Related papers: Bigraphical models for protein and membrane intera…
Mathematical and computational models can assist in gaining an understanding of cell behavior at many levels of organization. Here, we review models in the literature that focus on eukaryotic cell motility at 3 size scales: intracellular…
We advocate the use of qualitative models in the analysis of large biological systems. We show how qualitative models are linked to theoretical differential models and practical graphical models of biological networks. A new technique for…
Compared to pure fluids, binary mixtures display a very diverse phase behavior, which depends sensitively on the parameters of the microscopic potential. Here we investigate the phase diagrams of simple model mixtures by use of a…
Mixtures of several macromolecular species can lead to the formation of higher-order structures that often display non-ideal mixing behavior. In this work, we propose a minimal model of a quaternary system which considers the formation of a…
We report a numerical simulation for the phase diagram of a simple two dimensional model, similar to one proposed by Noro and Frenkel [J. Chem. Phys. \textbf{114}, 2477 (2001)] for membrane proteins, but one that includes the role of the…
Macromolecular complexation leading to coupling of two or more cellular membranes is a crucial step in a number of biological functions of the cell. While other mechanisms may also play a role, adhesion always involves the fluctuations of…
Active particle systems of interacting self-propelled particles offer a versatile framework for modeling complex systems. When employed to describe aspects of animal behavior, the complexity of animal movement and decision-making often…
Biological systems are notorious for complex behavior within short timescales (e.g. metabolic activity) and longer time scales (e.g. evolutionary selection), along with their complex spatial organization. Because of their complexity and…
Biomedical networks (or graphs) are universal descriptors for systems of interacting elements, from molecular interactions and disease co-morbidity to healthcare systems and scientific knowledge. Advances in artificial intelligence,…
As the frontiers of biology become increasingly interdisciplinary, the physics education community has engaged in ongoing efforts to make physics classes more relevant to life sciences majors. These efforts are complicated by the many…
We use dialgebras, generalising both algebras and coalgebras, as a complement of the standard coalgebraic framework, aimed at describing the semantics of an interactive system by the means of reaction rules. In this model, interaction is…
Complexes of physically interacting proteins are one of the fundamental functional units responsible for driving key biological mechanisms within the cell. Their identification is therefore necessary not only to understand complex formation…
The membrane curvature of cells and intracellular compartments continuously adapts to enable cells to perform vital functions, from cell division to signal trafficking. Understanding how membrane geometry affects these processes in vivo is…
We introduce Bi-GNN for modeling biological link prediction tasks such as drug-drug interaction (DDI) and protein-protein interaction (PPI). Taking drug-drug interaction as an example, existing methods using machine learning either only…
The structure and function of biological molecules are strongly influenced by the water and dissolved ions that surround them. This aqueous solution (solvent) exerts significant electrostatic forces in response to the biomolecule's…
Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists…
Cellular membranes are a heterogeneous mix of lipids, proteins and small molecules. Special groupings of saturated lipids and cholesterol form a liquid-ordered phase, known as `lipid rafts,' serving as platforms for signaling, trafficking…
We introduce a new model of proteins, which extends and enhances the traditional graphical representation by associating a combinatorial object called a fatgraph to any protein based upon its intrinsic geometry. Fatgraphs can easily be…
We present a method for logical specification of the behavior of a system based on the specification of its components and for representing and specifying the effect of a class of communication "signaling pathways" among them. Variations in…
Spherical symmetry is ubiquitous in nature. It's therefore unfortunate that spherical system simulations are so hard, and require complete spheres with millions of interacting particles. Here we introduce an approach to model spherical…