Related papers: 3D structure and stability prediction of DNA with …
We present a simple model which describes elastic response of single-stranded DNA (ssDNA) to stretching, including the regime of very high force (up to 1000 pN). ssDNA is modelled as a discreet persistent chain, whose ground state is a…
Molecular property prediction, crucial for early drug candidate screening and optimization, has seen advancements with deep learning-based methods. While deep learning-based methods have advanced considerably, they often fall short in fully…
This dissertation explores how deep generative models can advance the analysis of challenging biological problems by integrating domain knowledge with deep learning. It focuses on two areas: DNA reaction kinetics and cryogenic electron…
The equilibrium three dimensional shape of relatively short loops of DNA is studied using an elastic model that takes into account anisotropy in bending rigidities. Using a reasonable estimate for the anisotropy, it is found that cyclized…
Due to its polyionic character the DNA double helix is stable and biologically active only in salty aqueous media where its charge is compensated by solvent counterions. Monovalent metal ions are ubiquitous in DNA environment and they are…
Motivation: Thanks to the recent advances in structural biology, nowadays three-dimensional structures of various proteins are solved on a routine basis. A large portion of these contain structural repetitions or internal symmetries. To…
We present an end-to-end Convolutional Neural Network (CNN) approach for 3D reconstruction of knee bones directly from two bi-planar X-ray images. Clinically, capturing the 3D models of the bones is crucial for surgical planning, implant…
The distance-geometric graph representation adopts a unified scheme (distance) for representing the geometry of three-dimensional(3D) graphs. It is invariant to rotation and translation of the graph and it reflects pair-wise node…
Integrative biomolecular modeling of RNA relies on structural refined collections and accurate experimental data that reflect binding and folding behavior. However, the prediction of such collections remains challenging due to the rugged…
A systematic search for multicomponent crystal structures is carried out for five different ternary systems of nuclei in a polarizable background of electrons, representative of accreted neutron star crusts and some white dwarfs. Candidate…
Genome organization in eukaryotes during interphase stems from the delicate balance between non-random correlations present in the DNA polynucleotide linear sequence and the physico/chemical reactions which shape continuously the form and…
Understanding the relationship between atomic structure (order) and chemical composition (chemistry) is critical for advancing materials science, yet traditional spectroscopic techniques can be slow and damaging to sensitive samples.…
The 3D microstructure of solid oxide fuel cell anodes significantly influences their electrochemical performance, but conventional methods for acquiring high-resolution microstructural 3D data such as focused ion beam scanning electron…
The structure of DNA in the nucleosome core particle is studied using an elastic model that incorporates anisotropy in the bending energetics and twist-bend coupling. Using the experimentally determined structure of nucleosomal DNA [T.J.…
Predicting the stability of crystals is one of the central problems in materials science. Today, density functional theory (DFT) calculations are the computational tool of choice to obtain energies of crystals with quantitative accuracy.…
The data-based discovery of effective, coarse-grained (CG) models of high-dimensional dynamical systems presents a unique challenge in computational physics and particularly in the context of multiscale problems. The present paper offers a…
Ground-state 3D geometries of molecules are essential for many molecular analysis tasks. Modern quantum mechanical methods can compute accurate 3D geometries but are computationally prohibitive. Currently, an efficient alternative to…
Coherent diffraction imaging enables the imaging of individual defects, such as dislocations or stacking faults, in materials.These defects and their surrounding elastic strain fields have a critical influence on the macroscopic properties…
Short, partially complementary, single-stranded (ss)DNA strands can form nanostructures with a wide variety of shapes and mechanical properties. It is well known that semiflexible, linear dsDNA can undergo an isotropic to nematic (IN) phase…
RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, experimental determination of RNA structures through X-ray…