Related papers: Modelling the ATP production in mitochondria
Numerical methods based on matrix product states (MPSs) are currently the de facto standard for calculating the ground-state properties of (quasi-)one-dimensional quantum many-body systems. While the properties of the low-lying excitations…
Purpose: Phosphorus saturation-transfer experiments can quantify metabolic fluxes non-invasively. Typically, the forward flux through the creatine-kinase reaction is investigated by observing the decrease in phosphocreatine (PCr) after…
The Hamiltonian Mean Field (HMF) model has a low-energy phase where $N$ particles are trapped inside a cluster. Here, we investigate some properties of the trapping/untrapping mechanism of a single particle into/outside the cluster. Since…
Understanding stochastic thermodynamics of active Brownian particles (ABPs) system has been an important topic in very recent years. In this article we study a general model of active Brownian particle systems by introducing a…
We propose four novel mathematical models, describing the microscopic mechanisms of force generation in the cardiac muscle tissue, which are suitable for multiscale numerical simulations of cardiac electromechanics. Such models are based on…
A discrete-state model of the F1-ATPase molecular motor is developed which describes not only the dependences of the rotation and ATP consumption rates on the chemical concentrations of ATP, ADP, and inorganic phosphate, but also on…
Living systems operate far from thermal equilibrium by converting the chemical potential of ATP into mechanical work to achieve growth, replication or locomotion. Given time series observations of intra-, inter- or multicellular processes,…
FoF1-ATP synthase is the enzyme that provides the 'chemical energy currency' adenosine triphosphate, ATP, for living cells. The formation of ATP is accomplished by a stepwise internal rotation of subunits within the enzyme. We monitor…
The thermodynamic (TD) properties of biological membranes play a central role for living systems. It has been suggested, for instance, that nonlinear pulses such as action potentials (APs) can only exist if the membrane state is in vicinity…
Optogenetic modulation of adenosine triphosphatase (ATPase) expression represents a novel approach to maximize bioprocess efficiency by leveraging enforced adenosine triphosphate (ATP) turnover. In this study, we experimentally implement a…
The Na$^+$/K$^+$ ATPase is an essential component of cardiac electrophysiology, maintaining physiological Na$^+$ and K$^+$ concentrations over successive heart beats. Terkildsen et al. (2007) developed a model of the ventricular myocyte…
Within the Rayleigh-Helmholtz model of active Brownian particles activity is due to a non-linear velocity dependent force. In the presence of an external trapping potential or a constant force, the steady state of the system breaks detailed…
We discuss recent advances in developing a mode-coupling theory of the glass transition (MCT) of two-dimensional systems of active Brownian particles (ABP). We specifically discuss the case of a single ABP tracer in a glass-forming passive…
By embedding inert tracer particles (TPs) in a growing multicellular spheroid the local stresses on the cancer cells (CCs) can be measured. In order for this technique to be effective the unknown effect of the dynamics of the TPs on the CCs…
Muscle uses Ca2+ as a messenger to control contraction and relies on ATP to maintain the intracellular Ca2+ homeostasis. Mitochondria are the major sub-cellular organelle of ATP production. With a negative inner membrane potential,…
The theory describing action of medicines explored in this paper is based on assumption that vital activity of the cell may be described in terms of the model of two states: resting state and excitation. According to available physiological…
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…
The neuron consumes energy from ATP hydrolysis to maintain a far-from-equilibrium steady state inside the cell, thus all physiological functions inside the cell are modulated by thermodynamics. The neurons that manage information encoding,…
A jump-diffusion process is proposed to describe the displacements performed by single myosin heads along actin filaments during the rising phases. The process consists of the superposition of a Wiener and a jump process, with jumps…
Methods of stochastic thermodynamics and hydrodynamics are applied to the a recently introduced model of active particles. The model consists of an overdamped particle subject to Gaussian coloured noise. Inspired by stochastic…