相关论文: Quantum Field Theory and Phylogenetic Branching

We consider a general class of branching processes in discrete time, where particles have types belonging to a Polish space and reproduce independently according to their type. If the process is critical and the mean distribution of types…

Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees. Substitutions in sequences are modelled through a continuous-time Markov process, characterised by an instantaneous rate matrix, which standard…

Phylogenetic networks are becoming increasingly popular in phylogenetics since they have the ability to describe a wider range of evolutionary events than their tree counterparts. In this paper, we study Markov models on phylogenetic…

This paper investigates the formation and propagation of wavefunction `branches' through the process of entanglement with the environment. While this process is a consequence of unitary dynamics, and hence significant to many if not all…

Adapting a definition of Aaronson and Ambainis [Theory Comput. 1 (2005), 47--79], we call a quantum dynamics on a digraph "saturated Z-local" if the nonzero transition amplitudes specifying the unitary evolution are in exact correspondence…

Phylogenetic networks generalize phylogenetic trees, and have been introduced in order to describe evolution in the case of transfer of genetic material between coexisting species. There are many classes of phylogenetic networks, which can…

We observe $n$ sequences at each of $m$ sites, and assume that they have evolved from an ancestral sequence that forms the root of a binary tree of known topology and branch lengths, but the sequence states at internal nodes are unknown.…

The perennial formalism is applied to the real, massive Klein-Gordon field on a globally-hyperbolic background space-time with compact Cauchy hypersurfaces. The parametrized form of this system is taken over from the accompanying paper. Two…

Deterministic dynamical models are discussed which can be described in quantum mechanical terms. -- In particular, a local quantum field theory is presented which is a supersymmetric classical model. The Hilbert space approach of Koopman…

We discuss finite local extensions of quantum field theories in low space time dimensions in connection with categorical structures and the question of modular invariants in conformal field theory, also touching upon purely mathematical…

Rapid developments in genetics and biology have led to phylogenetic methods becoming an important direction in the study of cancer and viral evolution. Although our understanding of gene biology and biochemistry has increased and is…

The quasispecies theory is studied for dynamic replication landscapes. A meaningful asymptotic quasispecies is defined for periodic time dependencies. The quasispecies' composition is constantly changing over the oscillation period. The…

We point out that when a quadratic type Li\'enard equation is suitably interpreted shows branching due to the double valuedness of the governing Hamiltonian. Under certain approximation of the guiding coupling constant we derive its quantum…

We present a genealogy for superprocesses with a non-homogeneous quadratic branching mechanism, relying on a weighted version of the superprocess and a Girsanov theorem. We then decompose this genealogy with respect to the last individual…

The evolution of molecular and phenotypic traits is commonly modelled using Markov processes along a phylogeny. This phylogeny can be a tree, or a network if it includes reticulations, representing events such as hybridization or admixture.…

We develop the theory of ``branch algebras'', which are infinite-dimensional associative algebras that are isomorphic, up to taking subrings of finite codimension, to a matrix ring over themselves. The main examples come from groups acting…

We apply the theory of markov random fields on trees to derive a phase transition in the number of samples needed in order to reconstruct phylogenies. We consider the Cavender-Farris-Neyman model of evolution on trees, where all the inner…

We introduce new methods for phylogenetic tree quartet construction by using machine learning to optimize the power of phylogenetic invariants. Phylogenetic invariants are polynomials in the joint probabilities which vanish under a model of…

We consider a birth and death process in which death is due to both `natural death' and to competition between individuals, modelled as a quadratic function of population size. The resulting `logistic branching process' has been proposed as…

We study parton-branching solutions of QCD evolution equations and present a method to construct both collinear and transverse momentum dependent (TMD) parton densities from this approach. We work with next-to-leading-order (NLO) accuracy…