Related papers: Acceleration of enzymatic reactions due to nearby …
Biological molecular motors are high-performance nanomachines that convert chemical energy into mechanical motion via chemomechanical coupling. Their reaction cycles typically comprise a series of intermediate chemical states between the…
We propose a simple theoretical model for a molecular chemical engine that catalyzes a chemical reaction and converts the free energy released by the reaction into mechanical work. Binding and unbinding processes of reactant and product…
The rate-limiting step of some enzymatic reactions is a physical step, i.e. diffusion. The efficiency of such reactions can be improved through an increase in the arrival rate of the substrate molecules, e.g. by a directed passage of…
Metabolic reactions of single-cell organisms are routinely observed to become dispensable or even incapable of carrying activity under certain circumstances. Yet, the mechanisms as well as the range of conditions and phenotypes associated…
Most computer simulations of molecular dynamics take place under equilibrium conditions--in a closed, isolated system, or perhaps one held at constant temperature or pressure. Sometimes, extra tensions, shears, or temperature gradients are…
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…
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…
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…
Here, steady-state reaction networks are inspected from the viewpoint of individual tagged molecules jumping among their chemical states upon the occurrence of reactive events. Such an agent-based viewpoint is useful for selectively…
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 study of chemical reactions in environments under nonequilibrium conditions has been of interest recently in a variety of contexts, including current-induced reactions in molecular junctions and scanning tunneling microscopy…
In this work we study, at the single molecular level, the thermodynamic and dynamic characteristics of an enzymatic reaction comprising a rate limiting step. We investigate how the stability of the enzyme-state stationary probability…
We consider a general class of autocatalytic reactions, that has been shown to display stochastically switching behaviour (Discreteness Induced Transitions) in some parameter regimes. This behaviour was shown to occur when either 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.…
Parametrized polynomial ordinary differential equation systems are broadly used for modeling, specially in the study of biochemical reaction networks under the assumption of mass-action kinetics. Understanding the qualitative behavior of…
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…
The metabolic network of a living cell involves several hundreds or thousands of interconnected biochemical reactions. Previous research has shown that under realistic conditions only a fraction of these reactions is concurrently active in…
We propose a new way of quick and very efficient acceleration of protons and/or electrons in relativistic bulk flows. The new mechanism takes advantage of conversion of particles from the charged state (protons or electrons/positrons) into…
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…
Biological transport is supported by collective dynamics of enzymatic molecules that are called motor proteins or molecular motors. Experiments suggest that motor proteins interact locally via short-range potentials. We investigate the…