相关论文: Chromatin Folding in Relation to Human Genome Func…
The genome contains genetic information essential for cell's life. The genome's spatial organization inside the cell nucleus is critical for its proper function including gene regulation. The two major genomic compartments -- euchromatin…
Chromatin is a highly compact and dynamic nuclear structure that consists of DNA and associated proteins. The main organizational unit is the nucleosome, which consists of a histone octamer with DNA wrapped around it. Histone proteins are…
The correlations between the sequence of monomers in a polymer and its three-dimensional structure is a grand challenge in polymer science and biology. The properties and functions of macromolecules depend on their 3D shape that has…
During the life cycle of bacterial cells the non-mixing of the two ring-shaped daughter genomes is an important prerequisite for the cell division process. Mimicking the environments inside highly crowded biological cells, we study the…
Several processes in the cell, such as gene regulation, start when key proteins recognise and bind to short DNA sequences. However, as these sequences can be hundreds of million times shorter than the genome, they are hard to find by simple…
Biophysicists are modeling conformations of interphase chromosomes, often basing the strengths of interactions between segments distant on the genetic map on contact frequencies determined experimentally. Here, instead, we develop a…
At the cutting edge of materials science, matter is designed to self-organize into structures that perform a wide range of functions. The past two decades have witnessed major innovations in the versatility of building blocks, ranging from…
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…
The mechanism and driving forces of chromosome segregation in the bacterial cell cycle of E. coli is one of the least understood events in its life cycle. Using principles of entropic repulsion between polymer loops confined in a cylinder,…
Cortical folding exhibits substantial inter-individual variability while preserving stable anatomical landmarks that enable fine-scale characterization of cortical organization. Among these, the three-hinge gyrus (3HG) serves as a key…
Combining genome-wide structural models with phenomenological data is at the forefront of efforts to understand the organizational principles regulating the human genome. Here, we use chromosome-chromosome contact data as knowledge-based…
Physical mechanisms underlying the empirical correlation between relative contact order (CO) and folding rate among naturally-occurring small single-domain proteins are investigated by evaluating postulated interaction schemes for a set of…
The statistical properties of intra-chromosome maps obtained by a genome-wide chromosome conformation capture method (Hi-C) are described in the framework of the hierarchical crumpling model of heteropolymer chain with quenched disorder in…
Intact-organism imaging of Drosophila larvae reveals and quantifies chromatin-aqueous phase separation. The chromatin can be organized near the lamina layer of the nuclear envelope, conventionally fill the nucleus, be organized centrally,…
The cellular cytoplasm is organized into compartments. Phase separation is a simple manner to create membrane-less compartments in order to confine and localize particles like proteins. In many cases these particles are bound to fluctuating…
Protein folding cooperativity is defined by the nature of the finite-size thermodynamic transition exhibited upon folding: two-state transitions show a free energy barrier between the folded and unfolded ensembles, while downhill folding is…
A complex network approach to protein folding is proposed. The graph object is the network of shortcut edges present in a native-state protein (SCN0). Although SCN0s are found via an intuitive message passing algorithm (S. Milgram,…
Graphene is a new material that exhibits remarkable properties from both fundamental and applied issues. This is a 2D matter system whose physical and mechanical features have been approached by using tight binding model, first principle…
More than 30 years ago, we published a paper entitled as abnormal chromatin configuration and oncogenesis, which proposed the first hypothesis that links oncogenesis to abnormal three-dimensional (3D) genome structure. Recently, many…
The conformational complexity of linear polymers far exceeds that of point-like atoms and molecules. Polymers can bend, twist, even become knotted. Thus they may also display a much richer phase structure than point particles. But it is not…