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The textbook conceptualization of phenotype creation, "genotype (G) + environment (E) + genotype & environment interactions (GE) ↦ phenotype (Ph)", is modeled with open quantum systems theory (OQST) or more generally with adaptive dynamics theory (ADT). The model is quantum-like, i.e., it is not about quantum physical processes in biosystems. Generally such modeling is about applications of the quantum formalism and methodology outside of physics. Macroscopic biosystems, in our case genotypes and phenotypes, are treated as information processors which functioning matches the laws of quantum information theory. Phenotypes are the outputs of the E-adaptation processes described by the quantum master equation, Gorini-Kossakowski-Sudarshan-Lindblad equation (GKSL). Its stationary states correspond to phenotypes. We highlight the class of GKSL dynamics characterized by the camel-like graphs of (von Neumann) entropy: in the process of E-adaptation phenotype's state entropy (disorder) first increases and then falls down - a stable and well-ordered phenotype is created. Traits, an organism's phenotypic characteristics, are modeled within the quantum measurement theory, as generally unsharp observables given by positive operator valued measures (POVMs. This paper is also a review on the methods and mathematical apparatus of quantum information biology.

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The dynamical evolution of an open quantum system can be governed by the Lindblad equation of the density matrix. In this paper, we propose to characterize the density matrix topology by the topological invariant of its modular Hamiltonian. Since the topological classification of such Hamiltonians depends on their symmetry classes, a primary issue we address is determining the requirement for the Lindbladian operators, under which the modular Hamiltonian can preserve its symmetry class during the dynamical evolution. We solve this problem for the fermionic Gaussian state and for the modular Hamiltonian being a quadratic operator of a set of fermionic operators. When these conditions are satisfied, along with a nontrivial topological classification of the symmetry class of the modular Hamiltonian, a topological transition can occur as time evolves. We present two examples of dissipation-driven topological transitions where the modular Hamiltonian lies in the AIII class withU(1) symmetry and the DIII class withoutU(1) symmetry. By a finite size scaling, we show that this density matrix topology transition occurs at a finite time. We also present the physical signature of this transition.

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Entanglement engines are autonomous quantum thermal machines designed to generate entanglement from the presence of a particle current flowing through the device. In this work, we investigate the functioning of a two-qubit entanglement engine beyond the steady-state regime. Within a master equation approach, we derive the time-dependent state, the particle current, as well as the associated current correlation functions. Our findings establish a direct connection between coherence and internal current, elucidating the existence of a critical current that serves as an indicator for entanglement in the steady state. We then apply our results to investigate kinetic uncertainty relations (KURs) at finite times. We demonstrate that there is more than one possible definition for KURs at finite times. Although the two definitions agree in the steady-state regime, they lead to different parameter ranges for violating KUR at finite times.

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Kinetic theory provides modeling of open quantum systems subject to Markovian noise via the Wigner-Fokker-Planck equation, which is an alternate of the Lindblad master equation setting, having the advantage of great physical intuition as it is the quantum equivalent of the classical phase space description. We perform a numerical inspection of the Wehrl entropy for the benchmark problem of a harmonic potential, since the existence of a steady state and its analytical formula have been proven theoretically in this case. When there is friction in the noise terms, no theoretical results on the monotonicity of absolute entropy are available. We provide numerical results of the time evolution of the entropy in the case with friction using a stochastic (Euler-Maruyama-based Monte Carlo) numerical solver. For all the chosen initial conditions studied (all of them Gaussian states), up to the inherent numerical error of the method, one cannot disregard the possibility of monotonic behavior even in the case under study, where the noise includes friction terms.

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Establishing the fundamental chemical principles that govern molecular electronic quantum decoherence has remained an outstanding challenge. Fundamental questions such as how solvent and intramolecular vibrations or chemical functionalization contribute to the decoherence remain unanswered and are beyond the reach of state-of-the-art theoretical and experimental approaches. Here we address this challenge by developing a strategy to isolate electronic decoherence pathways for molecular chromophores immersed in condensed phase environments that enables elucidating how electronic quantum coherence is lost. For this, we first identify resonance Raman spectroscopy as a general experimental method to reconstruct molecular spectral densities with full chemical complexity at room temperature, in solvent, and for fluorescent and non-fluorescent molecules. We then show how to quantitatively capture the decoherence dynamics from the spectral density and identify decoherence pathways by decomposing the overall coherence loss into contributions due to individual molecular vibrations and solvent modes. We illustrate the utility of the strategy by analyzing the electronic decoherence pathways of the DNA base thymine in water. Its electronic coherences decay in [Formula: see text]30 fs. The early-time decoherence is determined by intramolecular vibrations while the overall decay by solvent. Chemical substitution of thymine modulates the decoherence with hydrogen-bond interactions of the thymine ring with water leading to the fastest decoherence. Increasing temperature leads to faster decoherence as it enhances the importance of solvent contributions but leaves the early-time decoherence dynamics intact. The developed strategy opens key opportunities to establish the connection between molecular structure and quantum decoherence as needed to develop chemical strategies to rationally modulate it.

