The respiratory system relies heavily on efficient species transport and transformations to maintain homeostasis. Disruptions in these processes are integral to the pathogenesis of numerous respiratory diseases. This section reviews the critical roles of species transport by diffusion and convection and the coupling with transformation such as reaction mechanisms and biomechanics in respiratory pathophysiology, with a specific emphasis on chronic obstructive pulmonary disease (COPD) and emphysema. Chemical species transport in the respiratory system predominantly occurs via diffusion. Diffusion is driven by concentration gradients, ensuring vital gases such as oxygen and carbon dioxide are adequately exchanged between alveoli and blood . The integrity of this process is essential; any impediments can significantly affect respiratory function. Recent studies highlight that impaired diffusion due to thickened alveolar membranes, common in pulmonary fibrosis, leads to decreased oxygen uptake and consequent systemic hypoxia .