Related papers: Computational studies of biomembrane systems: Theo…
A variety of computational models have been developed to describe active matter at different length and time scales. The diversity of the methods and the challenges in modeling active matter---ranging from molecular motors and cytoskeletal…
Scattering structure factors provide essential insight into material properties and are routinely obtained in experiments, computer simulations, and theoretical analyses. Different approaches favor different geometries of the material. In…
The organization of lipids in biological membranes is essential for cellular functions such as signal transduction and membrane trafficking. A major challenge is how to control lateral lipid composition in supported membranes which are…
Simulation models are an absolute necessity in the human and social sciences, which can only very exceptionally use experimental science methods to construct their knowledge. Models enable the simulation of social processes by replacing the…
The tensile force along a cylindrical lipid bilayer tube is proportional to the membrane's bending modulus and inversely proportional to the tube radius. We show that this relation, which is experimentally exploited to measure bending…
In tissues, cells in direct physical contact with each other can exchange ions or molecules via protein clusters called gap junctions that form channels across the membranes of adjacent cells. Here, we use a simplified biomimetic approach,…
This chapter reviews the purpose and use of models from the field of complex systems and, in particular, the implications of trying to use models to understand or make decisions within complex situations, such as policy makers usually face.…
Giant unilamellar vesicles (GUVs) composed of as few as three lipid species can phase separate into small-scale lipid domains with stripes and dots patterns. These patterns have been experimentally characterized in terms of how their size…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…
We consider the basic features of complex dynamical and control systems. Special attention is paid to the problems of synthesis of dynamical models of complex systems, construction of efficient control models, and to the development of…
Tubular and membranous shapes display a wide range of morphologies that are difficult to analyze within a common framework. By generalizing the classical Helfrich energy of biomembranes, we model them as solutions to a curvature…
Understanding and simulating how a quantum system interacts and exchanges information or energy with its surroundings is a ubiquitous problem, one which must be carefully addressed in order to establish a coherent framework to describe the…
Many living and physical systems such as cell aggregates, tissues or bacterial colonies behave as unconventional systems of particles that are strongly constrained by volume exclusion and shape interactions. Understanding how these…
Computer simulations have become an important tool across the biomedical sciences and beyond. For many important problems several different models or hypotheses exist and choosing which one best describes reality or observed data is not…
Relatively short peptides, such as toxins and antimicrobial-peptides, are known to insert themselves into cell membranes. On the basis of simple bead-spring models for the membrane lipids, the peptide, and water, detailed processes of the…
The mathematical models used to capture features of complex, biological systems are typically non-linear, meaning that there are no generally valid simple relationships between their outputs and the data that might be used to validate them.…
Recommender systems research is concerned with many aspects of recommender system behavior and effects than simply its effectiveness, and simulation can be a powerful tool for uncovering these effects. In this brief position paper, I…
Composition is a powerful principle for systems biology, focused on the interfaces, interconnections, and orchestration of distributed processes to enable integrative multiscale simulations. Whereas traditional models focus on the structure…
Recent development in computer processing power leads to new paradigms of how problems in many-body physics and especially polymer physics can be addressed. GPU parallel processors can be employed to generate millions of independent…
The cell membrane is inherently asymmetric and heterogeneous in its composition, a feature that is crucial for its function. Using atomistic molecular dynamics simulations, the physical properties of a 3-component asymmetric mixed lipid…