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One of the main obstacles toward building efficient quantum computing systems is decoherence, where the inevitable interaction between the qubits and the surrounding environment leads to a vanishing entanglement. We consider a system of two interacting asymmetric two-level atoms (qubits) in the presence of pure and correlated dephasing environments. We study the dynamics of entanglement while varying the interaction strength between the two qubits, their relative frequencies, and their coupling strength to the environment starting from different initial states of practical interest. The impact of the asymmetry of the two qubits, reflected in their different frequencies and coupling strengths to the environment, varies significantly depending on the initial state of the system and its degree of anisotropy. For an initial disentangled, or a Werner, state, as the difference between the frequencies increases, the entanglement decay rate increases, with more persistence at the higher degrees of anisotropy in the former state. However, for an initial anti-correlated Bell state, the entanglement decays more rapidly in the symmetric case compared with the asymmetric one. The difference in the coupling strengths of the two qubits to the pure (uncorrelated) dephasing environment leads to higher entanglement decay in the different initial state cases, though the rate varies depending on the degree of anisotropy and the initial state. Interestingly, the correlated dephasing environment, within a certain range, was found to enhance the entanglement dynamics starting from certain initial states, such as the disentangled, anti-correlated Bell, and Werner, whereas it exhibits a decaying effect in other cases such as the initial correlated Bell state.

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Scanning-tunneling microscopy (STM) combined with electron spin resonance (ESR) has enabled single-spin spectroscopy with nanoelectronvolt energy resolution and angstrom-scale spatial resolution, which allows quantum sensing and magnetic resonance imaging at the atomic scale. Extending this spectroscopic tool to a study of multiple spins, however, is nontrivial due to the extreme locality of the STM tunnel junction. Here we demonstrate double electron-electron spin resonance spectroscopy in an STM for two coupled atomic spins by simultaneously and independently driving them using two continuous-wave radio frequency voltages. We show the ability to drive and detect the resonance of a spin that is remote from the tunnel junction while read-out is achieved via the spin in the tunnel junction. Open quantum system simulations for two coupled spins reproduce all double-resonance spectra and further reveal a relaxation time of the remote spin that is longer by an order of magnitude than that of the local spin in the tunnel junction. Our technique can be applied to quantum-coherent multi-spin sensing, simulation, and manipulation in engineered spin structures on surfaces.

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The aim of this review is to highlight the possibility of applying the mathematical formalism and methodology of quantum theory to model behavior of complex biosystems, from genomes and proteins to animals, humans, and ecological and social systems. Such models are known as quantum-like, and they should be distinguished from genuine quantum physical modeling of biological phenomena. One of the distinguishing features of quantum-like models is their applicability to macroscopic biosystems or, to be more precise, to information processing in them. Quantum-like modeling has its basis in quantum information theory, and it can be considered one of the fruits of the quantum information revolution. Since any isolated biosystem is dead, modeling of biological as well as mental processes should be based on the theory of open systems in its most general form-the theory of open quantum systems. In this review, we explain its applications to biology and cognition, especially theory of quantum instruments and the quantum master equation. We mention the possible interpretations of the basic entities of quantum-like models with special interest given to QBism, as it may be the most useful interpretation.

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An interesting class of physical systems, including those associated with life, demonstrates the ability to hold thermalization at bay and perpetuate states of high free-energy compared to a local environment. In this work we study quantum systems with no external sources or sinks for energy, heat, work, or entropy that allow for high free-energy subsystems to form and persist. We initialize systems of qubits in mixed, uncorrelated states and evolve them subject to a conservation law. We find that four qubits make up the minimal system for which these restricted dynamics and initial conditions allow an increase in extractable work for a subsystem. On landscapes of eight co-evolving qubits, interacting in randomly selected subsystems at each step, we demonstrate that restricted connectivity and an inhomogeneous distribution of initial temperatures both lead to landscapes with longer intervals of increasing extractable work for individual qubits. We demonstrate the role of correlations that develop on the landscape in enabling a positive change in extractable work.

