- Institute of Physics, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
Quantum transport efficiency is influenced by mechanisms beyond coherence, including correlated disorder, which can balance localization and mobility to produce anomalous phenomena such as quantum rogue waves. Motivated by recent findings, we investigate the impact of correlated on-site energies in a linear quantum chain modeling a biological ion channel. The system is described by a tight-binding Hamiltonian with Lindblad operators representing source and drain. The average traversal time across the channel increases logarithmically with the correlation parameter, mirroring the growth of rogue-wave probability and indicating the emergence of temporary trapped states that slow transport. These results demonstrate that correlated disorder significantly influences ion transport even in small disordered systems.
1 Introduction
All living organisms share a fundamental characteristic: the presence of cells. Traditionally regarded as the basic structural and functional units of life, cells have also been described, according to Salari et al. (2017), as nano-machines capable of replication and information processing. This perspective not only emphasizes their complexity but also aligns with growing evidence of quantum mechanical phenomena in biological systems. For example, quantum coherence has been demonstrated in photosynthetic complexes during exciton energy transfer (Engel et al., 2007; Mohseni et al., 2008; Collini et al., 2010).
In addition, quantum superposition has been reported at the single-electron and single-photon levels in chiral molecular systems (Aiello et al., 2022), while quantum entanglement has been proposed as a mechanism underlying avian magnetoreception and navigation (Hore and Mouritsen, 2016). Specifically, the coherent spin dynamics of radical pair reactions, hypothesized to underlie avian magnetoreception, present a prime area for the application of digital quantum simulation (DQS) techniques on near-term hardware (Alvarez et al., 2024) or even in light-harvesting components of photosynthetic organisms (Sarovar et al., 2010).
Furthermore, quantum tunneling has been suggested to contribute to processes such as genetic mutations (McFadden and Al-Khalili, 1999), olfactory perception, and enzymatic catalysis (Brookes, 2017). These examples illustrate how quantum mechanical principles may underlie a wide range of biological processes, particularly those involving transport mechanisms. Since transport processes are essential for the functioning of biological systems, ion channels represent a critical case.
Ion channels are membrane-embedded proteins that play a crucial role in the propagation of electrical signals across cell membranes. They mediate the selective passage of ions through specialized pore structures. A defining feature of these channels is their remarkable ion selectivity, which is largely determined by a structural region known as the selectivity filter (SF), as illustrated in Figure 1.
Figure 1. Structure of the selectivity filter (SF), which comprises four potassium-binding sites formed by carbonyl groups and oxygen atoms (in red), as well as an external
Structural studies, particularly X-ray crystallography of the KcsA channel from the bacterium Streptomyces lividans, have provided detailed information about the SF, revealing an approximate diameter of 0.3 nm and a length of 1.2 nm (Doyle et al., 1998). The thermal energy of the potassium ion can be calculated as approximately
Since the thermal wavelength and dimensions of the SF are within a compatible order of magnitude, it is possible to view the transport of ions as a diffraction of the potassium wave matter off a one-dimensional series of potential wells formed by the SF binding sites. Despite these important insights, the precise molecular mechanisms underlying ion selectivity remain incompletely understood and continue to be actively investigated by the scientific community. In line with the tetrameric structure of the SF discussed by Doyle et al. (1998), which has four coordination sites, our model uses a linear chain of 6 sites (4 channel sites plus source and drain) as shown in Figure 1.
According to Vaziri and Plenio, (2010), quantum coherence may play a role in the selectivity and ion conduction of the SF. The authors propose that the mechanisms underlying high conduction rates and ion discrimination, as observed in potassium channels such as KcsA, may have a quantum origin, involving diffraction of the potassium matter wave or quantum tunneling through potential barriers. Their work also suggests an alternative experimental approach to ultrafast two-dimensional spectroscopy by showing that the application of an external alternating electric field (AC) could induce resonances in ion channel conductivity signatures of quantum coherence in the system.
Quantum coherence is a key factor underlying the high efficiency of quantum transport (Polakowski and Panfil, 2024). However, in realistic systems, interactions with the environment or with phonons arising from protein structural fluctuations introduce inevitable noise and disorder (Plenio and Huelga, 2008; Jalalinejad et al., 2018; Almeida et al., 2018). These fluctuations can disrupt coherence and modify transport properties. Depending on their nature, the resulting disorder may be completely random or exhibit spatial correlations (Izrailev et al., 2012). Understanding how such correlated disorder influences transport is therefore essential, particularly in open quantum systems that model biological ion channels, where coupling to external reservoirs and internal structural dynamics play a fundamental role.
