Related papers: Kinetics of proton pumping in cytochrome c oxidase
Realistic description of patient-specific mechanical properties of clotting dynamics presents a major challenge. Available patient-specific data falls short of robustly characterizing myriads of complex dynamic interactions that happen…
By employing single charge injections with an atomic force microscope, we investigated redox reactions of a molecule on a multilayer insulating film. First, we charged the molecule positively by attaching a single hole. Then we neutralized…
Kinetic equations for the stationary state distribution function of ions moving through narrow pores are solved for a number of one-dimensional models of single ion transport. Ions move through pores of length $L$, under the action of a…
A flexible membrane deforming its shape in time can self-propel in a viscous fluid. Alternatively, if the membrane is anchored, its deformation will lead to fluid transport. Past work in this area focused on situations where the deformation…
In this work a series of analyses are performed on ab initio molecular dynamics (AIMD) simulations of a hydrated excess proton in water to quantify the relative occurrence of concerted hopping events and <span>rattling</span> events, and…
We study the mobility of a charged colloidal particle in a constant homogeneous electric field by means of computer simulations. The simulation method combines a lattice Boltzmann scheme for the fluid with standard Langevin dynamics for the…
We present the results of the modeling of proton translocation in finite H-bonded chains in the framework of two-stage proton transport model. We explore the influence of reorientation motion of protons, as well as the effect of electric…
When redox active molecules are covalently tethered to the surface of the n-doped silicon, light induces their oxidation by the semiconductor. To visualize this charge separation we have followed the formation and decay of the surface…
We present in this paper an original approach to compute the electrophoretic mobility of rigid nucleo-protein complexes like nucleosomes. This model allows to address theoretically the influence of complex position along DNA, as well as…
We perform molecular dynamics simulations using the extended simple point charge SPC/E water model in order to investigate the dynamical behavior of supercooled-stretched water. We focus on the behavior of the translational diffusion…
We present a detailed study of proton dynamics in the hydrogen-bonded superprotonic conductor CsHSO4 from first-principles molecular dynamics simulations, isolating the subtle interplay between the dynamics of the O--H chemical bonds, the…
Herein (the first part of my work), I debunk the long-standing hypotheses that explain mitochondrial oxidative phosphorylation. Simple calculations point out that mitochondria are highly proton-deficient microcosms and therefore, elaborate…
A stochastic model for the dynamics of enzymatic catalysis in explicit, effective solvents under physiological conditions is presented. Analytically-computed first passage time densities of a diffusing particle in a spherical shell with…
Charge transport through single molecules can be influenced by the charge and spin states of redox-active metal centres placed in the transport pathway. These molecular intrinsic properties are usually addressed by varying the molecules…
The optimisation of the sensitive region of CMOS sensors with complex non-uniform electric fields requires precise simulations, and this can be achieved by a combination of electrostatic field simulations and Monte Carlo methods. This paper…
Two recent experimental (Li, J.~\emphj{et al}, \emph{Proc.\ Natl.\ Acad.\ Sci.\ U.~S.~A.} {\bf 2014}, 111, 1282-1287) and theoretical studies (B\^aldea, I, \emph{Phys.\ Chem.\ Chem.\ Phys.}\ {\bf 2014}, 16, 25942-25949) have addressed the…
A one-dimensional multi-phase flow model for thermomagnetically pumped ferrofluid with heat transfer is proposed. The thermodynamic model is a combination of a simplified particle model and thermodynamic equations of state for the base…
Enzymes show two distinct transport behaviors in the presence of their substrates in solution. First, their diffusivity enhances with increasing substrate concentration. In addition, enzymes perform directional motion toward regions with…
Pumping fluids is fundamental to a wide range of industrial, environmental, and biomedical applications. Among various pumping mechanisms, peristaltic pumps enable efficient and safe fluid transport by deforming an elastic tube without…
Here we study a pumping device capable of maintaining a density gradient and a flux of particles across a membrane. Its driving mechanism is based on the flashing ratchet effect powered by the random telegraph process in the presence of…