A polymer model for prediction of 3D structure and ...

A multicolour polymer model for the prediction of 3D structure and ...

We use Brownian dynamics simulations to study a polymer model for chromosomes accounting for multiple types (“colours”) of chromatin-binding proteins.

A polymer model for prediction of 3D structure and ... - YouTube

A multicolour polymer model facilitating prediction of 3D structure and transcriptional activity of human chromosomes Giuseppe Negro ...

A multicolour polymer model for the prediction of 3D ... - NASA ADS

Within each human cell, different kinds of RNA polymerases and a panoply of transcription factors bind chromatin to simultaneously determine 3D chromosome ...

A multicolour polymer model for the prediction of 3D structure and ...

Here, we use Brownian dynamics simulations to study a polymer model for chromosomes accounting for multiple types ('colours') of chromatin- ...

A multicolour polymer model for the prediction of 3D structure and ...

We introduce a polymer model which accounts for multiple types - or ``colours'' - of DNA-binding proteins. Molecular dynamics simulations shows a good ...

Polymer Simulations of Heteromorphic Chromatin Predict the 3D ...

LEs were removed from (and returned to) the polymer stochastically at a constant rate. The model was used to generate a population of conformations from which ...

[PDF] A multicolour polymer model for the prediction of 3D structure ...

Polymer Simulations of Heteromorphic Chromatin Predict the 3D Folding of Complex Genomic Loci · Biology, Materials Science. bioRxiv · 2018.

A multicolour polymer model for the prediction of 3D structure and ...

A multicolour polymer model for the prediction of. 3D structure and transcription in human chromatin. Monday, 19 December 2022 18:35 (20 minutes).

Polymer Simulations of Heteromorphic Chromatin Predict the 3D ...

Chromatin folded into 3D macromolecular structures is often analyzed by chromosome conformation capture (3C) and fluorescence in situ ...

Machine learning polymer models of three-dimensional chromatin ...

Furthermore, we design three-dimensional models of chromatin contact domains (CCDs) using real (ChIA-PET) and predicted looping interactions.

Modeling the 3D Spatiotemporal Organization of Chromatin ...

We propose a polymer model to investigate in silico the dynamics of chromatin replication in three dimensions (PolyRep).

Polymer Physics Models Reveal Structural Folding Features ... - MDPI

Here, we employ polymer physics models of chromatin to investigate the 3D folding of a 2 Mb wide genomic region encompassing the human LTN1 gene, ...

Predicting Polymer Properties Based on Multimodal Multitask ... - arXiv

Besides, to overcome the limited availability of polymer 3D data, we further propose the "Star Substitution" strategy to extract 3D structural ...

A maximum-entropy model to predict 3D structural ensembles of ...

Here, we introduce a computational method (Distance Matrix to Ensemble of Structures, DIMES), based on the maximum entropy principle, with ...

Polymer physics models to unveil the mechanisms that ... - YouTube

Polymer physics models to unveil the mechanisms that shape chromosome 3D ... A polymer model for prediction of 3D structure and transcriptional ...

Data-Driven Polymer Model for Mechanistic Exploration of Diploid ...

Computational tools that can efficiently reconstruct 3D structures from experimental data, and more importantly, that can provide mechanistic insight into the ...

Polymer physics reveals a combinatorial code linking 3D chromatin ...

(A) Our method combines machine learning and polymer physics to infer from only Hi-C data the genomic location of the minimal set of binding ...

Predicting the three-dimensional folding of cis-regulatory regions in ...

We present a polymer modeling scheme based on the assumption that chromosome architecture is maintained by protein bridges, which form chromatin loops.

Polymer Structure Predictor (PSP): A Python Toolkit for Predicting ...

3D models for multiple conformers of linear or circular oligomers are the output of PSP. 2.2. Infinite Polymer Chain Prediction. Oligomer and.

Polymer modelling unveils the roles of heterochromatin and ...

Using polymer modelling, we investigate the roles of nucleolus formation and epigenomics-driven interactions in shaping the 3D genome of A. thaliana.