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We start with a brief review on social laser theory which is newly framed with the notion of an infon-social energy quantum carrying coarse-grained information content. Infons are the excitations of the quantum social-information field. Humans are analogues of atoms-social atoms absorbing and emitting infons. Another new development is coupling of the social laser with the decision making model based on open quantum systems. The role of the environment for social atoms is played by the strong coherent social-information field-the output of social lasing. We analyse a simple quantum master equation generating decision jumps towards the coherent decision directed by the social laser beam. As an illustrative example, we analyse the possibility to create a societal benefit laser, i.e. directed for societal benefit. This article is part of the theme issue 'Thermodynamics 2.0: Bridging the natural and social sciences (Part 1)'.

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The conceptual analysis of quantum mechanics brings to light that a theory inherently consistent with observations should be able to describe both quantum and classical systems, i.e., quantum-classical hybrids. For example, the orthodox interpretation of measurements requires the transient creation of quantum-classical hybrids. Despite its limitations in defining the classical limit, Ehrenfest's theorem makes the simplest contact between quantum and classical mechanics. Here, we generalized the Ehrenfest theorem to bipartite quantum systems. To study quantum-classical hybrids, we employed a formalism based on operator-valued Wigner functions and quantum-classical brackets. We used this approach to derive the form of the Ehrenfest theorem for quantum-classical hybrids. We found that the time variation of the average energy of each component of the bipartite system is equal to the average of the symmetrized quantum dissipated power in both the quantum and the quantum-classical case. We expect that these theoretical results will be useful both to analyze quantum-classical hybrids and to develop self-consistent numerical algorithms for Ehrenfest-type simulations.

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The study of the human psyche has elucidated a bipartite structure of logic reflecting the quantum-classical nature of the world. Accordingly, we posited an approach toward studying the brain by means of the quantum-classical dynamics of a mixed Weyl symbol. The mixed Weyl symbol can be used to describe brain processes at the microscopic level and, when averaged over an appropriate ensemble, can provide a link to the results of measurements made at the meso and macro scale. Within this approach, quantum variables (such as, for example, nuclear and electron spins, dipole momenta of particles or molecules, tunneling degrees of freedom, and so on) can be represented by spinors, whereas the electromagnetic fields and phonon modes can be treated either classically or semi-classically in phase space by also considering quantum zero-point fluctuations. Quantum zero-point effects can be incorporated into numerical simulations by controlling the temperature of each field mode via coupling to a dedicated Nosé-Hoover chain thermostat. The temperature of each thermostat was chosen in order to reproduce quantum statistics in the canonical ensemble. In this first paper, we introduce a general quantum-classical Hamiltonian model that can be tailored to study physical processes at the interface between the quantum and the classical world in the brain. While the approach is discussed in detail, numerical calculations are not reported in the present paper, but they are planned for future work. Our theory of brain dynamics subsumes some compatible aspects of three well-known quantum approaches to brain dynamics, namely the electromagnetic field theory approach, the orchestrated objective reduction theory, and the dissipative quantum model of the brain. All three models are reviewed.

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We performed a theoretical study of the dephasing dynamics of a quantum two-state system under the influences of a non-equilibrium fluctuating environment. The effect of the environmental non-equilibrium fluctuations on the quantum system is described by a generalized random telegraph noise (RTN) process, of which the statistical properties are both non-stationary and non-Markovian. Due to the time-homogeneous property in the master equations for the multi-time probability distribution, the decoherence factor induced by the generalized RTN with a modulatable-type memory kernel can be exactly derived by means of a closed fourth-order differential equation with respect to time. In some special limit cases, the decoherence factor recovers to the expression of the previous ones. We analyzed in detail the environmental effect of memory modulation in the dynamical dephasing in four types of dynamics regimes. The results showed that the dynamical dephasing of the quantum system and the conversion between the Markovian and non-Markovian characters in the dephasing dynamics under the influence of the generalized RTN can be effectively modulated via the environmental memory kernel.

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A spin-boson-like model with two interacting qubits is analysed. The model turns out to be exactly solvable since it is characterized by the exchange symmetry between the two spins. The explicit expressions of eigenstates and eigenenergies make it possible to analytically unveil the occurrence of first-order quantum phase transitions. The latter are physically relevant since they are characterized by abrupt changes in the two-spin subsystem concurrence, in the net spin magnetization and in the mean photon number.

