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Gene regulatory networks with dynamics characterized by multiple stable states underlie cell fate-decisions. Quantitative models that can link molecular-level knowledge of gene regulation to a global understanding of network dynamics have…
We introduce a model of DNA sequence evolution which can account for biases in mutation rates that depend on the identity of the neighboring bases. An analytic solution for this class of non-equilibrium models is developed by adopting…
Neural quantum states (NQS) have emerged as a powerful tool for approximating quantum wavefunctions using deep learning. While these models achieve remarkable accuracy, understanding how they encode physical information remains an open…
Stochastic dynamics of chemical reactions in a mutually repressing two-gene circuit is numerically simulated. The circuit has a rich variety of different states when the kinetic change of DNA status is slow. The stochastic switching…
Evolution of genetic code is studied as the change in the choice of enzymes that are used to synthesize amino acids from the genetic information of nucleic acids. We propose the following theory: the differentiation of physiological states…
We consider non-equilibrium phenomena in a very simple model that displays a zero-temperature first-order phase transition. The quantum Ising model with a four-spin exchange is adopted as a general representative of first-order quantum…
We study the behavior of Quantum Darwinism (Zurek, [8]) within the iterative, random unitary operations qubit-model of pure decoherence (Novotny et al, [6]). We conclude that Quantum Darwinism, which describes the quantum mechanical…
Three coarse-grained models of the double-stranded DNA are proposed and compared in the context of mechanical manipulation such as twisting and various schemes of stretching. The models differ in the number of effective beads (between two…
A robust quantum state transfer scheme is discussed for three atoms that are trapped by separated cavities linked via optical fibers in ring-connection. It is shown that, under the effective three-atom Ising model, arbitrary quantum state…
Quantum annealing provides a promising way to solve combinational optimization problems where the solutions correspond to the ground state of the Ising Hamiltonian. We can implement quantum annealing using the Kerr non-linear resonators,…
This article is a short introduction to and review of the cluster-state model of quantum computation, in which coherent quantum information processing is accomplished via a sequence of single-qubit measurements applied to a fixed quantum…
A model of genome evolution is proposed. Based on three assumptions the evolutionary theory of a genome is formulated. The general law on the direction of genome evolution is given. Both the deterministic classical equation and the…
We consider a population evolving due to mutation, selection and recombination, where selection includes single-locus terms (additive fitness) and two-loci terms (pairwise epistatic fitness). We further consider the problem of inferring…
The classification of phases and the detection of phase transitions are central and challenging tasks in diverse fields. Within physics, it relies on the identification of order parameters and the analysis of singularities in the free…
The coherent control of multi-partite quantum systems presents one of the central prerequisites in state-of-the-art quantum information processing. With the added benefit of inherent high-fidelity detection capability, atomic quantum…
Neural-network quantum states have shown great potential for the study of many-body quantum systems. In statistical machine learning, transfer learning designates protocols reusing features of a machine learning model trained for a problem…
The dynamical behaviour of many-body systems is often richer than what can be anticipated from their static properties. Here we show that in closed quantum systems this becomes evident by considering time-integrated observables as order…
Neural Quantum States (NQS) are powerful tools used to represent complex quantum many-body states in an increasingly wide range of applications. However, despite their popularity, at present only a rudimentary understanding of their…
We present detailed analytical calculations for an 1D Ising ring of arbitrary number of spin-1/2 particles, in order to reveal entanglement properties of the stationary states. We show that the ground state and specific eigenstates of the…
We propose a solvable model of Quantum Darwinism to encoding transitions -- abrupt changes in how quantum information spreads in a many-body system under unitary dynamics. We consider a random Clifford circuit on an expanding tree, whose…