Related papers: Bigraphical models for protein and membrane intera…
It has recently been demonstrated that many biological networks exhibit a scale-free topology where the probability of observing a node with a certain number of edges (k) follows a power law: i.e. p(k) ~ k^-g. This observation has been…
Studying systems where many individual bodies in motion interact with one another is a complex and interesting area. Simple mechanisms that may be determined for biological, chemical, or physical reasons can lead to astonishingly complex…
Bigraphs are a versatile modelling formalism that allows easy expression of placement and connectivity relations in a graphical format. System evolution is user defined as a set of rewrite rules. This paper presents a practical, yet…
Cellular membranes exhibit a large variety of shapes, strongly coupled to their function. Many biological processes involve dynamic reshaping of membranes, usually mediated by proteins. This interaction works both ways: while proteins…
A distinguishing feature of a multicellular living system is that it operates at various scales, from the intracellular to organismal. Very little is known at present on how tissue level properties are related to cell and subcellular…
A notion of biologic system or just a system implies a functional wholeness of comprising system components. Positive and negative feedback are the examples of how the idea to unite anatomical elements in the whole functional structure was…
The inherent complexity of biological systems gives rise to complicated mechanistic models with a large number of parameters. On the other hand, the collective behavior of these systems can often be characterized by a relatively small…
Molecular interactions have widely been modelled as networks. The local wiring patterns around molecules in molecular networks are linked with their biological functions. However, networks model only pairwise interactions between molecules…
Quantitative modeling has become an essential tool in modern biophysics, driven by advances in both experimental techniques and theoretical frameworks. Powerful high-resolution techniques now provide detailed datasets spanning molecular to…
Membrane bending is an extensively studied problem from both modeling and experimental perspectives because of the wide implications of curvature generation in cell biology. Many of the curvature generating aspects in membranes can be…
The self-organization of proteins into enriched compartments and the formation of complex patterns are crucial processes for life on the cellular level. Liquid-liquid phase separation is one mechanism for forming such enriched compartments.…
Cellular function is widely believed to be organized in a modular fashion. On all scales and at all levels of complexity, relatively independent sub-units perform relatively independent sub-tasks of biological function. This functional…
The interaction between nano- or micro-sized particles and cell membranes is of crucial importance in many biological and biomedical applications such as drug and gene delivery to cells and tissues. During their cellular uptake, the…
We introduce a new, simplified model of proteins, which we call protein metastructure. The metastructure of a protein carries information about its secondary structure and $\beta$-strand conformations. Furthermore, protein metastructure…
We study membrane-protein interactions and membrane-mediated protein-protein interactions by Monte Carlo simulations of a generic coarse-grained model for lipid bilayers with cylindrical hydrophobic inclusions. The strength of the…
We study a physical model for the interaction between general inclusions bound to fluid membranes that possess finite tension, as well as the usual bending rigidity. We are motivated by an interest in proteins bound to cell membranes that…
We propose a variant of the CCS process algebra with new features aiming at allowing multiscale modelling of biological systems. In the usual semantics of process algebras for modelling biological systems actions are instantaneous. When…
We present an overview of phase field modeling of active matter systems as a tool for capturing various aspects of complex and active interfaces. We first describe how interfaces between different phases are characterized in phase field…
Numerous cellular functions rely on protein$\unicode{x2013}$protein interactions. Efforts to comprehensively characterize them remain challenged however by the diversity of molecular recognition mechanisms employed within the proteome. Deep…
We present the bond-calculus, a process algebra for modelling biological and chemical systems featuring nonlinear dynamics, multiway interactions, and dynamic bonding of agents. Mathematical models based on differential equations have been…