Related papers: Thermodynamic and Kinetic Analysis of Sensitivity …
Biomolecular machines consume free energy to break symmetry and make directed progress. Nonequilibrium ATP concentrations are the typical free energy source, with one cycle of a molecular machine consuming a certain number of ATP, providing…
A variety of biomolecular systems rely on exploratory dynamics to reach target locations or states within a cell. Without a mechanism to remotely sense and move directly towards a target, the system must sample over many paths, often…
Photovoltaic energy conversion in photovoltaic cells has been analyzed by the detailed balance approach or by thermodynamic arguments. Here we introduce a network representation to analyze the performance of such systems once a suitable…
Fueled by the hydrolysis of ATP, the motor protein kinesin literally walks on two legs along the biopolymer microtubule. The number of accidental backsteps that kinesin takes appears to be much larger than what one would expect given the…
Quasiperiodic systems are an intermediate class of systems between periodic crystals and disordered systems, famously exhibiting metal-insulator transitions (MITs) even in one dimension. While their transport properties have been studied…
In this study, we propose a theoretical framework to investigate the interactions between flexible polymer chains, specifically polyelectrolytes (PEs). By calculating the system's free energy while considering position-dependent mutual…
F1-ATPase catalyses ATP hydrolysis and converts the cellular chemical energy into mechanical rotation. The hydrolysis reaction in F1-ATPase does not follow the widely believed Michaelis-Menten mechanism. Instead, the hydrolysis mechanism…
We consider an arbitrary translationally invariant chain model with nearest neighbors interaction and satisfying periodic boundary condition. The approach developed here allows a thermodynamic description of the chain model directly in…
Cells can sense forces applied to them, but also the stiffness of their environment. These are two different phenomena, and here we investigate the mechanosensitivity of the IInd kind: how the cell can measure an elastic modulus at a single…
Quasi-parametric amplification (QPA) is a nonlinear interaction in which the idler wave is depleted through some loss mechanism. QPA plays an important role in signal amplification in ultrafast photonics and quantum light generation. The…
Electroporation is a complex, iterative, and nonlinear phenomenon that is often studied by numerical simulations. In recent years, tissue electroporation simulations have been performed using static models. However, the results of a static…
Harnessing the quantum coherence and tunability of molecular-scale structures, we theoretically explore thermoelectric transport in ring-shaped molecular junctions featuring dimerized hopping integrals. By engineering alternating strong and…
Accurate prediction of binding free energies is critical to streamlining the drug development and protein design process. With the advent of GPU acceleration, absolute alchemical methods, which simulate the removal of ligand electrostatics…
We propose a new statistical mechanics model for the melting transition of DNA. Base pairing and stacking are treated as separate degrees of freedom, and the interplay between pairing and stacking is described by a set of local rules which…
The synthesis of ATP, life's 'universal energy currency', is the most prevalent chemical reaction in biological systems, and is responsible for fueling nearly all cellular processes, from nerve impulse propagation to DNA synthesis. ATP…
On the microscopic level, biological signal transmission relies on coordinated structural changes in allosteric proteins that involve sensor and effector modules. The timescales and microscopic details of signal transmission in proteins are…
A system of N two-level atoms cooperatively interacting with a photonic field can be described as a single giant atom coupled to the field with interaction strength ~N^0.5. This enhancement, known as Dicke cooperativity in quantum optics,…
Mitochondria are critical organelles in eukaryotes that produce the energy currency ATP. In nerve axons, mitochondria are known to align at almost regular intervals to maintain a constant ATP concentration, but little is known about the…
Simple two-state folding kinetics of many small single-domain proteins are characterized by chevron plots with linear folding and unfolding arms consistent with a two-state description of equilibrium thermodynamics. This phenomenon is…
Thermoelectric energy conversion is a direct but low-efficiency process, which precludes the development of long-awaited wide-scale applications. As a breakthrough permitting a drastic performance increase is seemingly out of reach, we…