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Uğur Çetiner

Publications and source records attributed to Uğur Çetiner.

3 recordsLinked to original sources

Where Energy Is Spent Sets the Depth of Kinetic Proofreading

Kinetic proofreading buys accuracy with energy. Where the energy is spent, we show, caps how much accuracy it can buy. Drive layer $j$ of a $K$-checkpoint cascade and the error never falls below $\eeq^{K-j+1}$, where $\eeq$ is the error the same network reaches at equilibrium. The exponent is one plus the first Betti number of the downstream subgraph, which counts its independent cycles. Driving the first layer can recruit all $K$ checkpoints, whereas driving the final layer restricts the best possible scaling to $\eeq^2$, independently of network depth. We also derive the exact dependence on driving strength and show that the error either decreases monotonically or has a unique global minimum, beyond which stronger driving worsens accuracy. Drive placement therefore imposes a topological limit on nonequilibrium error correction.

physics.bio-ph↗

Energetic Protection, Monotonicity and Switching Far from Equilibrium

At equilibrium, the ratio of two steady-state probabilities is a Boltzmann factor, set by a free-energy difference. Such ratios are the natural, normalization-independent readouts of both thermodynamics and information processing, and are often used as a measure of fidelity in biophysical systems. What becomes of these ratios once a system is driven from equilibrium, where the Boltzmann factor no longer holds? Representing Markov processes as graphs and their steady states as averages over a distribution on spanning trees, the \emph{arboreal distribution}, we track the ratio $π_i/π_j$ under driving along \emph{energetic edges}, where detailed balance is broken, relative to its equilibrium value. Our central finding is that a chosen ratio can stay exactly locked to its equilibrium value arbitrarily far from equilibrium, a phenomenon we call \emph{energetic protection}, whenever an algebraic equality between spanning-tree weights holds. Just as detailed balance constrains rates around cycles, energetic protection constrains weights across trees, providing a new mechanism for robustness against fluctuations in the driving force, such as variations in ATP concentration. Away from this equality, single-edge driving collapses the response onto two arboreal coefficients and forces it to be monotonic, so nonmonotonic single-edge control is impossible at any strength. With two energetic edges, protection and monotonicity combine into a \emph{thermodynamic switch} that holds a function at its equilibrium value for as long as desired and releases it sharply. Equilibrium is known for the limits it places on information processing. We show that new constraints, both no-go principles and exact invariances, survive far from equilibrium. These results reveal how the localization of energy expenditure governs the functional logic of nonequilibrium systems in physics and biology.

physics.bio-ph↗

Mechanosensitive ion channels: Old but new

Ion channels orchestrate the communication between cells and their environment. These are special proteins capable of changing their shape to allow ions to pass through membranes in response to stimuli like membrane tension. As the letters are written and exchanged in the form of ionic currents, the energetic cost of this communication is of interest to many. To this end, we introduce the nanoscale thermodynamics of mechanosensitive ion channels, which amounts to defining work and heat for traces obtained during patch-clamp experiments. We also discuss the interplay between ion channel physics and evolution by showing how information-processing capabilities are coupled with the energy landscapes of channels.

physics.bio-ph↗