Related papers: Unravelling Mg$^{2+}$-RNA binding with atomistic m…
The accurate prediction of protein-RNA binding affinity remains an unsolved problem in structural biology, limiting opportunities in understanding gene regulation and designing RNA-targeting therapeutics. A central obstacle is the…
Adhesion processes of biological membranes that enclose cells and cellular organelles are essential for immune responses, tissue formation, and signaling. These processes depend sensitively on the binding constant K2D of the…
We study genetic networks that produce many species of non-coding RNA molecules that are present at a moderate density, as typically exists in the cell. The associations of the many species of these RNA are modeled physically, taking into…
We perform a theoretical study of the electronic structure and magnetic properties of the prototypical magnetic MAX-phase Mn$_2$GaC with the main focus given to the origin of magnetic interactions in this system. Using the density…
Theoretical and experimental investigation of the electronic and magnetic structure of transition metal atoms on an insulating interface with a metallic substrate at low temperatures is quite challenging. In this paper, we show a density…
This study address the computational determination of catalytic reaction rates by moving beyond traditional Transition State Theory (TST), addressing its limitations in complex systems. The Hill relation framework, integrated with Adaptive…
In biology, predicting RNA secondary structures plays a vital role in determining its physical and chemical properties. Although we have powerful energy models to predict them as well as parametric analysis to understand the models…
We utilize a multiscale modeling framework to study the effect of shape, size and ligand composition on the efficacy of binding of a ligand-coated-particle to a substrate functionalized with the target receptors. First, we show how…
The subcellular localization of RNAs, including long non-coding RNAs (lncRNAs), messenger RNAs (mRNAs), microRNAs (miRNAs) and other smaller RNAs, plays a critical role in determining their biological functions. For instance, lncRNAs are…
Ribonucleic acids (RNA) are unique in that they can store genetic information, replicate and perform catalysis. Importantly, RNA molecules are highly dynamic, and thus determining the ensemble of conformations that they populate is crucial…
RNA's diversity of structures and functions impacts all life forms since primordia. We use calorimetric force spectroscopy to investigate RNA folding landscapes in previously unexplored low-temperature conditions. We find that Watson-Crick…
We study deposition dynamics of Na and Na$_2$ on an Ar substrate, both species neutral as well as charged. The system is modeled by a hierarchical approach describing the Na valence electrons by time-dependent density-functional theory…
The computational study of conformational transitions in nucleic acids still faces many challenges. For example, in the case of single stranded RNA tetranucleotides, agreement between simulations and experiments is not satisfactory due to…
We study 1 or 2 neighboring Mn impurities, as well as complexes of 1 Mn and 1 or 2 Mg ions in a 64 atoms supercell of GaN by means of density functional calculations. Taking into account the electron correlation in the local spin density…
Phase-separated biomolecular condensates containing proteins and RNAs can assemble into higher-order structures by forming thermodynamically stable interfaces between immiscible phases. Using a minimal model of a protein/RNA interaction…
Biological adhesion often involves several pairs of specific receptor-ligand molecules. Using rate equations, we study theoretically the rupture of such multiple parallel bonds under dynamic loading assisted by thermal activation. For a…
RNA function crucially depends on its structure. Thermodynamic models currently used for secondary structure prediction rely on computing the partition function of folding ensembles, and can thus estimate minimum free-energy structures and…
Nuclear magnetic dipole properties of ground bands and gamma-vibrational bands are studied for the first time using the triaxial projected shell model approach. The study is carried out for the Dy and Er isotopic chains, ranging from…
Magnesium (Mg) and its alloys hold great potential as an energy-saving structural material for automative, aerospace applications. However, the use of Mg alloys has been limited due to poor ductility and formability. Poor mechanical…
By exerting mechanical force it is possible to unfold/refold RNA molecules one at a time. In a small range of forces, an RNA molecule can hop between the folded and the unfolded state with force-dependent kinetic rates. Here, we introduce a…