Related papers: A framework for protein and membrane interactions

Multi-omics studies often rely on pathway enrichment to interpret heterogeneous molecular changes, but pathway enrichment (PE)-based workflows inherit structural limitations of pathway resources, including curation lag, functional…

Starting from the concept of binary interactions between pairs of particles, a kinetic framework for the description of the action potential dynamics on a neural network is proposed. It consists of two coupled levels: the description of a…

Biofilms are complex structures which are inhabited by numerous amount of different species of microorganisms. Due to their ubiquity, they influence human life on an everyday basis. It is therefore important to understand the interactions…

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 and analyse a model for cell signalling processes in biological tissues. The model includes diffusion and nonlinear reactions on the cell surfaces, and both inter- and intracellular signalling. Using techniques from the theory of…

Our understanding of the physics of biological molecules, such as proteins and DNA, is limited because the approximations we usually apply to model inert materials are not in general applicable to soft, chemically inhomogeneous systems. The…

Context-free and context-sensitive formal grammars are often regarded as more appropriate to model proteins than regular level models such as finite state automata and Hidden Markov Models. In theory, the claim is well founded in the fact…

Biomolecular condensates constitute a newly recognized form of spatial organization in living cells. Although many condensates are believed to form as a result of phase separation, the physicochemical properties that determine the phase…

We construct a model to explore the hydrodynamic interactions of active inclusions in curved biological membranes. The curved membrane is modelled as a two dimensional layer of highly viscous fluid, surrounded by external solvents of…

The interaction of fluid membranes with a scaffold, which can be a planar surface or a more complex structure, is intrinsic to a number of systems - from artificial supported bilayers and vesicles to cellular membranes. In principle, these…

At the heart of the structured architecture and complex dynamics of biological systems are specific and timely interactions operated by biomolecules. In many instances, biomolecular agents are spatially confined to flexible lipid membranes…

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…

Protein-peptide interactions play essential functional roles in living organisms and their structural characterization is a hot subject of current experimental and theoretical research. Computational modeling of the structure of…

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…

A cell's behavior is a consequence of the complex interactions between its numerous constituents, such as DNA, RNA, proteins and small molecules. Cells use signaling pathways and regulatory mechanisms to coordinate multiple processes,…

We introduce a simulation strategy to consistently couple continuum biomembrane dynamics to the motion of discrete biological macromolecules residing within or on the membrane. The methodology is used to study the diffusion of integral…

Dialectical frameworks are a unifying model of formal argumentation, where argumentative relations between arguments are represented by assigning acceptance conditions to atomic arguments. Their generality allow them to cover a number of…

In this work, we present a computational formulation based on continuum mechanics to study the interaction of fluid membranes embedded with semiflexible filaments. This is motivated by systems in membrane biology, such as cytoskeletal…

Behavior Engineering (BE) provides a rigorous way to derive a formal specification of a software system from the requirements written in natural language. Its graphical specification language, Behavior Tree (BT), has been used with success…

Biomedical Question Answering systems play a critical role in processing complex medical queries, yet they often struggle with the intricate nature of medical data and the demand for multi-hop reasoning. In this paper, we propose a model…