Related papers: Bayesian dictionary learning estimation of cell me…
To maintain homeostasis, living cells process information with networks of interacting molecules. Traditional models for cellular information processing have focused on networks of chemical reactions between molecules. Here, we describe how…
Drug efficacy depends on its capacity to permeate across the cell membrane. We consider the prediction of passive drug-membrane permeability coefficients. Beyond the widely recognized correlation with hydrophobicity, we additionally…
Previous research based on electronic structure calculations and molecular dynamics (MD) simulations have demonstrated that graphdiyne (GDY) is a very suitable two-dimensional membrane for the separation of small molecules in a gas mixture…
In this paper, we present an approach for modeling bio-tissues that incorporates the variability in properties as part of their characteristics. This is achieved by considering the parameters of the model of a biomaterial to themselves be…
This paper concerns the use of the expectation-maximisation (EM) algorithm for inference in partially observed diffusion processes. In this context, a well known problem is that all except a few diffusion processes lack closed-form…
This paper is an introduction to the membrane potential equation for neurons. Its properties are described, as well as sample applications. Networks of these equations can be used for modeling neuronal systems, which also process images and…
This thesis investigates how the sub-structure of words can be accounted for in probabilistic models of language. Such models play an important role in natural language processing tasks such as translation or speech recognition, but often…
Liquid-liquid phase separation has emerged as a fundamental mechanism underlying intracellular organization, with evidence for it being reported in numerous different systems. However, there is a growing concern regarding the lack of…
We consider subdiffusion of a particle in a one-dimensional system with a thin partially permeable wall. Passing through the wall, the particle can be absorbed with a certain probability. We call such a wall partially permeable partially…
We present a theoretical model for the evolution of mixture concentrations in a micro-pervaporation device, similar to those recently presented experimentally. The described device makes use of the pervaporation of water through a thin PDMS…
Populations of heterogeneous cells play an important role in many biological systems. In this paper we consider systems where each cell can be modelled by an ordinary differential equation. To account for heterogeneity, parameter values are…
Diffusion of molecules within biological cells and tissues is strongly influenced by crowding. A key quantity to characterize diffusion is the particle lifetime, which is the time taken for a diffusing particle to exit by hitting an…
The analysis of diffusion processes in real-world propagation scenarios often involves estimating variables that are not directly observed. These hidden variables include parental relationships, the strengths of connections between nodes,…
We study both theoretically and experimentally the process of subdiffusive substance releasing from a thick membrane. The theoretical model uses the subdiffusion equation with fractional time derivative and specific boundary conditions at…
Understanding the oscillating behaviors that govern organisms' internal biological processes requires interdisciplinary efforts combining both biological and computer experiments, as the latter can complement the former by simulating…
Porous membranes are thin solid structures that allow the flow to pass through their tiny openings, called pores. Flow inertia may play a significant role in several filtration flows of natural and engineering interest. Here, we develop a…
Cells regulate themselves via dizzyingly complex biochemical processes called signaling pathways. These are usually depicted as a network, where nodes represent proteins and edges indicate their influence on each other. In order to…
We study the permeability of quasi two-dimensional porous structures of randomly placed overlapping monodisperse circular and elliptical grains. Measurements in microfluidic devices and lattice Boltzmann simulations demonstrate that the…
Diffusion rates through a membrane can be asymmetric, if the diffusing particles are spatially extended and the pores in the membrane have asymmetric structure. This phenomenon is demonstrated here via a deterministic simulation of a…
We propose a novel density based numerical method for uncertainty propagation under certain partial differential equation dynamics. The main idea is to translate them into objects that we call cellular probabilistic automata and to evolve…