相关论文: Active Hydrodynamic Theory of Euchromatin and Hete…
Spatiotemporal coordination of chromatin and subnuclear compartments is crucial for cells. Numerous enzymes act inside nucleus\textemdash some of those transiently link and pass two chromatin segments. Here we study how such an active…
In higher organisms, all cells share the same genome, but every cell expresses only a limited and specific set of genes that defines the cell type. During cell division, not only the genome, but also the cell type is inherited by the…
Enhanced dynamical fluctuations of RNAs, facilitated by a network of water molecules with strong interactions with RNA, are suspected to be critical in their ability to respond to a variety of cellular signals. Using atomically detailed…
1. Role of inter-domain water clusters in large-scale dynamics of proteins; 2. Description of large-scale dynamics of proteins based on generalized Stokes-Einstein and Eyring-Polany equation; 3. Dynamic model of protein-ligand complexes…
We derive the Hydrodynamics for a system of N active, spherical, underdamped particles, interacting through conservative forces. At the microscopic level, we represent the evolution of the particles in terms of the Kramers equation for the…
The nature of emergent collective behaviors of moving physical agents interacting with their neighborhood is a long-standing open issue in physical and biological systems alike. This calls for studies on the control of synchronization and…
Epigenetics plays a key role in cellular differentiation and maintaining cell identity, enabling cells to regulate their genetic activity without altering the DNA sequence. Epigenetic regulation occurs within the context of hierarchically…
Transcriptional activity has been shown to relate to the organization of chromosomes in the eukaryotic nucleus and in the bacterial nucleoid. In particular, highly transcribed genes, RNA polymerases and transcription factors gather into…
For a dense and strongly interacting system, such as a nucleus or a strongly-coupled quark-gluon plasma, the foundation of hydrodynamics can be better found in the quantum description of constituents moving in the strong mean fields…
The contributions of active deformation dynamics in cell nuclei to the intra-nuclear positioning of hetero- and euchromatin are investigated. We analyzed the behaviors of model chains containing two types of regions, one with high and the…
The development of multicellular organisms relies on the precise coordination of molecular events across multiple spatial and temporal scales. Understanding how information flows from molecular interactions to cellular processes and tissue…
Droplets are essential for spatially controlling biomolecules in cells. To work properly, cells need to control the emergence and morphology of droplets. On the one hand, driven chemical reactions can affect droplets profoundly. For…
Recent research has shown that motile cells can adapt their mode of propulsion to the mechanical properties of the environment in which they find themselves--crawling in some environments while swimming in others. The latter can involve…
Water is vital for life, and without it biomolecules and cells cannot maintain their structures and functions. The remarkable properties of water originate from its ability to form hydrogen-bonding networks and dynamics, which the…
Mirroring their role in electrical and optical physics, two-dimensional crystals are emerging as novel platforms for fluid separations and water desalination, which are hydrodynamic processes that occur in nanoscale environments. For…
The three dimensional structure of DNA in the nucleus (chromatin) plays an important role in many cellular processes. Recent experimental advances have led to high-throughput methods of capturing information about chromatin conformation on…
Spatial organization of chromatin plays a critical role in genome regulation. Various types of affinity mediators and enzymes have been attributed to regulate spatial organization of chromatin from a thermodynamics perspective. However, at…
Recent progress has been made in the understanding of the physical properties of chromatin -- the dense complex of DNA and histone proteins that occupies the nuclei of plant and animal cells. Here I will focus on the two lowest levels of…
The cell nucleus houses the chromosomes, which are linked to a soft shell of lamin filaments. Experiments indicate that correlated chromosome dynamics and nuclear shape fluctuations arise from motor activity. To identify the physical…
Within the nucleus, structural maintenance of chromosome protein complexes, namely condensin and cohesin, create an architecture to facilitate the organization and proper function of the genome. Condensin, in addition to performing loop…