相关论文: Modelling the ATP production in mitochondria
Using an additivity property, we study particle-number fluctuations in a system of interacting self-propelled particles, called active Brownian particles (ABPs), which consists of repulsive disks with random self-propulsion velocities. From…
The two-dimensional Active Brownian Particles system is meant to be composed of hard disks, that show excluded volume interactions, usually simulated via molecular dynamics using pure repulsive potentials. We show that the softness of the…
We apply a holistic 2D Tetris-like model, where particles move based on prescribed rules, to investigate the flow rate enhancement from a hopper. This phenomenon was originally reported in the literature as a feature of placing an obstacle…
We study the stationary states of an over-damped active Brownian particle (ABP) in a harmonic trap in two dimensions, via mathematical calculations and numerical simulations. In addition to translational diffusion, the ABP self-propels with…
Molecular machines are stochastic systems that catalyze the energetic processes keeping living cells alive and structured. Inspired by the examples of F1-ATP synthase and the bacterial flagellum, we present a minimal model of an externally…
Motivated by the biologically important and complex phenomena of A\beta\ peptide aggregation in Alzheimer's disease, we introduce a model and simulation methodology for studying protein aggregation that includes extra-cellular aggregation,…
Changes in stoichiometric NiTi allotropes induced by hydrostatic pressure have been studied employing density functional theory. By modelling the pressure-induced transitions in a way that imitates quasi-static pressure changes, we show…
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…
We develop a physiological model of granulopoiesis which includes explicit modelling of the kinetics of the cytokine granulocyte colony-stimulating factor (G-CSF) incorporating both the freely circulating concentration and the concentration…
We present a rigorous statistical-mechanics theory of nonlinear many mode laser systems. An important example is the passively mode-locked laser that promotes pulse operation when a saturable absorber is placed in the cavity. It was shown…
We study the stochastic motion of a particle subject to spatially varying Lorentz force in the small-mass limit. The limiting procedure yields an additional drift term in the overdamped equation that cannot be obtained by simply setting…
Cytoplasmic dynein exhibits a directional processive movement on microtubule filaments and is known to move in steps of varying length based on the number of ATP molecules bound to it and the load that it carries. It is experimentally…
A general framework to describe a vast majority of biology-inspired systems is to model them as stochastic processes in which multiple couplings are in play at the same time. Molecular motors, chemical reaction networks, catalytic enzymes,…
We investigate bulk thermodynamic and microscopic structural properties of amorphous solids in the framework of the phase-field crystal (PFC) model. These are metastable states with a non-uniform density distribution having no long-range…
The theory of entropy production in nonequilibrium, Hamiltonian systems, previously described for steady states using partitions of phase space, is here extended to time dependent systems relaxing to equilibrium. We illustrate the main…
The structural dynamics of biological macromolecules, such as proteins, DNA/RNA, or complexes thereof, are strongly influenced by protonation changes of their typically many titratable groups, which explains their sensitivity to pH changes.…
This work introduces novel unconditionally stable operator splitting methods for solving the time dependent nonlinear Poisson-Boltzmann (NPB) equation for the electrostatic analysis of solvated biomolecules. In a pseudo-transient…
The synthesis of ATP, life's 'universal energy currency', is the most prevalent chemical reaction in biological systems, and is responsible for fueling nearly all cellular processes, from nerve impulse propagation to DNA synthesis. ATP…
A generic approach is proposed for the estimation of advanced biocrudes properties from liquefied biomass and the enthalpy of formation of biomass feedstocks applicable to the modeling of biomass conversion processes where the exact…
A novel mathematical model for the hypothalamic pituitary adrenal (HPA) axis is proposed to comprehend the oscillations observed in hormone concentration and potential dysfunction within the HPA axis in stressful situation. This model…