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It is a standard exercise in mechanical engineering to infer the external forces and torques on a body from its static shape and known elastic properties. Here we apply this kind of analysis to distorted double-helical DNA in complexes with…
The central dogma of molecular biology is the principal framework for understanding how nucleic acid information is propagated and used by living systems to create complex biomolecules. Here, by integrating the structural and dynamic…
A repair protein like RecG moves the stalled replication fork in the direction from the zipped to the unzipped state of DNA. It is proposed here that a softening of the zipped-unzipped interface at the fork results in the front propagating…
In the framework of algebraic topology the closed sequence of 4-dimensional polyhedra (algebraic polytopes) was defined. This sequence is started by the polytope {240}, discovered by Coxeter, and is determined by the second coordination…
RNA's diverse biological functions stem from its structural versatility, yet accurately predicting and designing RNA sequences given a 3D conformation (inverse folding) remains a challenge. Here, I introduce a deep learning framework that…
Solid-state nanopore DNA sequencers present mechanical and chemical stability, reusability, and large-scale integrability. However, their development is hindered by the absence of a protein-free mechanism for controlling DNA translocation,…
We present Molecular Dynamics simulations of a single stranded unprotonated DNA i-motif in explicit solvent. Our results indicate that the native structure in non-acidic solution at 300 K is unstable and completely vanishes on a time scale…
We demonstrate high-resolution non-iterative holographic coherent diffraction imaging with hard X-rays using a novel phase-shifting reference, fabricated by atomic layer deposition to produce nanosharp 3D structure. The method surpasses the…
DNA nanostructures with programmable shape and interactions can be used as building blocks for the self-assembly of crystalline materials with prescribed nanoscale features, holding a vast technological potential. Structural rigidity and…
For an understanding of DNA elasticity at high mechanical loads (F > 30 pN), its helical nature needs to be taken into account, in the form of coupling between the twist and stretch degrees of freedom. The prevailing model for DNA…
The theoretical study of deformability of special sequence of DNA double helix TATA-box is presentated. The paper elaborates on the mechanisms of abnormal deformation of DNA TATA-box double helix that cannot be explained using the standard…
We introduce a probabilistic model for protein sliding motion along DNA during the search of a target sequence. The model accounts for possible effects due to sequence-dependent interaction between the nonspecific DNA and the protein. As an…
Homologous gene shuffling between DNA promotes genetic diversity and is an important pathway for DNA repair. For this to occur, homologous genes need to find and recognize each other. However, despite its central role in homologous…
We study the rank 4 linear matroid $M(H_4)$ associated with the 4-dimensional root system $H_4$. This root system coincides with the vertices of the 600-cell, a 4-dimensional regular solid. We determine the automorphism group of this…
DNA G-hairpins are potential key structures participating in folding of human telomeric guanine quadruplexes (GQ). We examined their properties by standard MD simulations starting from the folded state and long T-REMD starting from the…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…
The forming and melting of complementary base pairs in RNA duplexes are conformational transitions required to accomplish a plethora of biological functions. Yet the dynamic steps of these transitions have not been quantitatively…
DDX3X is a human DEAD-box RNA helicase implicated in many cancers and in viral progression. In addition to the RecA-like catalytic core, DDX3X contains N- and C-terminal domains. Here, we investigate the substrate and protein requirements…
We study the resonance behaviour of the forbidden 600 and 222 x-ray Bragg peaks in Ge using LDA band structure methods. These Bragg peaks remain forbidden in the resonant dipole scattering approximation even taking into account the non…
In this paper we study the existence of heteroclinic cycles in generic unfoldings of nilpotent singularities. Namely we prove that any nilpotent singularity of codimension four in $\mathbb{R}^4$ unfolds generically a bifurcation…