Time delay during intra-base proton tunneling in the guanine base of the single stranded DNA

Ozcelik, Elif; Akar, Demet Eda; Zaman, Semih; Demir, Durmuş A.

doi:10.1016/j.pbiomolbio.2022.05.009

Cited by 4 publications

(6 citation statements)

References 41 publications

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“…In contrast, QM simulations give a realistic description of the potassium tunneling in G-quadruplex because, quoting from Villani [38], "it is more accurate in the treatment of hydrogen-bonding and stacking interactions." It is in light of this fact [38] and it is with our experience from our earlier studies on proton tunneling in DNA [27,28] that our analysis of the G-quadruplex is based on quantum simulations [38].…”

Section: Resultsmentioning

confidence: 99%

“…(MD, for instance, is classical in nature [8].) In fact, entropic tunneling time formula we use here was applied before to inter-base and intra-base proton tunnelings in DNA (whose potentials were calculated with DFT), and tunneling delay was found to be in picoseconds range [27,28], which is seen to agree with recent experimental results [52,68]. It is in this sense that entropic time remains in the ballpark of conformational transition times in biological systems, and we expect it to be so also for potassium ion tunneling in G-quadruplex.…”

Section: Resultsmentioning

confidence: 99%

“…There are two statements for enabling quantum mechanics in complex biological systems: (i) quantum phenomena can take place over very short time scales before wash away by its surroundings and (ii) quantum dynamics can be enhanced by a finely tuned and constructive interplay with its surroundings [16]. In the last decades, the growing number of theoretical and experimental studies supported quantum tunneling and quantum coherence effects on biology [22,27,28], however, other areas of quantum biology remain speculative such as magnetoreception [29] and olfaction [30,31]. Even though its fast progression, the main limitation of studies in quantum biology is the difficulty of monitoring experimental systems for precise physical measurement.…”

Section: Introductionmentioning

confidence: 99%

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Quantum tunneling time delay investigation of $${{\varvec{K}}}^{+}$$ ion in human telomeric G-quadruplex systems

Çelebi

Demir

2023

J Biol Inorg Chem

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Guanine-rich quadruplex DNA (G-quadruplex) is of interest both in cell biology and nanotechnology. Its biological functions necessitate a G-quadruplex to be stabilized against escape of the monovalent metal cations. The potassium ion ( K + ) is particularly important as it experiences a potential energy barrier while it enters and exits the G-quadruplex systems which are normally found in human telomere. In the present work, we analyzed the time it takes for the K + cations to get in and out of the G-quadruplex. Our time estimate is based on entropic tunneling time-a time formula which gave biologically relevant results for DNA point mutation by proton tunneling. The potential energy barrier experienced by K + ions is determined from a quantum mechanical simulation study, Schrodinger equation is solved using MATLAB, and the computed eigenfunctions and eigenenergies are used in the entropic tunneling time formula to compute the time delay and charge accumulation rate during the tunneling of K + in G-quadruplex. The computations have shown that ion tunneling takes picosecond times. In addition, average K + accumulation rate is found to be in the picoampere range. Our results show that time delay during the K + ion tunneling is in the ballpark of the conformational transition times in biological systems, and it could be an important parameter for understanding its biological role in human DNA as well as for the possible applications in biotechnology. To our knowledge, for the first time in the literature, time delay during the ion tunneling from and into G-quadruplexes is computed.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Quantum tunneling time delay investigation of $${{\varvec{K}}}^{+}$$ ion in human telomeric G-quadruplex systems

Çelebi

Demir

2023

J Biol Inorg Chem

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“…It is concordant with the wavefront delay, and respects therefore fundamentals of the relativity and quantum. Needless to say, (ATT) F gives the durations of tunneling-enabled phenomena in nature, which range from nuclear fusion [1] in physics to smell perception [45] in chemistry to DNA mutation [46,47,48,49] in biology. Likewise, it sets operation speeds of all tunneling-driven processes such as quantum annealing [50,51] -a tunneling-enabled quantum computation mechanism [52,53,26] which has already been implemented on an 1,800-qubit chip [27] by D-Wave Systems.…”

Section: Discussionmentioning

confidence: 99%

Tunneling time from spin fluctuations in Larmor clock

Demir

2022

Preprint

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Tunneling time, time needed for a quantum particle to tunnel through a potential energy barrier, can be measured by a duration marker. One such marker is spin reorientation due to Larmor precession. With a weak magnetic field in z direction, the Larmor clock reads two times, τ y and τ z , for a potential energy barrier along the y axis. The problem is to determine the actual tunneling time (ATT). Büttiker defines τ 2 y + τ 2 z to be the ATT. Steinberg and others, on the other hand, identify τ y with the ATT. The Büttiker and Steinberg times are based on average spin components but in non-commuting spin system average of one component requires the other two to fluctuate. In the present work, we study the effects of spin fluctuations and show that the ATT can well be τ y + τ 2 z τy . We analyze the ATT candidates and reveal that the fluctuation-based ATT acts as a transmission time in all of the low-barrier, high-barrier, thick-barrier and classical dynamics limits. We extract this new ATT using the most recent experimental data by the Steinberg group. The new ATT qualifies as a viable tunneling time formula.

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“…The hand should not seek neutrality or silence; the hand should be looking for functional entropy. The latter is the maximum adaptability of the organism which is expressed in health [ 48 , 49 ]. Conversely, the presence of dysfunctional syntropy implies the presence of a predominant pattern that disrupts the balance and leads to disease [ 48 , 49 ].…”

Section: Reviewmentioning

confidence: 99%

The Osteopath’s Imprint: Osteopathic Medicine Under the Nanoscopic Lens

Bordoni¹,

Escher²

2023

Cureus

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Scientific literature demonstrates how osteopathic manipulative treatments (OMT) are able to improve various somatic functional parameters, change somato-visceral and viscero-somatic reflexes toward a more physiological mechano-metabolic environment and, consequently, bring benefits to patients. These benefits can be long-lasting or short-lived. Multiple reasons can be found to explain the positive responses to OMT, ranging from neurological, vascular, lymphatic, and endocrine explanations. Not only the techniques, but the touch of the clinician prove to be important factors for a favorable adaptation by the patient. Another science capable of explaining the change in cellular status and from which reflections that pave the way for observing the human body in a different light can be extrapolated is quantum physics. The latter is rarely taken into consideration to obtain possible explanations of the physical events that occur between the clinician and the patient. The article tries to put the effects of OMT under the light of a new lens: the nanoscopic.

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Time delay during intra-base proton tunneling in the guanine base of the single stranded DNA

Cited by 4 publications

References 41 publications

Quantum tunneling time delay investigation of $${{\varvec{K}}}^{+}$$ ion in human telomeric G-quadruplex systems

Quantum tunneling time delay investigation of $${{\varvec{K}}}^{+}$$ ion in human telomeric G-quadruplex systems

Tunneling time from spin fluctuations in Larmor clock

The Osteopath’s Imprint: Osteopathic Medicine Under the Nanoscopic Lens

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