  Decomposition of biomolecular reaction networks into pathways is a powerful
approach to the analysis of metabolic and signalling networks. Current
approaches based on analysis of the stoichiometric matrix reveal information
about steady-state mass flows (reaction rates) through the network. In this
work we show how pathway analysis of biomolecular networks can be extended
using an energy-based approach to provide information about energy flows
through the network. This energy-based approach is developed using the
engineering-inspired bond graph methodology to represent biomolecular reaction
networks.
  The approach is introduced using glycolysis as an exemplar; and is then
applied to analyse the efficiency of free energy transduction in a biomolecular
cycle model of a transporter protein (Sodium-Glucose Transport Protein 1,
SGLT1).
  The overall aim of our work is to present a framework for modelling and
analysis of biomolecular reactions and processes which considers energy flows
and losses as well as mass transport.
