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Genome organization within the cell nucleus is a result of chromatin condensation achieved by histone tail-tail interactions and other nuclear proteins that counter the outward entropic pressure of the polymeric DNA. We probed the entropic swelling of chromatin driven by enzymatic disruption of these interactions in isolated mammalian cell nuclei. The(More)
Over the past two decades, measurements on individual stretched and twisted DNA molecules have helped define the basic elastic properties of the double helix and enabled real-time functional assays of DNA-associated molecular machines. Recently, new magnetic tweezers approaches for simultaneously measuring freely fluctuating twist and extension have begun(More)
DNA gyrase is a molecular motor that harnesses the free energy of ATP hydrolysis to introduce negative supercoils into DNA. A critical step in this reaction is the formation of a chiral DNA wrap. Here we observe gyrase structural dynamics using a single-molecule assay in which gyrase drives the processive, stepwise rotation of a nanosphere attached to the(More)
Single-molecule measurements of DNA twist and extension have been used to reveal physical properties of the double helix and to characterize structural dynamics and mechanochemistry in nucleoprotein complexes. However, the spatiotemporal resolution of twist measurements has been limited by the use of angular probes with high rotational drag, which prevents(More)
Many ribosomes simultaneously move on the same messenger RNA (mRNA), each synthesizing separately a copy of the same protein. In contrast to the earlier models, here we develop a "unified" theoretical model that not only incorporates the mutual exclusions of the interacting ribosomes, but also describes explicitly the mechanochemistry of each of these(More)
Debashish Chowdhury†,1 Aakash Basu, Ashok Garai, Philip Greulich, Katsuhiro Nishinari, Andreas Schadschneider, and Tripti Tripathi Department of Physics, Indian Institute of Technology, Kanpur 208016, India Institute for Theoretical Physics, University of Cologne, D-50937 Köln, Germany 3 Department of Aeronautics and Astronautics, Faculty of Engineering,(More)
Many ribosomes simultaneously move on the same messenger RNA (mRNA), each separately synthesizing the protein coded by the mRNA. Earlier models of ribosome traffic represent each ribosome by a “self-propelled particle” and capture the dynamics by an extension of the totally asymmetric simple exclusion process (TASEP). In contrast, here we develope a(More)
We show that arrival times for electromagnetic pulses measured through the rate of absorption in an ideal impedance matched detector are equivalent to the arrival times using the average flow of optical energy as proposed by Peatross [Phys. Rev. Lett. 84, 2370 (2000)]. We then investigate the transport of optical pulses through dispersive media with(More)
1 Department of Applied Physics, Stanford University, Stanford, California, USA 2 Department of Bioengineering, Stanford University, Stanford, California, USA 3 Department of Molecular and Cell Biology, University of California, Berkeley, California, USA 4 Department of Structural Biology, Stanford University Medical Center, Stanford, California, USA 5(More)