Related papers: Quantum Simulation of Phylogenetic Trees
We introduce an analytically treatable spin decoherence model for quantum walk on a line that yields the exact position probability distribution of an unbiased classical random walk at all-time scales. This spin decoherence model depicts a…
Quantum random walks use interference to obtain faster state space exploration, which can be used for algorithmic purposes. Photonic technologies provide a natural platform for many recent experimental demonstrations. Here we analyze…
As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic…
Classical randomized algorithms use a coin toss instruction to explore different evolutionary branches of a problem. Quantum algorithms, on the other hand, can explore multiple evolutionary branches by mere superposition of states. Discrete…
Besides serving as prediction models, classification trees are useful for finding important predictor variables and identifying interesting subgroups in the data. These functions can be compromised by weak split selection algorithms that…
A dynamical picture of phylogenetic evolution is given in terms of Markov models on a state space, comprising joint probability distributions for character types of taxonomic classes. Phylogenetic branching is a process which augments the…
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.…
Invariance under translation is exploited to efficiently simulate one-dimensional quantum lattice systems in the limit of an infinite lattice. Both the computation of the ground state and the simulation of time evolution are considered.
Recently Quantum Computation has generated a lot of interest due to the discovery of a quantum algorithm which can factor large numbers in polynomial time. The usefulness of a quantum com puter is limited by the effect of errors. Simulation…
Classically simulating quantum circuits is crucial when developing or testing quantum algorithms. Due to the underlying exponential complexity, efficient data structures are key for performing such simulations. To this end, tensor networks…
Simulating quantum circuits on classical computers is a notoriously hard, yet increasingly important task for the development and testing of quantum algorithms. In order to alleviate this inherent complexity, efficient data structures and…
We study the evolution of sexual and asexual populations in general fitness landscapes. We find deep relations between the mathematics of biological evolution and the formalism of quantum mechanics. We give the general structure of the…
We introduce a model for simulating mutation of prokaryote DNA sequences. Using that model we can then evaluated traditional techniques like parsimony and maximum likelihood methods for computing phylogenetic relationships. We also use the…
This manuscript gathers and subsumes a long series of works on using QW to simulate transport phenomena. Quantum Walks (QWs) consist of single and isolated quantum systems, evolving in discrete or continuous time steps according to a…
Quantum simulation uses a well-known quantum system to predict the behavior of another quantum system. Certain limitations in this technique arise, however, when applied to specific problems, as we demonstrate with a theoretical and…
Quantum algorithms reformulate computational problems as quantum evolutions in a large Hilbert space. Most quantum algorithms assume that the time-evolution is perfectly unitary and that the full Hilbert space is available. However, in…
Many real-world systems studied are governed by complex, nonlinear dynamics. By modeling these dynamics, we can gain insight into how these systems work, make predictions about how they will behave, and develop strategies for controlling…
This paper presents a novel quantum walk approach to simulating parton showers on a quantum computer. We demonstrate that the quantum walk paradigm offers a natural and more efficient approach to simulating parton showers on quantum…
We investigated testing the likelihood of a phylogenetic tree by comparison to its subtree pruning and regrafting (SPR) neighbors, with or without re-optimizing branch lengths. This is inspired by aspects of Bayesian significance tests, and…
Computer modelling for evolutionary systems consists in: 1) to store in the memory the individual features of each member of a large population; and 2) to update the whole system repeatedly, as time goes by, according to some prescribed…