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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…
Implementing a laboratory activity involves a complex interplay among learning goals, available resources, feedback about the existing course, best practices for teaching, and an overall philosophy about teaching labs. Building on our…
We present a multilevel Monte Carlo simulation method for analysing multi-scale physical systems via a hierarchy of coarse-grained representations, to obtain numerically-exact results, at the most detailed level. We apply the method to a…
Computer simulations of coarse-grained molecular models for amphiphilic systems can provide insight into the the structure of amphiphiles at interfaces. They can help to identify the factors that determine the phase behavior, and they can…
We discuss the role coarse-grained models play in the investigation of the structure and thermodynamics of bilayer membranes, and we place them in the context of alternative approaches. Because they reduce the degrees of freedom and employ…
A brief review of modeling and simulation methods for a study of polymers at interfaces is provided. When studying truly multiscale problems as provided by realistic polymer systems, coarse graining is practically unavoidable. In this…
A simulation technique is described for quantifying the contribution of three-body interactions to the thermodynamical properties of coarse-grained representations of complex fluids. The method is based on comparing the third virial…
Integrative biological simulations have a varied and controversial history in the biological sciences. From computational models of organelles, cells, and simple organisms, to physiological models of tissues, organ systems, and ecosystems,…
During the last decades, medical observations and multiscale data concerning tumor growth are mounting. At the same time, contemporary imaging techniques well established in clinical practice, provide a variety of information on real-time,…
This paper presents a comprehensive survey of various established mathematical models pertaining to Somitogenesis, a biological process. The study begins by revisiting and replicating the findings from prominent research papers in this…
We provide a visualization model that targets the visualization of Protein-Protein Interactions(PPI) and combines it with a super view based on publications and methods to extract interactions. Although there are several existing tools, our…
Mathematical models are increasingly a part of microbiological research. Here, we share our perspective on how modeling advances the discipline by: (i) enforcing logical consistency, (ii) enabling quantitative prediction, (iii) extracting…
Coupled natural systems are generally modeled at multiple abstraction levels. Both structural scale and behavioral complexity of these models are determinants in the kinds of questions that can be posed and answered. As scale and complexity…
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…
The rapid advances in 3D scanning and acquisition techniques have given rise to the explosive increase of volumetric digital models in recent years. This dissertation systematically trailblazes a novel volumetric modeling framework to…
We present LayerPCM, an extension of the polarizable-continuum model coupled to real-time time-dependent density-functional theory for an efficient and accurate description of the electrostatic interactions between molecules and…
The aim of this chapter is to provide a brief introduction into the basics of a top-down multilevel tumor dynamics modeling method primarily based on discrete entity consideration and manipulation. The method is clinically oriented, one of…
Functional aspects as well as the influence of integration technology on the system behavior have to be considered in the 3D integration design process of micro systems. Therefore, information from different physical domains has to be…
This paper presents a theoretical model for interactive visualization literacy to describe how people use interactive data visualizations and systems. Literacies have become an important concept in describing modern life skills, with…
Organogenesis is a tightly regulated process that has been studied experimentally for decades. Computational models can help to integrate available knowledge and to better understand the underlying regulatory logic. We are currently…