Related papers: Simulating topological domains in human chromosome…
Transcriptional regulation of gene expression is one of the main processes that affect cell diversification from a single set of genes. Regulatory proteins often interact with DNA regions located distally from the transcription start sites…
The function of protein, RNA, and DNA is modulated by fast, dynamic exchanges between three-dimensional conformations. Conformational sampling of biomolecules with exact and nullspace inverse kinematics, using rotatable bonds as revolute…
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,…
We introduce the coherent state mapping ring-polymer molecular dynamics (CS-RPMD), a new method that accurately describes electronic non-adiabatic dynamics with explicit nuclear quantization. This new approach is derived by using coherent…
We investigate a densely packed, non-random arrangement of forty-six chromosomes (46,XY) in human nuclei. Here, we model systems-level chromosomal crosstalk by unifying intrinsic parameters (chromosomal length and number of genes) across…
We propose a model for the formation of chromatin loops based on the diffusive sliding of a DNA-bound factor which can dimerise to form a molecular slip-link. Our slip-links mimic the behaviour of cohesin-like molecules, which, along with…
Topology has emerged as a fundamental property of many systems, manifesting in cosmology, condensed matter, high-energy physics and waves. Despite the rich textures, the topology has largely been limited to low dimensional systems that can…
We present a real-space view of one-dimensional (1D) to three-dimensional (3D) topological materials with 13 representative samples selected from each class, including 1D trans-polyacetylene, two-dimensional (2D) graphene, and 3D…
We have studied the excited states of a one-dimensional donor dimer array by using time-dependent Hartree-Fock and density-functional theories. We find that tuning the inter-donor distances can induce a topological phase transition from a…
A theoretical framework for evaluating the approximate energy and dynamic properties associated with the folding of DNA into nucleosomes and chromatin is presented. For this purpose experimentally determined elastic constants of linear DNA…
Flat band (FB) systems provide ideal playgrounds for studying correlation physics, whereas multi-orbital characteristics in real materials are distinguished from most simple FB models. Here, we propose a systematic and versatile framework…
We propose that protein loops can be interpreted as topological domain-wall solitons. They interpolate between ground states that are the secondary structures like alpha-helices and beta-strands. Entire proteins can then be folded simply by…
To gain a deeper insight into cellular processes such as transcription and translation, one needs to uncover the mechanisms controlling the configurational changes of nucleic acids. As a step toward this aim, we present here a novel…
A single semiflexible polymer chain folds into a toroidal object under poor solvent conditions. In this study, we examined the morphological change in such a toroidal state as a function of the width and stiffness of the chain together with…
Traditional molecular string representations, such as SMILES, often pose challenges for AI-driven molecular design due to their non-sequential depiction of molecular substructures. To address this issue, we introduce Sequential…
We investigate the phase diagram of a one-dimensional model of hardcore bosons or spinless fermions with tunable nearest-neighbor interactions. By introducing alternating repulsive and attractive interactions on consecutive bonds, we show…
We explicitly show that the differences, with respect to the appearance of topological phases, between the traditional Haldane model, which utilises a honeycomb lattice structure, to that of the Haldane model imbued onto a brick-wall…
Spatial transcriptomics (ST) enables gene expression mapping within anatomical context but remains costly and low-throughput. Hematoxylin and eosin (H\&E) staining offers rich morphology yet lacks molecular resolution. We present…
Traditional models of wormlike chains in shear flows at finite temperature approximate the equation of motion via finite difference discretization (bead and rod models). We introduce here a new method based on a spectral representation in…
We present a multi-phase design parameterization to obtain optimized heterogeneous lattice structures. The 3D domain is discretized into a cubical grid wherein each cube has eight distinct unit cell types or phases. When all phases are…