104 citations · 143 across the 5 of their papers we have counts for
5 papers
Scaffold-mediated Nucleation of Protein Signaling Complexes: Elementary Principles
Jin Yang, William S. Hlavacek
Proteins with multiple binding sites play important roles in cell signaling systems by nucleating protein complexes in which, for example, enzymes and substrates are co-localized.…
Monte Carlo Algorithm for Simulating Reversible Aggregation of Multisite Particles
Qiang Chang, Jin Yang
We present an efficient and exact Monte Carlo algorithm to simulate reversible aggregation of particles with dedicated binding sites. This method introduces a novel data structure…
Rule-based Modeling and Simulation of Biochemical Systems with Molecular Finite Automata
Jin Yang, Xin Meng, William S. Hlavacek
We propose a theoretical formalism, molecular finite automata (MFA), to describe individual proteins as rule-based computing machines. The MFA formalism provides a framework for mo…
Rejection-free kinetic Monte Carlo simulation of multivalent biomolecular interactions
Jin Yang, William S. Hlavacek
The system-level dynamics of multivalent biomolecular interactions can be simulated using a rule-based kinetic Monte Carlo method in which a rejection sampling strategy is used to…
Kinetic Monte Carlo Method for Rule-based Modeling of Biochemical Networks
Jin Yang, Michael I. Monine, James R. Faeder +1
We present a kinetic Monte Carlo method for simulating chemical transformations specified by reaction rules, which can be viewed as generators of chemical reactions, or equivalentl…