Related papers: Simulating and model checking membrane systems usi…
Most available tools propose simulation frameworks to study models of biological systems, but simulation only explores a few of the most probable behaviours of the system. On the contrary, techniques such as model checking, coming from…
The molecular computing has been successfully employed to solve more and more complex computation problems. However, as an important complex problem, the model checking are still far from fully resolved under the circumstance of molecular…
The analysis of cyber-physical systems (CPS) is challenging due to the large state space and the continuous changes occurring in their constituent parts. Design practices favor modularity to help reducing this complexity. In a previous…
Many complex systems can be modeled as multiagent systems in which the constituent entities (agents) interact with each other. The global dynamics of such a system is determined by the nature of the local interactions among the agents.…
The application of systems and control theory to membrane physiology is presented here. Modeling efforts have focused on describing those physiologically realistic mechanisms which govern the regulation of membrane permeability in nerve.…
Rule-based modeling is a powerful way to model kinetic interactions in biochemical systems. Rules enable a precise encoding of biochemical interactions at the resolution of sites within molecules, but obtaining an integrated global view…
Many of the most important processes in cells take place on and across membranes. With the rise of an impressive array of powerful quantitative methods for characterizing these membranes, it is an opportune time to reflect on the structure…
System correctness is one of the most crucial and challenging objectives in software and hardware systems. With the increasing evolution of connected and distributed systems, ensuring their correctness requires the use of formal…
Recent developments in lipid membrane models for simulations are reviewed. To reduce computational costs, various coarse-grained molecular models have been proposed. Among them, implicit solvent (solvent-free) molecular models are…
The Plan Execution Interchange Language (PLEXIL) is a synchronous language developed by NASA to support autonomous spacecraft operations. In this paper, we propose a rewriting logic semantics of PLEXIL in Maude, a high-performance logical…
Biological membranes constitute boundaries of cells and cell organelles. Physico-chemical mechanisms at the atomic scale are dictated by protein-lipid interaction strength, lipid composition, lipid distribution in the vicinity of the…
Reconfigurable multi-agent systems consist of a set of autonomous agents, with integrated interaction capabilities that feature opportunistic interaction. Agents seemingly reconfigure their interactions interfaces by forming collectives,…
ELAN is a powerful language and environment for specifying and prototyping deduction systems in a language based on rewrite rules controlled by strategies. Timed automata is a class of continuous real-time models of reactive systems for…
ELAN is a powerful language and environment for specifying and prototyping deduction systems in a language based on rewrite rules controlled by strategies. Timed automata is a class of continuous real-time models of reactive systems for…
Cells control fluid flows with a spatial and temporal precision that far exceeds the capabilities of current microfluidic technologies. Cells achieve this superior spatio-temporal control by harnessing dynamic networks of cytoskeleton and…
As an effective method to deliver external materials into biological cells, microinjection has been widely applied in the biomedical field. However, the cognition of cell mechanical property is still inadequate, which greatly limits the…
A discourse strategy is a strategy for communicating with another agent. Designing effective dialogue systems requires designing agents that can choose among discourse strategies. We claim that the design of effective strategies must take…
Multiset rewriting systems provide a formalism particularly suitable for the description of biological systems. We present an extension of this formalism with additional controls on the derivations as a tool for reducing possible…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
Peripheral membrane proteins can reversibly and specifically bind to biological membranes to carry out functions such as cell signalling, enzymatic activity, or membrane remodelling. Structures of these proteins and of their lipid-binding…