Although chromatin organization and dynamics play a critical role in gene transcription, how they interplay remains unclear. To approach this issue, we investigated genome-wide chromatin behavior under various transcriptional conditions in living human cells using single-nucleosome imaging. While transcription by RNA polymerase II (RNAPII) is generally thought to need more open and dynamic chromatin, surprisingly, we found that active RNAPII globally constrains chromatin movements. RNAPII inhibition or its rapid depletion released the chromatin constraints and increased chromatin dynamics. Perturbation experiments of P-TEFb clusters, which are associated with active RNAPII, had similar results. Furthermore, chromatin mobility also increased in resting G0 cells and UV-irradiated cells, which are transcriptionally less active. Our results demonstrated that chromatin is globally stabilized by loose connections through active RNAPII, which is compatible with models of classical transcription factories or liquid droplet formation of transcription-related factors. Together with our computational modeling, we propose the existence of loose chromatin domain networks for various intra-/interchromosomal contacts via active RNAPII clusters/droplets.

Understanding chromatin organization and dynamics is important, since they crucially affect DNA functions. In this study, we investigate chromatin dynamics by statistically analyzing single-nucleosome movement in living human cells. Bimodal nature of the mean square displacement distribution of nucleosomes allows for a natural categorization of the nucleosomes as fast and slow. Analyses of the nucleosome–nucleosome correlation functions within these categories along with the density of vibrational modes show that the nucleosomes form dynamically correlated fluid regions (i.e., dynamic domains of fast and slow nucleosomes). Perturbed nucleosome dynamics by global histone acetylation or cohesin inactivation indicate that nucleosome–nucleosome interactions along with tethering of chromatin chains organize nucleosomes into fast and slow dynamic domains. A simple polymer model is introduced, which shows the consistency of this dynamic domain picture. Statistical analyses of single-nucleosome movement provide rich information on how chromatin is dynamically organized in a fluid manner in living cells.

The project was financed by the British Economic and Social Research Council and by INTAS. The Russian side of the project was directed by Vadim Borisov, Director of ISITO and concurrently ICFTU Representative for the CIS countries. We are very grateful to our colleagues, especially to Vadim, and to all the Russian trade unionists who collaborated with the research, none of whom bears any responsibility for the errors and omissions or the judgements in this book. We would also like to thank those Western colleagues with whom we have shared this research field over the past ten years, particularly Peter Fairbrother, David Mandel, Rick Simon, Jochen Tholen and Frank Hoffer. Researching Russian trade unions can be a depressing occupation unless one works with colleagues who are also friends and comrades. Some sections of the book are based on a report prepared by the authors for the ILO Task Force on Industrial Relations in 1996. We are grateful to the ILO for permission to use this material.

Computer simulations, using the Stillinger-Weber potential, have previously been employed to demonstrate a liquid-liquid transition in supercooled silicon near 1060 K. From calculations of electronic structure using an empirical psuedopotential, we show that silicon undergoes an associated metal to semimetal transition with a resistivity jump of roughly 1 order of magnitude. We show that the electronic states near the Fermi energy become localized in the low temperature phase, and that changes in electronic structure between the two phases arise from a change in atomic structure, and not from a change in density.

Experimental and computational model systems composed of frictionless particles in a fixed geometry have a finite number of distinct mechanically stable (MS) packings. The frequency of occurrence for each MS packing is highly variable and depends strongly on preparation protocol. Despite intense work, it is extremely difficult to predict a priori the MS packing probabilities. We describe a novel computational method for calculating the volume and other geometrical properties of the 'basin of attraction' for each MS packing. The basin of attraction for a MS packing contains all initial conditions in configuration space that map to that MS packing using a given preparation protocol. We find that the basin is a highly complex structure. For a compressive-quench-from-zero-density protocol, we show the existence of a small core volume of the basin around each MS packing for which all points map to that MS packing. However, in contrast to previous studies for supercooled liquids, glasses, and over-compressed jammed systems, we find that the MS packing probabilities are very weakly correlated with this core volume. Instead, MS packing probabilities obtained from compression protocols that use initially dilute configurations and do not allow particle overlaps (i.e. those relevant to granular media) are determined by complex geometric features of the basin of attraction that are distant from the MS packing. In particular, we find that the shape of the average basin profile function S(l), which gives the probability for a point on a hyper-spherical shell a distance l from a given MS packing to map back to that packing, can be described by a Γ-distribution with a peak that increases as the system size increases and as the quench rate decreases. We find a simple model which predicts S(l) for the extreme cases of very slow and fast quench rates.