A recent study by Buarque et al. (2023) shows that spatially correlated site energies in a one-dimensional lattice with hopping can produce highly localized intensities in the wave functions due to anomalous quantum amplitudes, controlled by a parameter that sets the correlation length. Similar effects have also been observed in a variety of wave phenomena, from ocean waves to optical systems (da Silva and Prado, 2020; Bonatto et al., 2020). Nonetheless, the role of correlated disorder in transport efficiency within open quantum systems that simulate the selectivity filter (SF) of ion channels, modeled as small lattices with a source and a drain, has not yet been fully explored. The selectivity filter is an open system in contact with ionic reservoirs and is characterized by structural fluctuations which might introduce disorder into the site energies.
In this work, we address this gap by investigating transport dynamics in an open quantum system inspired by the KcsA selectivity filter structure under the influence of correlated disorder. We employ the Lindblad master equation to model the SF coupled to a source and a drain. The disorder is introduced into the on-site potentials using a method that allows explicit control over the correlation length. Although a six-site lattice would not ordinarily be expected to capture the subtleties introduced by spatial correlations, our ensemble analysis with 10,000 disorder realizations shows that the mean traversal time increases significantly under strong on-site potential correlations. This demonstrates that the underlying mechanism responsible for correlation-induced delays persists even in small open systems, a result that is both unexpected and noteworthy, and which we aim to highlight in this paper.
The remainder of this paper is organized as follows. Section 2 introduces the theoretical model used to simulate ion transport through the channel and outlines the governing dynamical equations. Section 3 presents the numerical results and discusses their physical implications in the context of correlated disorder and environmental effects. Section 4 summarizes the main conclusions and relates our findings to the mechanisms of ion transport in ion-channel systems.
2 Model and methods
We modeled the selectivity filter (SF) as a linear lattice composed of a source (site 1), four sites (2–5) representing the ion channel and a drain (site 6) (see Figure 1). The source acts as an emitter to the channel, while the extracellular site (site 6) acts like a drain, removing particles from the channel. The entry and exit processes are irreversible: once a particle enters the channel, it cannot return to the source. This configuration was adopted to simulate the interaction between the SF and its surrounding environment.
According to experimental studies (Berneche and Roux, 2001; Gwan and Baumgaertner, 2007), the distance between two adjacent potential minima is approximately 0.24 nm, requiring each ion to cross an energy barrier
where
The crucial element in this analysis is the set of on-site energies
where
After generating each correlated sequence
The on-site energy sequences used in Equation 2 are intended to represent spatial fluctuations of the local site energies with a tunable degree of long-range correlation. The motivation for this choice is twofold. First, long-range correlations are known to alter interference patterns in wave systems and to produce rare, extreme amplitude events that strongly influence transport statistics in both classical and quantum settings. These extreme events correspond, in our discrete open chain, to configurations that transiently concentrate amplitude at certain sites, producing resonant trapping and markedly increasing traversal times. Second, spatial correlations of the kind modeled here can plausibly arise in biological ion channels: correlated positioning of charged or polar residues along the pore, collective conformational fluctuations of the protein scaffold, and correlated variations of the solvent/protein electrostatic environment (including lipid–protein coupling) can induce slowly varying, spatially correlated shifts of local site energies (Gu and de Groot, 2020; Chowdhury and Chanda, 2012; Goforth et al., 2003). Thus, Equation 2 represents a phenomenological, statistically controlled model for spatially correlated energetic landscapes whose transport consequences we explore in this paper.
