We study by molecular dynamics simulations supercooled water with the TIP4P/2005 potential. This model is able to predict many properties of water in a large range of the thermodynamic space in agreement with experiments. We explore the dynamical behavior and, in particular, the self intermediate scattering function of the oxygen atoms. We find that the structural relaxation in the range of mild supercooling is in agreement with the Mode Coupling Theory (MCT). The ideal MCT crossover takes place at decreasing temperature with increasing density. Deviations from the MCT behavior are found upon further supercooling. A crossover from the MCT, fragile, regime to a strong, Arrhenius, regime is found and it is connected to the presence of a liquid-liquid phase transition and the Widom line emanating from the liquid-liquid critical point.

To image the accessible genome at nanometer scale in situ , we developed 3D ATAC-PALM which integrates Assay for Transposase-Accessible Chromatin with visualization, PALM super-resolution imaging and lattice light-sheet microscopy. Multiplexed with Oligopaint DNA-FISH, RNA-FISH and protein fluorescence, 3D ATAC-PALM connected microscopy and genomic data, revealing spatially-segregated accessible chromatin domains (ACDs) that enclose active chromatin and transcribed genes. Using these methods to analyze genetically perturbed cells, we demonstrated that genome architectural protein CTCF prevents excessive clustering of accessible chromatin and decompacts ACDs. These results highlight 3D ATAC-PALM as a useful tool to probe the structure and organizing mechanism of the genome.

We study the translational single particle dynamics of hydration water of lysozyme upon cooling by means of molecular dynamics simulations. We find that water close to the protein exhibits two distinct relaxations. By characterizing their behavior upon cooling, we are able to assign the first relaxation to the structural α-relaxation also present in bulk water and in other glass-forming liquids. The second, slower, relaxation can be ascribed to a dynamic coupling of hydration water motions to the fluctuations of the protein structure. Both relaxation times exhibit crossovers in the behavior upon cooling. For the α-process, we find upon cooling a crossover from a fragile behavior to a strong behavior at a temperature which is about five degrees higher than that of bulk water. The long-relaxation time appears strictly connected to the protein motion as it shows upon cooling a temperature crossover from a strong behavior with a lower activation energy to a strong behavior with a higher activation energy. The crossover temperature coincides with the temperature of the protein dynamical transition. These findings can help experimentalists to disentangle the different information coming from total correlators and to better characterize hydration water relaxations in different biomolecules.

Mammalian chromosomes are organized into megabase-sized compartments that are further subdivided into topologically associated domains (TADs). While the formation of TADs is dependent on Cohesin, the mechanism behind compartmentalization remains enigmatic. Here, we show that the bromodomain and extraterminal (BET) family scaffold protein BRD2 promotes spatial mixing and compartmentalization of active chromatin after Cohesin loss. This activity is independent of transcription but requires BRD2 to recognize acetylated targets through its double bromodomain and interact with binding partners with its low complexity domain. Notably, genome compartmentalization mediated by BRD2 is antagonized on one hand by Cohesin and on This work is licensed under a Creative Commons Attribution 4.0 International License, which allows reusers to distribute, remix, adapt, and build upon the material in any medium or format, so long as attribution is given to the creator. The license allows for commercial use.

Bronchospasm compresses the bronchial epithelium, and this compressive stress has been implicated in asthma pathogenesis. However, the molecular mechanisms by which this compressive stress alters pathways relevant to disease are not well understood. Using air-liquid interface cultures of primary human bronchial epithelial cells derived from non-asthmatic donors and asthmatic donors, we applied a compressive stress and then used a network approach to map resulting changes in the molecular interactome. In cells from non-asthmatic donors, compression by itself was sufficient to induce inflammatory, late repair, and fibrotic pathways. Remarkably, this molecular profile of non-asthmatic cells after compression recapitulated the profile of asthmatic cells before compression. Together, these results show that even in the absence of any inflammatory stimulus, mechanical compression alone is sufficient to induce an asthma-like molecular signature. Bronchial epithelial cells (BECs) form a physical barrier that protects pulmonary airways from inhaled irritants and invading pathogens 1,2. Moreover, environmental stimuli such as allergens, pollutants and viruses can induce constriction of the airways 3 and thereby expose the bronchial epithelium to compressive mechanical stress. In BECs, this compressive stress induces structural, biophysical, as well as molecular changes 4,5 , that interact with nearby mesenchyme 6 to cause epithelial layer unjamming 1 , shedding of soluble factors, production of matrix proteins, and activation matrix modifying enzymes, which then act to coordinate inflammatory and remodeling processes 4,7-10. Growing evidence supports the notion that mechanical stress in the airway induces not only developmental, homeostatic and reparative responses in the healthy lung but also pathophysiologic processes in the asthmatic lung 2,11-13. For example, mechanical stimuli induce early inflammatory and remodeling factors 6,7,14,15 , microRNAs (miRs) 16,17 , and cell proliferation 18. Using protein-protein interaction networks, here we compare responses to compressive stress in human BECs (HBECs) obtained from non-asthmatic versus asthmatic donors. Our hypothesis was, that using a systems biology approach to examine the effect of mechanical forces acting on structural cells in the airway, will elucidate the complex transcriptional programs that contribute to disease development and pathophysiology.

