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arXiv:2311.10222 · Scientific Reports

Mimicking classical noise in ion channels by quantum decoherence

Mina Seifi, Ali Soltanmanesh, Afshin Shafiee

Published Jul 12, 2024• 6 citations
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Abstract

The mechanism of selectivity in ion channels is still an open question in biology. Recent studies suggest that the selectivity filter may exhibit quantum coherence, which could help explain how ions are selected and conducted. However, environmental noise causes decoherence and loss of quantum effects. It is hoped that the effect of classical noise on ion channels can be modeled using the framework provided by quantum decoherence theory. In this paper, the behavior of the ion channel system was simulated using two models: the Spin-Boson model and the stochastic Hamiltonian model under classical noise. Additionally, using a different approach, the system's evolution was modeled as a two-level Spin-Boson model with tunneling, interacting with a bath of harmonic oscillators, based on decoherence theory. We investigated under what conditions the decoherence model approaches and deviates from the noise model. Specifically, we examined Gaussian noise and Ornstein-Uhlenbeck noise in our model. Gaussian noise shows a very good agreement with the decoherence model. By examining the results, it was found that the Spin-Boson model at a high hopping rate of potassium ions can simulate the behavior of the system in the classical noise approach for Gaussian noise.

DOI
10.1038/s41598-024-67106-6

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The mechanism of selectivity in ion channels is still an open question in biology. Recent studies suggest that the selectivity filter may exhibit quantum coherence, which could help explain how ions are selected and conducted. However, environmental noise causes decoherence and loss of quantum effects. It is hoped that the effect of classical noise on ion channels can be modeled using the framework provided by quantum decoherence theory. In this paper, the behavior of the ion channel system was simulated using two models: the Spin-Boson model and the stochastic Hamiltonian model under classical noise. Additionally, using a different approach, the system's evolution was modeled as a two-level Spin-Boson model with tunneling, interacting with a bath of harmonic oscillators, based on decoherence theory. We investigated under what conditions the decoherence model approaches and deviates from the noise model. Specifically, we examined Gaussian noise and Ornstein-Uhlenbeck noise in our model. Gaussian noise shows a very good agreement with the decoherence model. By examining the results, it was found that the Spin-Boson model at a high hopping rate of potassium ions can simulate the behavior of the system in the classical noise approach for Gaussian noise.
Abstract Recently, it has been suggested that ion channel selectivity filter may exhibit quantum coherence, which may be appropriate to explain ion selection and conduction processes. Potassium channels play a vital role in many physiological processes. One of their main physiological functions is the efficient and highly selective transfer of K + ions through the membranes into the cells. To do this, ion channels must be highly selective, allowing only certain ions to pass through the membrane, while preventing the others. The present research is an attempt to investigate the relationship between hopping rate and maintaining coherence in ion channels. Using the Lindblad equation to describe a three-level system, the results in different quantum regimes are examined. We studied the distillable coherence and the second order coherence function of the system. The oscillation of distillable coherence from zero, after the decoherence time, and also the behavior of the coherence function clearly show the point that the system is coherent in ion channels with high throughput rates.
Quantum decoherence arises due to uncontrollable entanglement between a system and its environment. However, the effects of decoherence are often thought of and modeled through a simpler picture in which the role of the environment is to introduce classical noise in the system's degrees of freedom. Here, we establish necessary conditions that the classical noise models need to satisfy to quantitatively model the decoherence. Specifically, for pure-dephasing processes, we identify well-defined statistical properties for the noise that are determined by the quantum many-point time correlation function of the environmental operators that enter into the system-bath interaction. In particular, for the exemplifying spin-boson problem with a Lorentz-Drude spectral density, we show that the high-temperature quantum decoherence is quantitatively mimicked by colored Gaussian noise. In turn, for dissipative environments, we show that classical noise models cannot describe decoherence effects due to relaxation through spontaneous emission of photons/phonons. These developments provide a rigorous platform to assess the validity of classical noise models of decoherence.
Assuming the selectivity filter of KcsA potassium ion channel may exhibit quantum coherence, we extend a previous model by Vaziri and Plenio (2010 New J. Phys. 12 085001) to take into account Coulomb repulsion between potassium ions. We show that typical ion transit timescales are determined by this interaction, which imposes optimal input/output parameter ranges. Also, as observed in other examples of quantum tunneling in biological systems, the addition of moderate noise helps coherent ion transport.
The mechanism of selectivity in ion channels is still an open question in biology for more than half a century. Here, we suggest that quantum interference can be a solution to explain the selectivity mechanism in ion channels since interference happens between similar ions through the same size of ion channels. In this paper, we simulate two neighboring ion channels on a cell membrane with the famous double-slit experiment in physics to investigate whether there is any possibility of matter-wave interference of ions via movement through ion channels. Our obtained decoherence timescales indicate that the quantum states of ions can only survive for short times, i.e. ≈100 picoseconds in each channel and ≈17-53 picoseconds outside the channels, giving the result that the quantum interference of ions seems unlikely due to environmental decoherence. However, we discuss our results and raise few points, which increase the possibility of interference.
discrimination rate between ions). It is made of four strands as the backbone, and each strand is composed of sequences of five amino acids connected by peptide units H-N-C=O in which the main molecules in the backbone that interact with ions in the filter are carbonyl (C=O) groups that mimic the transient interactions of ion with binding sites during ion conduction. It has been suggested that quantum coherence and possible emergence of resonances in the backbone carbonyl groups may play a role in mediating ion conduction and selectivity in the filter. Here, we investigate the influence of noise and disorder on the efficiency of excitation energy transfer (EET) in a linear harmonic chain of N = 5 sites with dipole-dipole couplings as a simple model for one P-loop strand of the selectivity filter backbone in biological ion channels. We include noise and disorder inherent in real biological systems by including spatial disorder in the chain, and random noise within a weak coupling quantum master equation approach. Our results show that disorder in the backbone considerably reduces EET, but the addition of noise helps to recover high EET for a wide range of system parameters. Our analysis may help for better understanding of the coordination of ions in the filter as well as the fast and efficient functioning of the selectivity filters in ion channels.
The efficiency of the future devices for quantum information processing will be limited mostly by the finite decoherence rates of the qubits. Recently, substantial progress was achieved in enhancing the time within which a solid-state qubit demonstrates coherent dynamics. This progress is based mostly on a successful isolation of the qubits from external decoherence sources. Under these conditions, the material-inherent sources of noise start to play a crucial role. In most cases, the noise that the quantum device demonstrates has a 1/ f spectrum. This suggests that the environment that destroys the phase coherence of the qubit can be thought of as a system of two-state fluctuators, which experience random hops between their states. In this short review, the current state of the theory of the decoherence due to the qubit interaction with the fluctuators is discussed. The effect of such an environment on two different protocols of the qubit manipulations, free induction and echo signal, is described. It turns out that in many important cases the noise produced by the fluctuators is non-Gaussian. Consequently, the results of the interaction of the qubit with the fluctuators are not determined by the pair correlation function alone. We describe the effect of the fluctuators using the so-called spin-fluctuator model. Being quite realistic, this model allows one to exactly evaluate the qubit dynamics in the presence of one fluctuator. This solution is found, and its features, including non-Gaussian effects, are analyzed in detail. We extend this consideration to systems of large numbers of fluctuators, which interact with the qubit and lead to the 1/ f noise. We discuss existing experiments on the Josephson qubit manipulation and try to identify non-Gaussian behavior.