Related papers: Modeling compartmentalization within intracellular…
Most models of biological pattern formation are simulated on continuous domains even though cells are discrete objects that provide internal boundaries to the diffusion of regulatory components. In our previous papers on simulating…
Cellular membranes are elastic lipid bilayers that contain a variety of proteins, including ion channels, receptors, and scaffolding proteins. These proteins are known to diffuse in the plane of the membrane and to influence the bending of…
Multicellular organisms comprise a diverse collection of stable tissues built from different cell types. It remains unclear how large numbers of interacting cells can precisely coordinate their gene expression during tissue…
Diffusion generative models have emerged as a powerful framework for addressing problems in structural biology and structure-based drug design. These models operate directly on 3D molecular structures. Due to the unfavorable scaling of…
We analyze oscillatory instabilities for a coupled PDE-ODE system modeling the communication between localized spatially segregated dynamically active signaling compartments that are coupled through a passive extracellular bulk diffusion…
Continuum or hybrid modeling of bilayer membrane morphological dynamics induced by embedded proteins necessitates the identification of protein-membrane interfaces and coupling of deformations of two surfaces. In this article we developed…
Many cell functions are accomplished thanks to intracellular transport mechanisms of macromolecules along filaments. Molecular motors such as dynein or kinesin are proteins playing a primary role in these processes. The behavior of such…
Phenomena taking place in capacitively coupled plasmas with large electrodes and driven at very high frequencies are studied numerically utilizing a novel energy- and charge-conserving implicit fully electromagnetic particle-in-cell / Monte…
Extending deterministic compartments pharmacokinetic models as diffusions seems not realistic on biological side because paths of these stochastic processes are not smooth enough. In order to extend one compartment intra-veinous bolus…
Formulating quantitative and predictive models for tissue development requires consideration of the complex, stochastic gene expression dynamics, its regulation via cell-to-cell interactions, and cell proliferation. Including all of these…
Motor proteins are key players in intracellular transport processes and biological motion. Theoretical modeling of these systems has been achieved by the use of step processes on one-dimensional lattices. After a comprehensive introduction…
Temporally and spatially resolved measurements of protein transport inside cells provide important clues to the functional architecture and dynamics of biological systems. Fluorescence Recovery After Photobleaching (FRAP) technique has been…
Understanding the rules underlying organismal development is a major unsolved problem in biology. Each cell in a developing organism responds to signals in its local environment by dividing, excreting, consuming, or reorganizing, yet how…
The problem of reconstructing and identifying intracellular protein signaling and biochemical networks is of critical importance in biology today. We sought to develop a mathematical approach to this problem using, as a test case, one of…
The response of cells during spreading and motility is dictated by several multi-physics events, which are triggered by extracellular cues and occur at different time-scales. For this sake, it is not completely appropriate to provide a cell…
Complex systems often have features that can be modeled by advanced mathematical tools [1]. Of special interests are the features of complex systems that have a network structure as such systems are important for modeling technological and…
The dynamics of stochastic reaction networks within cells are inevitably modulated by factors considered extrinsic to the network such as for instance the fluctuations in ribsome copy numbers for a gene regulatory network. While several…
We consider molecular communication networks consisting of transmitters and receivers distributed in a fluidic medium. In such networks, a transmitter sends one or more signalling molecules, which are diffused over the medium, to the…
Multi-compartment Hodgkin-Huxley models are biophysical models of how electrical signals propagate throughout a neuron, and they form the basis of our knowledge of neural computation at the cellular level. However, these models have many…
We propose a novel approach to modeling cell migration in an anisotropic environment with biochemical heterogeneity and interspecies interactions, using as a paradigm glioma invasion in brain tissue under the influence of hypoxia-triggered…