We derive by computer simulation the radial distribution functions of water confined in a silica pore modeled to reproduce MCM-41. We perform the calculations in a range of temperatures from ambient to deep supercooling for the subset of water molecules that reside in the inner shell (free water) by applying the excluded volume corrections. By comparing with bulk water we find that the first shell of the oxygen-oxygen and hydrogen-hydrogen radial distribution functions is less sharp and the first minimum fills in while the oxygen-hydrogen structure does not significantly change, indicating that the free water keeps the hydrogen bond short range order. The two body excess entropy of supercooled water is calculated from the radial distribution functions. We connect the behavior of this function to the relaxation time of the same system already studied in previous simulations. We show that the two body entropy changes its behavior in coincidence with the crossover of the relaxation time from the mode coupling fragile to the strong Arrhenius regime. As for bulk water also in confinement, the two body entropy has a strict connection with the dynamical relaxation.

In development of an embryo, healing of a wound, or progression of a carcinoma, a requisite event is collective epithelial cellular migration. For example, cells at the advancing front of a wound edge tend to migrate collectively, elongate substantially, and exert tractions more forcefully compared with cells many ranks behind. With regards to energy metabolism, striking spatial gradients have recently been reported in the wounded epithelium, as well as in the tumor, but within the wounded cell layer little is known about the link between mechanical events and underlying energy metabolism. Using the advancing confluent monolayer of MDCKII cells as a model system, here we report at single cell resolution the evolving spatiotemporal fields of cell migration speeds, cell shapes, and traction forces measured simultaneously with fields of multiple indices of cellular energy metabolism. Compared with the epithelial layer that is unwounded, which is non-migratory, solid-like and jammed, the leading edge of the advancing cell layer is shown to become progressively more migratory, fluid-like, and unjammed. In doing so the cytoplasmic redox ratio becomes progressively smaller, the NADH lifetime becomes progressively shorter, and the mitochondrial membrane potential and glucose uptake become progressively larger. These observations indicate that a metabolic shift toward glycolysis accompanies collective cellular migration but show, further, that this shift occurs throughout the cell layer, even in regions where associated changes in cell shapes, traction forces, and migration velocities have yet to penetrate. In characterizing the wound healing process these morphological, mechanical, and metabolic observations, taken on a cell-by-cell basis, comprise the most comprehensive set of biophysical data yet reported. Together, these data suggest the novel hypothesis that the unjammed phase evolved to accommodate fluid-like migratory dynamics during episodes of tissue wound healing, development, and plasticity, but is more energetically expensive compared with the jammed phase, which evolved to maintain a solid-like non-migratory state that is more energetically economical.

We perform an accurate analysis of the density self-correlation functions of TIP4P/2005 supercooled water on approaching the region of the liquid-liquid critical point. In a previous work on this model, we provided evidence of a fragile to strong crossover of the dynamical behavior in the deep supercooled region. The structural relaxation follows the Mode Coupling theory in the fragile region and then deviates from Mode Coupling regime to a strong Arrhenius behavior. This crossover is particularly important in water because it is connected to the thermodynamics of the supercooled region. To better understand the origin of this crossover, we compute now the Van Hove self-correlation functions. In particular we aim at investigating the presence and the role of the hopping phenomena that are the cause of the fragile to strong crossover in simple liquids. In TIP4P/2005 water, we find hopping processes too and we analyze how they depend on temperature and density upon approaching the fragile to strong crossover and the Mode Coupling ideal crossover temperature. Our results show that water behaves like a simple glass former. After an initial ballistic regime, the cage effect dominates the mild supercooled region, with diffusion taking place at long time. At the fragile to strong crossover, we find that hopping (activated) processes start to play a role. This is evidenced by the appearance of peaks in the Van Hove correlation functions. In the deep supercooled regime, our analysis clearly indicates that activated processes dominate the dynamics. The comparison between the Van Hove functions and the radial distribution functions allows to better understand the mechanism of hopping phenomena in supercooled water and to connect their onset directly with the crossing of the Widom Line.