CHARMM‐GUI 10 years for biomolecular modeling and simulation

Hybrid Modeling and Simulation of Biomolecular Networks

In a biological cell, cellular functions and the genetic regulatory apparatus are implemented and controlled by a network of chemical reactions in which regulatory proteins can control genes that produce other regulators, which in turn control other genes. Further, the feedback pathways appear to incorporate switches that result in changes in the dynamic behavior of the cell. This paper describ...

Visual Programming for Modeling and Simulation of Biomolecular Regulatory Networks

In this paper we introduce our new tool BIOSKETCHPAD that allows visual programming and modeling of biological regulatory networks. The tool allows biologists to create dynamic models of networks using a menu of icons, arrows, and pop-up menus, and translates the input model into CHARON, a modeling language for modular design of interacting multi-agent hybrid systems. Hybrid systems are systems...

Modeling, Analysis, Simulation, and Synthesis of Biomolecular Networks

Agent-based Modeling and Simulation of Biomolecular Reactions

We present an agent-based, three-dimensional model of phage lambda, a virus infecting E. coli which exhibits two phases, lysogenic and lytic. This process is useful for bio-based sensors or switches and is a widely studied gene regulatory system. We model system constituents as software agents. Complex system behavior emerges from local agent interactions. Agent based modeling lets us study how...

Variational Methods for Biomolecular Modeling

Structure, function and dynamics of many biomolecular systems can be characterized by the energetic variational principle and the corresponding systems of partial differential equations (PDEs). This principle allows us to focus on the identification of essential energetic components, the optimal parametrization of energies, and the efficient computational implementation of energy variation or m...