Force-clamp experiments reveal the free energy profile and diffusion coefficient of the collapse of proteins

We present force-clamp data on the collapse of ubiquitin polyproteins in response to a quench in the force. These nonequilibrium trajectories are analyzed using a general method based on a diffusive assumption of the end-to-end length to reconstruct a downhill free energy profile at 5pN and an energy plateau at 10pN with a slow diffusion coefficient on the order of~100nm^2/s. The shape of the free energy and its linear scaling with the protein length give validity to a physical model for the collapse. However, the length independent diffusion coefficient suggests that internal rather than viscous friction dominates and thermal noise is needed to capture the variability in the measured times to collapse.Comment: 12 pages, 4 figure

On the Structure of the Orion A Cloud and the Formation of the Orion Nebula Cluster

We suggest that the Orion A cloud is gravitationally collapsing on large scales, and is producing the Orion Nebula Cluster due to the focusing effects of gravity acting within a finite cloud geometry. In support of this suggestion, we show how an elliptical rotating sheet of gas with a modest density gradient along the major axis can collapse to produce a structure qualitatively resembling Orion A, with a fan-shaped structure at one end, ridges or filaments along the fan, and a narrow curved filament at the other end reminiscent of the famous integral-shaped filament. The model produces a local concentration of mass within the narrow filament which in principle could form a dense cluster of stars like that of the Orion Nebula. We suggest that global gravitational contraction might be a more common feature of molecular clouds than previously recognized, and that the formation of star clusters is a dynamic process resulting from the focusing effects of gravity acting upon the geometry of finite clouds.Comment: 23 pages, 6 figures, to appear in the Astrophysical Journa