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The study of noise assisted-transport in quantum systems is essential in a wide range of applications, from near-term NISQ devices to models for quantum biology. Here, we study a generalized XXZ model in the presence of stochastic collision noise, which allows describing environments beyond the standard Markovian formulation. Our analysis through the study of the local magnetization, the inverse participation ratio (IPR) or its generalization, and the inverse ergodicity ratio (IER) showed clear regimes, where the transport rate and coherence time could be controlled by the dissipation in a consistent manner. In addition, when considering various excitations, we characterized the interplay between collisions and system interactions, identifying regimes in which transport was counterintuitively enhanced when increasing the collision rate, even in the case of initially separated excitations. These results constitute an example of an essential building block for the understanding of quantum transport in structured noisy and warm-disordered environments.

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An efficient algorithm to simulate dynamics of open quantum system is presented. The method describes the dynamics by unraveling stochastic wave functions converging to a density operator description. The stochastic techniques are based on the quantum collision model. Modeling systems dynamics with wave functions and modeling the interaction with the environment with a collision sequence reduces the scale of the complexity significantly. The algorithm developed can be implemented on quantum computers. We introduce stochastic methods that exploit statistical characteristics of the model such as Markovianity, Brownian motion, and binary distribution. The central limit theorem is employed to study the convergence of distributions of stochastic dynamics of pure quantum states represented by wave vectors. By averaging a sample of functions in the distribution we prove and demonstrate the convergence of the dynamics to the mixed quantum state described by a density operator.

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We use optimal control theory to obtain shortcuts to adiabaticity which maximize population transfer in a three-level stimulated Raman adiabatic passage system, for a given finite duration of the process and a specified dissipation rate at the intermediate state. We fix the sum of the intensities of the pump and Stokes pulses and use the mixing angle of the fields as the sole control variable. We determine the optimal variation of this angle and reveal the role of the singular arc in the optimal trajectory, in order to minimize the effect of dissipation. This article is part of the theme issue 'Shortcuts to adiabaticity: theoretical, experimental and interdisciplinary perspectives'.

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The development of a self-consistent thermodynamic theory of quantum systems is of fundamental importance for modern physics. Still, despite its essential role in quantum science and technology, there is no unifying formalism for characterizing the thermodynamics within general autonomous quantum systems, and many fundamental open questions remain unanswered. Along these lines, most current efforts and approaches restrict the analysis to particular scenarios of approximative descriptions and semi-classical regimes. Here, we propose a novel approach to describe the thermodynamics of arbitrary bipartite autonomous quantum systems based on the well-known Schmidt decomposition. This formalism provides a simple, exact, and symmetrical framework for expressing the energetics between interacting systems, including scenarios beyond the standard description regimes, such as strong coupling. We show that this procedure allows straightforward identification of local effective operators suitable for characterizing the physical local internal energies. We also demonstrate that these quantities naturally satisfy the usual thermodynamic notion of energy additivity.

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We study the generalized one-dimensional (1D) quantum dissipative models corresponding to a Majorana wire which can possess more than one Majorana bound state at each end. The system consists of a 1D fermionic open quantum system whose dynamics is governed by a quadratic Lindblad equation. Using the adjoint Lindblad equation for the fermionic two-point correlations, we find the gaps in the damping and purity spectra of a generic 1D model. Then, using the symmetry-based classification, we show that a winding number as the topological invariant can be defined which distinguishes different steady states of the system in the presence of damping and purity gaps. Then we focus on certain models with different Lindblad quantum jump terms and explore their phase diagrams by calculating the damping and the purity gaps as well as the winding number. In particular, we show that by inclusion of quantum jumps between next-nearest-neighbor sites, higher winding numbers and equivalently more Majorana bound states can be achieved. Also, by introducing imbalanced couplings we can switch between states with negative and positive winding numbers. Finally, we should mention that since our formulation is based on the fermionic correlations rather than the Majorana operators, it can be easily extended to the dissipative topological phases belonging to other symmetry classes.

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In recent years, quantum collision models, sometimes dubbed repeated interaction models, have gained much attention due to their simplicity and their capacity to convey ideas without resorting to technical complications typical of many approaches and techniques used in the field of open quantum systems. In this tutorial, we show how to use these models, highlighting their strengths and some technical subtleties often overlooked in the literature. We do this by deriving the Markovian master equation and comparing the standard collisional derivation with the standard microscopic one. We then use the collision model to derive the master equation of a two-level system interacting with either a bosonic or fermionic bath to give the reader a flavour of the real use of the model.