Since the ion channel operates as an open quantum system, its dynamics are governed by the Lindblad master equation
where
and
where
In this framework, Equation 4,
where the dephasing rate is
3 Results and discussion
All results presented in this work were obtained from an ensemble of 10,000 independent realizations of the disordered system. For each realization, the correlated on-site energies
For simplicity, we set
Ensemble averages were then computed over all realizations to obtain statistically representative quantities. We define
A physically grounded estimate for the hopping rate in quantum models of ion transport can be obtained from prior theoretical and computational studies of potassium channels. The effective site-to-site hopping rate in the selectivity filter was estimated to lie in the range
As the traversal time
Figure 2. Average traversal time,
Figure 3. Traversal-time distributions obtained from an ensemble of 10,000 realizations, comparing weak (
As shown in Figure 3, the distribution undergoes a slight broadening while its peak position remains unchanged. For a drain occupation of 0.65, we see that while most realizations are concentrated at short times, a larger value of
It is important to emphasize that the presence of transient trapping is not any trivial consequence of any broadening of the energy distribution generated by Equation 2, but rather a genuine effect of the correlations. To make this clear, Figure 4 shows the distributions of the on-site energies,
Figure 4. Distributions of on-site energies
The role of dephasing is expected to mitigate correlation effects, as biological environments are inherently noisy. Estimates for biomolecular systems indicate that realistic environmental dephasing rates in proteins at physiological temperature lie in the range
The impact of random dephasing, implemented through the Lindblad operator in Equation 6, is shown in Figure 5. As indicated by the dephasing rates
Figure 5. Mean traversal time
Having addressed the environmental impact, we now consider the intrinsic transport scales. The interplay between the correlation parameter
Figure 6. Mean traversal time,
4 Conclusion
In this work, we investigated the impact of correlated disorder, environmental dephasing, and intrinsic transport parameters on quantum dynamics in a minimal model of the selectivity filter (SF) of ion channels. Using an open quantum system framework with a source, a drain, and four internal sites, we analyzed how correlations in the on-site energies influence the mean traversal time of particles crossing the channel.
Our numerical results show that increasing the correlation parameter
Environmental dephasing, modeled through the Lindblad formalism, attenuates correlation-induced effects when the dephasing rate is sufficiently large. However, signatures of correlated disorder remain visible under weak dephasing, consistent with estimated biomolecular dephasing rates reported in the literature for ion channels. Likewise, increasing the hopping rate,
Taken together, these results demonstrate that transport efficiency in quantum models of biological ion channels arises from a subtle interplay between coherence and disorder. Correlated fluctuations can induce transient trapping even in small, open architectures, while moderate environmental noise and realistic hopping strengths allow transport to remain efficient. The parameter regimes explored here align with those proposed in the biophysical literature, reinforcing the physical relevance of the model and the robustness of the conclusions.
Data availability statement
The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.
Author contributions
ID: Conceptualization, Data curation, Formal Analysis, Investigation, Methodology, Software, Visualization, Writing – original draft, Writing – review and editing. RG: Conceptualization, Formal Analysis, Investigation, Methodology, Visualization, Writing – review and editing. LB: Conceptualization, Data curation, Formal Analysis, Investigation, Methodology, Project administration, Supervision, Validation, Visualization, Writing – original draft, Writing – review and editing. SP: Conceptualization, Data curation, Formal Analysis, Investigation, Methodology, Project administration, Software, Supervision, Validation, Visualization, Writing – original draft, Writing – review and editing.
Funding
The author(s) declared that financial support was received for this work and/or its publication. The authors declare that this research was conducted during the tenure of a scholarship from CNPq (Brazil). No specific funding from CNPq was received for the publication fees of this article.
Acknowledgements
IPSR acknowledges the financial support provided by CNPq. IPSR and RGL also express their gratitude to the Ciência Pioneira initiative for organizing the Quantum Biology School, which was instrumental to this work, and especially thank Dr. Clarice Aiello, Dr. Marcelo Sousa, and the entire Ciência Pioneira team.
Conflict of interest
The author(s) declared that this work was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
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Supplementary material
The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/frqst.2025.1725290/full#supplementary-material
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Keywords: conduction, correlated disorder, quantum ion channels, tight-binding Hamiltonian, trapping localization
Citation: Da Silva Ramos IP, Gandolfi Lanzini R, Brunnet L and Prado SD (2025) Correlated disorder as a tunable switch between trapping and conduction in quantum ion channels. Front. Quantum Sci. Technol. 4:1725290. doi: 10.3389/frqst.2025.1725290
Received: 16 October 2025; Accepted: 11 December 2025;
Published: 29 December 2025.
Edited by:
Sebastiano Pilati, University of Camerino, ItalyReviewed by:
Xianlong Gao, Zhejiang Normal University, ChinaGuilherme Almeida, Federal University of Alagoas, Brazil
Copyright © 2025 Da Silva Ramos, Gandolfi Lanzini, Brunnet and Prado. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: Iara Patrícia Da Silva Ramos, aWFyYS5yYW1vc0B1ZnJncy5icg==; Rafael Gandolfi Lanzini, cmFmYWVsLmxhbnppbmlAdWZyZ3MuYnI=; Leonardo Brunnet, bGVvbkBpZi51ZnJncy5icg==; Sandra D. Prado, cHJhZG9AaWYudWZyZ3MuYnI=
Rafael Gandolfi Lanzini*