Related papers: Unravelling Mg$^{2+}$-RNA binding with atomistic m…
Elastic network models (ENMs) are valuable and efficient tools for characterizing the collective internal dynamics of proteins based on the knowledge of their native structures. The increasing evidence that the biological functionality of…
RNA molecules exhibit various biological functions intrinsically dependent on their diverse ecosystem of highly flexible structures. This flexibility arises from complex hydrogen-bonding networks defined by canonical and non-canonical base…
Non-coding RNA molecules fold into precise base pairing patterns to carry out critical roles in genetic regulation and protein synthesis. We show here that coupling systematic mutagenesis with high-throughput SHAPE chemical mapping enables…
We study the folding of RNA secondary structures with quenched sequence randomness by means of the constrained annealing method. A thermodynamic phase transition is induced by including the conformational weight of loop structures. In…
In this study, we investigate the effect of Mg incorporation on the relative phase stability of the four primary Ga$_2$O$_3$ polymorphs using density functional theory (DFT) calculations, with the goal of rationalizing experimental…
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…
Double-exchange mechanisms in RE$_{1-x}$AE$_{x}$MnO$_{3}$ manganites (where RE is a trivalent rare-earth ion and AE is a divalent alkali-earth ion) relies on the strong exchange interaction between two Mn$^{3+}$ and Mn$^{4+}$ ions through…
The structural and magnetic properties of spinel compounds $CoB_2O_4$ (B=Cr,Mn and Fe) are studied using the DFT+U method and generalized gradient approximation (GGA). We concentrate on understanding the trends in the properties of these…
We present results of tight-binding spin-dynamics simulations of individual and pairs of substitutional Mn impurities in GaAs. Our approach is based on the mixed quantum-classical scheme for spin dynamics, with coupled equations of motions…
The statistical mechanics of heteropolymer structure formation is studied in the context of RNA secondary structures. A designed RNA sequence biased energetically towards a particular native structure (a hairpin) is used to study the…
Using force as a probe to map the folding landscapes of RNA molecules has become a reality thanks to major advances in single molecule pulling experiments. Although the unfolding pathways under tension are complicated to predict studies in…
Rate theory and DFT calculations of hydrogen evolution reaction (HER) on MoS2 with Co, Ni and Pt impurities show the significance of dihydrogen (H2*) complex where both hydrogen atoms are interacting with the surface. Stabilization of such…
Understanding the role of network structure in the evolution of cooperation is a key research goal at the intersection between physics and biology. Recent studies have particularly focused on multiplex networks given that multiple social…
The functioning of double-stranded (ds) nucleic acids (NAs) in cellular processes is strongly mediated by their elastic response. These processes involve proteins that interact with dsDNA or dsRNA and distort their structures. The…
We present large-scale molecular dynamics (MD) simulations based on a machine-learning interatomic potential to investigate the wet etching behavior of various GaN facets in alkaline solution-a process critical to the fabrication of…
The temperature-induced structural and electronic transformation in VO$_2$ between the monoclinic M1 and tetragonal rutile phases was studied by means of \textit{ab initio} molecular dynamics, based on density functional theory with Hubbard…
Motivation: RNA design aims to find RNA sequences that fold into a given target secondary structure, a problem also known as RNA inverse folding. However, not all target structures are designable. Recent advances in RNA designability have…
By using single-DNA observation with fluorescence microscopy, we observed the effects of divalent and trivalent cations on the higher-order structure of giant DNA (T4 DNA with 166 kbp). It was found that divalent cations, such as Mg(2+) and…
Systemic properties of living cells are the result of molecular dynamics governed by so-called genetic regulatory networks (GRN). These networks capture all possible features of cells and are responsible for the immense levels of adaptation…
microRNAs (miRNAs) regulate gene expression at post-transcriptional level by repressing target RNA molecules. Competition to bind miRNAs tends in turn to correlate their targets, establishing effective RNA-RNA interactions that can…