arXiv subjects

Onur Pusuluk

Publications and source records attributed to Onur Pusuluk.

24 records · Page 2Linked to original sources

arXiv2021

Quantum Rayleigh problem and thermocoherent Onsager relations

The role of quantum coherence and correlations in heat flow and equilibration is investigated by exploring the Rayleigh's dynamical problem to equilibration in the quantum regime and following Onsager's approach to thermoelectricity. Specifically, we consider a qubit bombarded by two-qubit projectiles from a side. For arbitrary collision times and initial states, we develop the master equation for sequential and collective collisions. By deriving the Fokker-Planck equation out of the master equation, we identify the quantum version of the Rayleigh's heat conduction equation. We find that quantum discord and entanglement shared between the projectiles can contribute to genuine heat flow only when they are associated with so-called heat-exchange coherences. Analogous to Onsager's use of Rayleigh's principle of least dissipation of energy, we use the entropy production rate to identify the coherence current. Both coherence and heat flows can be written in the form of quantum Onsager relations, from which we predict coherent Peltier and coherent Seebeck effects. The effects can be optimized by the collision times and collectivity. Finally, we discuss some of the possible experimental realizations and technological applications of the thermocoherent phenomena in different platforms.

quant-ph↗

arXiv2019

Emergence of correlated proton tunneling in water ice

Several experimental and theoretical studies report instances of concerted or correlated multiple proton tunneling in solid phases of water. Here, we construct a pseudo-spin model for the quantum motion of protons in a hexameric H$_2$O ring and extend it to open system dynamics that takes environmental effects into account in the form of O$-$H stretch vibrations. We approach the problem of correlations in tunneling using quantum information theory in a departure from previous studies. Our formalism enables us to quantify the coherent proton mobility around the hexagonal ring by one of the principal measures of coherence, the $l_1$ norm of coherence. The nature of the pairwise pseudo-spin correlations underlying the overall mobility is further investigated within this formalism. We show that the classical correlations of the individual quantum tunneling events in long-time limit is sufficient to capture the behaviour of coherent proton mobility observed in low-temperature experiments. We conclude that long-range intra-ring interactions do not appear to be a necessary condition for correlated proton tunneling in water ice.

quant-ph↗

arXiv2018

Proton tunneling in hydrogen bonds and its implications in an induced-fit model of enzyme catalysis

The role of proton tunneling in biological catalysis is investigated here within the frameworks of quantum information theory and thermodynamics. We consider the quantum correlations generated through two hydrogen bonds between a substrate and a prototypical enzyme that first catalyzes the tautomerization of the substrate to move on to a subsequent catalysis, and discuss how the enzyme can derive its catalytic potency from these correlations. In particular, we show that classical changes induced in the binding site of the enzyme spreads the quantum correlations among all of the four hydrogen-bonded atoms thanks to the directionality of hydrogen bonds. If the enzyme rapidly returns to its initial state after the binding stage, the substrate ends in a new transition state corresponding to a quantum superposition. Open quantum system dynamics can then naturally drive the reaction in the forward direction from the major tautomeric form to the minor tautomeric form without needing any additional catalytic activity. We find that in this scenario the enzyme lowers the activation energy so much that there is no energy barrier left in the tautomerization, even if the quantum correlations quickly decay.

physics.chem-ph↗

arXiv2018

Quantum entanglement shared in hydrogen bonds and its usage as a resource in molecular recognition

Quantum tunneling events occurring through biochemical bonds are capable to generate quantum correlations between bonded systems, which in turn makes the conventional second law of thermodynamics approach insufficient to investigate these systems. This means that the utilization of these correlations in their biological functions could give an evolutionary advantage to biomolecules to an extent beyond the predictions of molecular biology that are generally based on the second law in its standard form. To explore this possibility, we first compare the tunneling assisted quantum entanglement shared in the ground states of covalent and hydrogen bonds. Only the latter appears to be useful from a quantum information point of view. Also, significant amounts of quantum entanglement can be found in the thermal state of hydrogen bond. Then, we focus on an illustrative example of ligand binding in which a receptor protein or an enzyme is restricted to recognize its ligands using the same set of proton-acceptors and donors residing on its binding site. In particular, we show that such a biomolecule can discriminate between $3^n - 1$ agonist ligands if it uses the entanglement shared in $n$ intermolecular hydrogen bonds as a resource in molecular recognition. Finally, we consider the molecular recognition events encountered in both the contemporary genetic machinery and its hypothetical primordial ancestor in pre-DNA world, and discuss whether there may have been a place for the utilization of quantum entanglement in the evolutionary history of this system.

quant-ph↗

arXiv2011

Entanglement Swapping Model of DNA Replication

Molecular biology explains function of molecules by their geometrical and electronical structures that are mainly determined by utilization of quantum effects in chemistry. However, further quantum effects are not thought to play any significant role in the essential processes of life. On the contrary, consideration of quantum circuits/protocols and organic molecules as software and hardware of living systems that are co-optimized during evolution, may be useful to overcome the difficulties raised by biochemical complexity and to understand the physics of life. In this sense, we review quantum information-theoretic approaches to the process of DNA replication and propose a new model in which 1) molecular recognition of a nucleobase is assumed to trigger an intrabase entanglement corresponding to a superposition of different tautomer forms and 2) pairing of complementary nucleobases is described by swapping intrabase entanglements with interbase entanglements. We examine possible biochemical realizations of quantum circuits/protocols to be used to obtain intrabase and interbase entanglements. We deal with the problem of cellular decoherence by using the theory of decoherence-free subspaces and subsystems. Lastly, we discuss feasibility of the computational or experimental verification of the model and future research directions.

quant-ph↗

arXiv2011

DNA Replication via Entanglement Swapping

Quantum effects are mainly used for the determination of molecular shapes in molecular biology, but quantum information theory may be a more useful tool to understand the physics of life. Organic molecules and quantum circuits/protocols can be considered as hardware and software of living systems that are co-optimized during evolution. We try to model DNA replication in this sense as a multi-body entanglement swapping with a reliable qubit representation of the nucleotides. In our model molecular recognition of a nucleotide triggers an intrabase entanglement corresponding to a superposition state of different tautomer forms. Then, base pairing occurs by swapping intrabase entanglements with interbase entanglements. We examine possible realizations of quantum circuits to be used to obtain intrabase entanglement and swapping protocols to be employed to obtain interbase entanglement. Finally, we discuss possible ways for computational and experimental verification of the model.

quant-ph↗