Related papers: 3D structure and stability prediction of DNA with …
A series of coarse-grained models have been developed for the study of the molecular dynamics of RNA nanostructures. The models in the series have one to three beads per nucleotide and include different amounts of detailed structural…
Diffusion generative models have emerged as a powerful framework for addressing problems in structural biology and structure-based drug design. These models operate directly on 3D molecular structures. Due to the unfavorable scaling of…
In this paper, we present a deep-learning based method for estimating the 3D structure of a bone from a pair of 2D X-ray images. Our triplet loss-trained neural network selects the most closely matching 3D bone shape from a predefined set…
The objective of the present study was to develop an understanding of short single-stranded DNA (ssDNA) to assist the development of new DNA-based biosensors. A ssDNA model containing twelve bases was constructed from the 130-145 codon…
The Histone-like Nucleoid Structuring protein (H-NS) is a nucleoid-associated protein, which is involved in both gene regulation and DNA compaction. Although it is a key player in genome organization by forming bridges between DNA duplexes,…
Gel electrophoresis is a powerful experimental method to probe the topology of DNA and other biopolymers. While there is a large body of experimental work which allows us to accurately separate different topoisomers of a molecule, a full…
Self-assembly is traditionally described as the process through which an initially disordered system relaxes towards an equilibrium ordered phase only driven by local interactions between its building blocks. However, This definition is too…
This paper tackles the pressing challenge of mutagenicity prediction by introducing three ground-breaking approaches. First, it showcases the superior performance of 2D scattering coefficients extracted from molecular images, compared to…
Grain boundaries (GBs) in complex oxides play critical roles in governing their functional properties, which are intrinsically linked to their three-dimensional (3D) atomic configurations and local chemical environments that can deviate…
In this letter, we study the structure-transport property relationships of small ligand intercalated DNA molecules using a multiscale modelling approach where extensive ab-initio calculations are performed on numerous MD-simulated…
The spectrum of two-dimensional (2D) materials beyond graphene offers a remarkable platform to study new phenomena in condensed matter physics. Among these materials, layered hexagonal boron nitride (hBN), with its wide bandgap energy…
Discrete dislocation dynamics (DDD) is a widely employed computational method to study plasticity at the mesoscale that connects the motion of dislocation lines to the macroscopic response of crystalline materials. However, the…
In the course of evolution, proteins show a remarkable conservation of their three-dimensional structure and their biological function, leading to strong evolutionary constraints on the sequence variability between homologous proteins. Our…
Recognition and binding of specific sites on DNA by proteins is central for many cellular functions such as transcription, replication, and recombination. In the process of recognition, a protein rapidly searches for its specific site on a…
We construct a theoretical model for the dynamics of a microscale colloidal particle, modeled as an interval, moving horizontally on a DNA-coated surface, modelled as a line coated with springs that can stick to the interval. Averaging over…
Chain-like macromolecules in solution, whether biological or synthetic, transform from a spatially extended conformation to a compact one upon change of temperature or solvent qualities. This sharp transition plays a key role in various…
The binding of proteins onto DNA contributes to the shaping and packaging of genome as well as to the expression of specific genetic messages. With a view to understanding the interplay between the presence of proteins and the deformation…
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…
Advanced three-dimensional (3D) tracking methods are essential for studying particle dynamics across a wide range of complex systems, including multiphase flows, environmental and atmospheric sciences, colloidal science, biological and…
In this work we propose a model for DNA double helix within the tight-binding framework that incorporates the helicity of the molecules. We have studied localization properties of three DNAsequences,the periodic poly(dG)-poly(dC) and…