Inherent structure versus geometric metric for state space discretization.

Inherent structure (IS) and geometry-based clustering methods are commonly used for analyzing molecular dynamics trajectories. ISs are obtained by minimizing the sampled conformations into local minima on potential/effective energy surface. The conformations that are minimized into the same energy basin belong to one cluster. We investigate the influence of the applications of these two methods of trajectory decomposition on our understanding of the thermodynamics and kinetics of alanine tetrapeptide. We find that at the microcluster level, the IS approach and root-mean-square deviation (RMSD)-based clustering method give totally different results. Depending on the local features of energy landscape, the conformations with close RMSDs can be minimized into different minima, while the conformations with large RMSDs could be minimized into the same basin. However, the relaxation timescales calculated based on the transition matrices built from the microclusters are similar. The discrepancy at the microcluster level leads to different macroclusters. Although the dynamic models established through both clustering methods are validated approximately Markovian, the IS approach seems to give a meaningful state space discretization at the macrocluster level in terms of conformational features and kinetics.

The combined influence of body weight support and running direction on self-selected movement patterns.

We investigated metabolic costs, muscle activity, and perceptual responses during forward and backward running at matched speeds at different body weight support (BWS) conditions. Participants ran forward and backward on a lower body positive pressure treadmill at 0%BWS, 20%BWS, and 50%BWS conditions. We measured oxygen uptake, carbon dioxide production, heart rate, muscle activity, and stride frequency. Additionally, we calculated metabolic cost of transport. Furthermore, we used rating of perceived exertion and feeling scale to investigate perceptual responses. Feeling scale during running was higher with increasing BWS (0-50%BWS), regardless of running direction (p < 0.05). Oxygen uptake, heart rate, and metabolic cost of transport were influenced by the interaction of running direction and BWS (p < 0.01). For example, metabolic cost of transport during backward running was greater than when running forward only when running at 0%BWS (i.e., 4.4 ± 1.1 and 5.8 ± 1.4 J/kg/m for forward and backward running, respectively: p < 0.001). However, rectus femoris muscle activity, stride frequency, and rating of perceived exertion during backward running were averages of 113.5%, 11.3%, and 2.8 rankings greater than when running forward, respectively, regardless of BWS (p < 0.001). We interpret our observations to indicate that environment (in the context of effective body weight) is a critical factor that determines self-selected movement patterns during forward and backward running.