characterize when a set of binary phylogenetic trees is displayed by a unicyclic network in terms of tree rearrangement operations. This leads to a triple-wise compatibility theorem and a simple, fast algorithm to determine 1-cycle compatibility. We also use generating function techniques to provide closed-form expressions that enumerate unicyclic networks with specified or unspecified cycle length, and we provide an extension to enumerate a class of multicyclic networks.
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http://dx.doi.org/10.1109/TCBB.2006.14 | DOI Listing |
Phys Rev Lett
September 2024
Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg.
We consider Markov jump processes on a graph described by a rate matrix that depends on various control parameters. We derive explicit expressions for the static responses of edge currents and steady-state probabilities. We show that they are constrained by the graph topology (i.
View Article and Find Full Text PDFPhys Rev E
August 2022
Institute of Molecular Physics, Polish Academy of Sciences, Mariana Smoluchowskiego 17, 60-179 Poznań, Poland.
Current fluctuations are a powerful tool to unravel the underlying physics of the observed transport process. This work discusses some general properties of the third and the fourth current cumulant (skewness and kurtosis) related to dynamics and thermodynamics of a transport setup. Specifically, several distinct bounds on these quantities are either analytically derived or numerically conjectured, which are applicable to (1) noninteracting fermionic systems, (2) noninteracting bosonic systems, (3) thermally driven classical Markovian systems, and (4) unicyclic Markovian networks.
View Article and Find Full Text PDFJ Appl Math Comput
May 2022
Department of Applied Mathematics with Oceanology and Computer Programming, Vidyasagar University, Midnapore, 721102 India.
From the mid-nineteenth century, the railway network has been the most important mode of conveying people and goods in India. 22.15 million passengers used this network and 3.
View Article and Find Full Text PDFJ Phys Chem B
February 2021
Dept. of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India.
In this paper, we consider a macromolecule with two competitive binding sites where a ligand can bind to and gives rise to a unicyclic reaction network consisting of four states-(i) a single state with both binding sites vacant, (ii) two states with one bound site and one free binding site, and (iii) an another single state with both sites occupied. We obtain probability densities of the time-integrated current along the clockwise direction and the dynamical activity or mean number of jumps between different states for finite times at a fast diffusion limit. On the other hand, in the diffusion-limited case, ligand diffusion between the two binding sites directly connects the mono-ligated states-changing the reaction scheme.
View Article and Find Full Text PDFPhys Rev Lett
October 2015
II. Institut für Theoretische Physik, Universität Stuttgart, 70550 Stuttgart, Germany.
We obtain lower and upper bounds on the skewness and kurtosis associated with the cycle completion time of unicyclic enzymatic reaction schemes. Analogous to a well-known lower bound on the randomness parameter, the lower bounds on skewness and kurtosis are related to the number of intermediate states in the underlying chemical reaction network. Our results demonstrate that evaluating these higher order moments with single molecule data can lead to information about the enzymatic scheme that is not contained in the randomness parameter.
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