Related papers: Output-input coupling in thermally fluctuating bio…
We study coupled quantum systems as the working media of thermodynamic machines. Under a suitable phase-space transformation, the coupled systems can be expressed as a composition of independent subsystems. We find that for the coupled…
The biological cell exhibits a fantastic range of behaviors, but ultimately these are governed by a handful of physical and chemical principles. Here we explore simple theory, known for decades and based on the simple thermodynamics of…
We use a free energy functional theory to elucidate general properties of heterogeneously ordering, fast folding proteins, and we test our conclusions with lattice simulations. We find that both structural and energetic heterogeneity can…
Chemical affinities are responsible for driving active matter systems out of equilibrium. At the nano-scale, molecular machines interact with the surrounding environment and are subjected to external forces. The mechano-chemical coupling…
We investigate the weak-strong coupling transition of two linearly coupled systems under the influence of a phase fluctuating coupling. In the weak coupling regime the exponential decay of quantum properties is well known. A different…
Living cells use readout molecules to record the state of receptor proteins, similar to measurements or copies in typical computational devices. But is this analogy rigorous? Can cells be optimally efficient, and if not, why? We show that,…
Motor proteins are active enzymatic molecules that drive a variety of biological processes, including transfer of genetic information, cellular transport, cell motility and muscles contraction. It is known that these biological molecular…
Mechanochemical coupling was studied for two different types of myosin motors in cells: myosin V, which carries cargo over long distances by as a single molecule; and myosin II, which generates a contracting force in cooperation with other…
Enzymatic molecules that actively support many cellular processes, including transport, cell division and cell motility, are known as motor proteins or molecular motors. Experimental studies indicate that they interact with each other and…
A protein undergoes conformational dynamics with multiple time scales, which results in fluctuating enzyme activities. Recent studies in single molecule enzymology have observe this "age-old" dynamic disorder phenomenon directly. However,…
The dynamics of flow within a material transport network is dependent upon the dynamics of its power source. Responding to a change of these dynamics is critical for the fitness of living flow networks, e.g. the animal vasculature, which…
During overflow metabolism, cells excrete glycolytic byproducts when growing under aerobic conditions in a seemingly wasteful fashion. While potentially advantageous for microbes with finite oxidative capacity, its role in higher organisms…
A class of analog computers built from large numbers of microscopic probabilistic machines is discussed. It is postulated that such computers are implemented in biological systems as ensembles of protein molecules. The formalism is based on…
We provide a rigorous definition of free-energy transduction and its efficiency in arbitrary -- linear or nonlinear -- open chemical reaction networks (CRNs) operating at steady state. Our method is based on the knowledge of the…
Information thermodynamics relates the rate of change of mutual information between two interacting subsystems to their thermodynamics when the joined system is described by a bipartite stochastic dynamics satisfying local detailed balance.…
Enzymes are nano-scale machines that have evolved to drive chemical reactions out of equilibrium in the right place at the right time. Given the complexity and specificity of enzymatic function, bottom-up design of enzymes presents a…
The possibility that evolutionary forces -- together with a few fundamental factors such as thermodynamic constraints, specific computational features enabling information processing, and ecological processes -- might constrain the logic of…
Neither of the two prevalent theories, namely thermodynamic stability and kinetic stability, provides a comprehensive understanding of protein folding. The thermodynamic theory is misleading because it assumes that free energy is the…
An activated process consists of energy activation and barrier crossing; the former is a prerequisite for the latter. Barrier crossing has been studied extensively, but energy activation has been overlooked due to a lack of means to gauge…
Proteins change their charge state through protonation and redox reactions as well as through binding charged ligands. The free energy of these reactions are dominated by solvation and electrostatic energies and modulated by protein…