相关论文: Modelling the ATP production in mitochondria
Active Brownian particles (ABPs) function as self-driving agents that display non-equilibrium behavior through their pairwise interactions which lead to phase separation and vortex patterns in both soft matter and living systems. A…
Often gaining insight into the functioning of biomolecular systems requires to follow their dynamics along a microscopic reaction coordinate (RC) on a macroscopic time scale, which is beyond the reach of current all atom molecular dynamics…
We develop and evaluate two novel purpose-built deep learning (DL) models for synthesis of the arterial blood pressure (ABP) waveform in a cuff-less manner, using a single-site photoplethysmography (PPG) signal. We train and evaluate our DL…
We analyse a non-equilibrium exclusion process in which particles are created and annihilated in pairs and hop to the the right or to the left with different transition rates, $p$ and $q$, respectively. We have studied the dynamics of a…
In this work, we report a new method to simulate active Brownian particles (ABPs) in molecular dynamics (MD) simulations. Immersed in a fluid, each ABP consists of a head particle and a spherical phantom region of fluid where the flagellum…
Living systems maintain or increase local order by working against the Second Law of Thermodynamics. Thermodynamic consistency is restored as they dissipate heat, thereby increasing the net entropy of their environment. Recently introduced…
To sustain metabolism, intracellular ATP concentration must be regulated within an appropriate range. This coordination is achieved through the function of the AMP-activated protein kinase (AMPK), a cellular "fuel gauge" that is expressed…
The selection of an equilibrium state by maximising the entropy of a system, subject to certain constraints, is often powerfully motivated as an exercise in logical inference, a procedure where conclusions are reached on the basis of…
The stochastic entropy generated during the evolution of a system interacting with an environment may be separated into three components, but only two of these have a non-negative mean. The third component of entropy production is…
Active transport of biomolecular condensates and cell migration in collectives are fundamental to development, homeostasis, and processes such as cancer progression, wound healing, and infection response. Yet how these assemblies are…
F1F0 ATP synthase (ATPase) either facilitates the synthesis of ATP in the mitochondrial membranes and bacterial inner membranes in a process driven by the proton moving force (pmf), or uses the energy from ATP hydrolysis to pump protons…
The dynamics of cellular pattern formation is crucial for understanding embryonic development and tissue morphogenesis. Recent studies have shown that human dermal fibroblasts cultured on liquid crystal elastomers can exhibit an increase in…
We derive a mode-coupling theory (MCT) to describe the dynamics of tracer particles in dense systems of active Brownian particles (ABPs) in two spatial dimensions. The ABP undergo translational and rotational Brownian dynamics, and are…
This paper presents a novel blood pressure (BP) estimation method based on pulse transit time (PTT) and pulse arrival time (PAT) to estimate the systolic BP (SBP) and the diastolic BP (DBP). A data acquisition hardware is designed for…
Most of the calcium in the body is stored in bone. The rest is stored elsewhere, and calcium signalling is one of the most important mechanisms of information propagation in the body. Yet, many questions remain open. In this work, we…
Active Brownian particles (ABPs) are a model for nonequilibrium systems in which the constituent particles are self-propelled in addition to their Brownian motion. Compared to the well-studied mean first passage time (MFPT) of passive…
Cells generally convert external nutrient resources to support metabolismand growth. Understanding the thermodynamic efficiency of this conversion is essential to determine the general characteristics of cellular growth. Using a simple…
An ensemble of trajectories with dynamical activity and first-passage time (FPT) is considered in the context of the thermodynamics of trajectories. The relationship between the average FPT and the total change in entropy is determined,…
A comprehensive characterization of lattice Boltzmann (LB) schemes to perform warm fluid numerical simulations of particle wakefield acceleration (PWFA) processes is discussed in this paper. The LB schemes we develop hinge on the moment…
In this work, we study the dynamics of complex systems with time-dependent transition rates, focusing on $p$-adic analysis in modeling such systems. Starting from the master equation that governs the stochastic dynamics of a system with a…