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A brief review is presented of the scaling of complex fluids, polymers and polyelectrolytes in solution and in confined geometry, in thermodynamical, structural and rheology properties using equilibrium and nonequilibrium dissipative…
3D modeling is becoming a well-developed field of medicine, but its applicability can be limited due to the lack of software allowing for easy utilizations of generated 3D visualizations. By leveraging recent advances in virtual reality, we…
We describe a 3D percolation-type approach to modeling of the processes of aging and certain other properties of tissues analyzed as systems consisting of interacting cells. Lattice sites are designated as regular (healthy) cells, senescent…
Simulations of biophysical systems inevitably include steps that correspond to time integrations of ordinary differential equations. These equations are often related to enzyme action in the synthesis and destruction of molecular species,…
Computational biomechanics of the brain for neurosurgery is an emerging area of research recently gaining in importance and practical applications. This review paper presents the contributions of the Intelligent Systems for Medicine…
With the increasing interplay between experimental and computational approaches at multiple length scales, new research directions are emerging in materials science and computational mechanics. Such cooperative interactions find many…
Diffusion models are important in tissue engineering as they enable an understanding of molecular delivery to cells in tissue constructs. As three-dimensional (3D) tissue constructs become larger, more intricate, and more clinically…
We investigate the convergence of solutions of a recently proposed diffuse interface/phase field model for cell blebbing by means of matched asymptotic expansions. It is a biological phenomenon that increasingly attracts attention by both…
Systems biology and whole-cell modelling are demanding increasingly comprehensive mathematical models of cellular biochemistry. These models require the development of simplified models of specific processes which capture essential…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
Mathematical modelling has a long history in the context of collective cell migration, with applications throughout development, disease and regenerative medicine. The aim of modelling in this context is to provide a framework in which to…
Tracking of plant cells in images obtained by microscope is a challenging problem due to biological phenomena such as large number of cells, non-uniform growth of different layers of the tightly packed plant cells and cell division.…
Colorization involves the synthesis of colors on a target image while preserving structural content as well as the semantics of the target image. This is a well-explored problem in 2D with many state-of-the-art solutions. We propose a novel…
Obtaining a rigorous and reliable method for linking computer simulations of polymer blends and composites at different length scales of interest is a highly desirable goal in soft matter physics. In this paper a multiscale modeling…
This paper provides a tutorial and survey for a specific kind of illustrative visualization technique: feature lines. We examine different feature line methods. For this, we provide the differential geometry behind these concepts and adapt…
Essential life processes take place across multiple space and time scales in living organisms but understanding their mechanistic interactions remains an ongoing challenge. Advanced multiscale modeling techniques are providing new…
Fueled by breakthrough technology developments, the biological, biomedical, and behavioral sciences are now collecting more data than ever before. There is a critical need for time- and cost-efficient strategies to analyze and interpret…
Bioscientists frequently seek to visualize the biological systems they have empirically characterized and reported in the literature. Realizing such visualizations requires biological structure modeling, an inherently complex process that…
We employ a multiscale approach to model the translocation of biopolymers through nanometer size pores. Our computational scheme combines microscopic Molecular Dynamics (MD) with a mesoscopic Lattice Boltzmann (LB) method for the solvent…
Declarative modeling uses symbolic expressions to represent models. With such expressions one can formalize high-level mathematical computations on models that would be difficult or impossible to perform directly on a lower-level simulation…