Related papers: Multiscale Computational Modeling of Biofilm
Model biomembrane systems play a crucial role in advancing biomedical research by providing simplified yet effective platforms for exploring complex biological mechanisms. These systems span a wide range of scales, from…
A surface integral representation of Maxwell's equations allows the efficient electromagnetic (EM) modeling of three-dimensional structures with a two-dimensional discretization, via the boundary element method (BEM). However, existing BEM…
The evolution of local defects such as dislocations and cracks often determines the performance of engineering materials. For a proper description and understanding of these phenomena, one needs to descend to a very small scale, at which…
This chapter provides a brief introduction to the theory and practice of spatial stochastic simulations. It begins with an overview of different methods available for biochemical simulations highlighting their strengths and limitations.…
The fundamental understanding of how cells physically interact with each other and their environment is key to understanding their organisation in living tissues. Over the past decades several computational methods have been developed to…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
Formation of bacterial colonies as biofilm on the surface/interface of various objects has the potential to impact not only human health and disease but also energy and environmental considerations. Biofilms can be regarded as soft…
Even though the term `organic electronics' evokes rather organic devices, a significant part of its scope deals with physical properties of `active elements' such as organic films and interfaces. Examination of the film growth and the…
Accurate and scalable universal interatomic potentials are key for understanding material properties at the atomic level, a task often hindered by the steep computational scaling. Although recent developments of machine learning potential…
Cell blebs are protrusions of the cell membrane and can be instrumental for cell migration. We derive a continuum model for the mechanical and geometrical aspects of the onset of blebbing in terms of a force balance. It is abstract and…
The current study explores an artificial intelligence framework for measuring the structural features from microscopy images of the bacterial biofilms. Desulfovibrio alaskensis G20 (DA-G20) grown on mild steel surfaces is used as a model…
Biofilms are communities of microorganisms that grow on virtually all surfaces with sufficient nutrients including aquatic and industrial water systems and medical devices. Biofilms are complex, structured communities where the interplay of…
The discrete element method (DEM) is a powerful tool for simulating granular soils, but its high computational demand often results in extended simulation times. While the effect of particle size has been extensively studied, the potential…
The understanding of morphogenesis in living organisms has been renewed by tremendous progressin experimental techniques that provide access to cell-scale, quantitative information both on theshapes of cells within tissues and on the genes…
Structure, function and dynamics of many biomolecular systems can be characterized by the energetic variational principle and the corresponding systems of partial differential equations (PDEs). This principle allows us to focus on the…
The applicability of computational models to the biological world is an active topic of debate. We argue that a useful path forward results from abandoning hard boundaries between categories and adopting an observer-dependent, pragmatic…
Cellular bioelectricity describes the biological phenomenon in which cells in living tissue generate and maintain patterns of voltage gradients induced by differing concentrations of charged ions. A growing body of research suggests that…
We propose a general multiscale approach for the mechanical behavior of three-dimensional networks of macromolecules undergoing strain-induced unfolding. Starting from a (statistically based) energetic analysis of the macromolecule…
This chapter summarizes several approaches combining theory, simulation and experiment that aim for a better understanding of phenomena in lipid bilayers and membrane protein systems, covering topics such as lipid rafts, membrane mediated…
We introduce a scheme for molecular simulations, the Deep Potential Molecular Dynamics (DeePMD) method, based on a many-body potential and interatomic forces generated by a carefully crafted deep neural network trained with ab initio data.…