Correlative light and soft X-ray tomography of in situ mesoscale heterochromatin structure in intact cells.

Heterochromatin organization is critical to many genome-related programs including transcriptional silencing and DNA repair. While super-resolution imaging, electron microscopy, and multiomics methods have provided indirect insights into the heterochromatin organization, a direct measurement of mesoscale heterochromatin ultrastructure is still missing. We use a combination of correlative light microscopy and cryo-soft X-ray tomography (CLXT) to analyze heterochromatin organization in the intact hydrated state of human mammary fibroblast cells.

Analysis of Structural Change across the Liquid-Liquid Transition and the Widom Line in Supercooled Stillinger-Weber Silicon.

We consider the changes in the structure of supercooled Stillinger-Weber silicon at pressures at which the studied range of temperatures traverses the liquid-liquid transition or the "Widom line" (at which the isothermal compressibility or the specific heat exhibits a maximum). In addition to the conventional characterizations in terms of the pair-correlation function and bond orientational order, we analyze the statistics of rings in the bond network as well as the statistics of clusters of low density liquid (LDL)- and high density liquid (HDL)-like atoms. We investigate the nature of the change in these structural characterizations when the liquid-liquid transition line or the Widom line is crossed.

Kinetic reconstruction of free energies as a function of multiple order parameters.

A vast array of phenomena, ranging from chemical reactions to phase transformations, are analyzed in terms of a free energy surface defined with respect to a single or multiple order parameters. Enhanced sampling methods are typically used, especially in the presence of large free energy barriers, to estimate free energies using biasing protocols and sampling of transition paths. Kinetic reconstructions of free energy barriers of intermediate height have been performed, with respect to a single order parameter, employing the steady state properties of unconstrained simulation trajectories when barrier crossing is achievable with reasonable computational effort.

Liquid-liquid phase transition in deeply supercooled Stillinger-Weber silicon.

The existence of a phase transition between two distinct liquid phases in single-component network-forming liquids (e.g. water, silica, silicon) has elicited considerable scientific interest.

Thermodynamics and kinetics of crystallization in deeply supercooled Stillinger-Weber silicon.

We study the kinetics of crystallization in deeply supercooled liquid silicon employing computer simulations and the Stillinger-Weber three-body potential. The free energy barriers to crystallization are computed using umbrella sampling Monte Carlo simulations and from unconstrained molecular dynamics simulations using a mean first passage time formulation. We focus on state points that have been described in earlier work [S.