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Cells generally convert nutrient resources to useful products via energy transduction. Accordingly, the thermodynamic efficiency of this conversion process is one of the most essential characteristics of living organisms. However, although…
Recent fluorescence spectroscopy measurements of the turnover time distribution of single-enzyme turnover kinetics of $\beta$-galactosidase provide evidence of Michaelis-Menten kinetics at low substrate concentration. However, at high…
The rate of a chemical reaction can often be determined by the properties of a rank-1 saddle and the associated transition state separating reactants and products. We have found evidence that such rates can be controlled and even enhanced…
Genetically identical cells under the same environmental conditions can show strong variations in protein copy numbers due to inherently stochastic events in individual cells. We here develop a theoretical framework to address how…
Molecular motors transduce chemical energy obtained from hydrolizing ATP into mechanical work exerted against an external force. We calculate their efficiency at maximum power output for two simple generic models and show that the…
To understand the behaviour of complex systems it is often necessary to use models that describe the dynamics of subnetworks. It has previously been established using projection methods that such subnetwork dynamics generically involves…
The driving force for active physical and biological systems is determined by both the underlying landscape and the non-equilibrium curl flux. While landscape can be quantified in the experiments by the histograms of the collecting…
In this paper we study noise-induced bistability in a specific circuit with many biological implications, namely a single-step enzymatic cycle described by Michaelis Menten equations with quasi-steady state assumption. We study the system…
The appealing feature of molecular electronics is the possibility of exploiting functionality built within a single molecule. This functionality can be employed, for example, for sensing or switching purposes. Thus, ideally, the associated…
Biological molecular machines are bifunctional enzymes that catalyze two processes: one donating free energy and the other accepting it. Recent studies show that most protein enzymes have rich stochastic dynamics of transitions between the…
A theoretical model of nuclear spin conversion in molecules controlled by an external electromagnetic radiation resonant to rotational transition has been developed. It has been shown that one can produce an enrichment of spin isomers 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,…
We present a model of an ATP-fueled molecular machine which push a polymer through a pore channel. The machine acts between two levels (working-waiting), and the working one remains active for a fixed time giving a constant force. The…
A simple model of the two-state ratchet type is proposed for molecular chemical engines that convert chemical free energy into mechanical work and vice versa. The engine works by catalyzing a chemical reaction and turning a rotor.…
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 concept of allostery in which macromolecules switch between two different conformations is a central theme in biological processes ranging from gene regulation to cell signaling to enzymology. Allosteric enzymes pervade metabolic…
The hyperbolic dependence of catalytic rate on substrate concentration is a classical result in enzyme kinetics, quantified by the celebrated Michaelis-Menten equation. The ubiquity of this relation in diverse chemical and biological…
Enzyme-catalysed reactions involve two distinct timescales. There is a short timescale on which enzymes bind to substrate molecules to produce bound complexes, and a comparatively long timescale on which the complex is transformed into a…
The movement of single kinesin molecules was observed while applying noisy external forces that mimic intracellular active fluctuations. We found kinesin accelerates under noise, especially when a large hindering load is added. The behavior…
The theory of biochemical processes needs simple but realistic models of phenomena underlying microscopic dynamics of proteins. Many experiments performed in the 1980s have demonstrated that within the protein native state, apart from usual…