Related papers: Multiscale Computational Modeling of Biofilm
We present teraflop-scale calculations of biomolecular electrostatics enabled by the combination of algorithmic and hardware acceleration. The algorithmic acceleration is achieved with the fast multipole method (FMM) in conjunction with a…
Single particle cryo-electron microscopy (EM) is an increasingly popular method for determining the 3-D structure of macromolecules from noisy 2-D images of single macromolecules whose orientations and positions are random and unknown. One…
Flowing granular materials segregate due to differences in particle size (driven by percolation) and density (driven by buoyancy). Modelling the segregation of mixtures of large/heavy particles and small/light particles is challenging due…
A micro-hydromechanical model for granular materials is presented. It combines the discrete element method (DEM) for the modeling of the solid phase and a pore-scale finite volume (PFV) formulation for the flow of an incompressible pore…
This work presents a microscale approach for simulating the dielectrophoresis (DEP) assembly of polarizable particles under an external electric field. The model is shown to capture interesting dynamical and topological features, such as…
We introduce a model for describing the dynamics of large numbers of interacting cells. The fundamental dynamical variables in the model are sub-cellular elements, which interact with each other through phenomenological intra- and…
An efficient computational approach for imaging binary-type physical properties suitable for various models in biomedical applications is developed and validated. The proposed methodology includes gradient-based multiscale optimization with…
Bacterial biofilms play a significant role in various fields that impact our daily lives, from detrimental public health hazards to beneficial applications in bioremediation, biodegradation, and wastewater treatment. However,…
Individual-based model (IBM) has been used to simulate and to design control strategies for dynamic systems that are subject to stochasticity and heterogeneity, such as infectious diseases. In the IBM, an individual is represented by a set…
Biological membranes constitute boundaries of cells and cell organelles. Physico-chemical mechanisms at the atomic scale are dictated by protein-lipid interaction strength, lipid composition, lipid distribution in the vicinity of the…
We propose a model of antibiotic diffusion through a bacterial biofilm when diffusion and/or absorption barriers develop in the biofilm. The idea of this model is: We deduce details of the diffusion process in a medium in which direct…
Over the last two decades, scientific literature has been blooming with various means of simulating epithelial cell colonies. Each of these simulations can be separated by their respective efficiency (expressed in terms of consumed…
Faceted shapes, such as polyhedra, are commonly found in systems of nanoscale, colloidal, and granular particles. Many interesting physical phenomena, like crystal nucleation and growth, vacancy motion, and glassy dynamics are challenging…
Ordinary differential equation models have become a standard tool for the mechanistic description of biochemical processes. If parameters are inferred from experimental data, such mechanistic models can provide accurate predictions about…
Biofilms are bacterial aggregates encased in a self-produced polymeric matrix which attach to moist surfaces and are extremely resistant to chemicals and antibiotics. Recent experiments show that their structure is defined by the interplay…
Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations…
This review examines the current state of research on microscale cellular changes during the drying of plant-based food materials (PBFM), with particular emphasis on computational modelling approaches. The review addresses the critical need…
The segmentation and tracking of living cells play a vital role within the biomedical domain, particularly in cancer research, drug development, and developmental biology. These are usually tedious and time-consuming tasks that are…
Advancements in computing power have made it possible to numerically simulate large-scale fluid-mechanical and/or particulate systems, many of which are integral to core industrial processes. Among the different numerical methods available,…
Nowadays, multiscale modelling is recognized as the most suitable way to study biological processes. Indeed, almost every phenomenon in nature exhibits a multiscale behaviour, i.e., it is the outcome of interactions that occur at different…