Related papers: Stem-loop formation drives RNA folding in mechanic…
In this paper we study irreducibility in RNA structures. By RNA structure we mean RNA secondary as well as RNA pseudoknot structures. In our analysis we shall contrast random and minimum free energy (mfe) configurations. We compute various…
We present Monte Carlo simulations of hysteresis loops of a model of a magnetic nanoparticle with a ferromagnetic core and an antiferromegnetic shell with varying values of the core/shell interface exchange coupling which aim to clarify the…
The formation of DNA loops by proteins and protein complexes that bind at distal DNA sites plays a central role in many cellular processes, such as transcription, recombination, and replication. Here we review the basic thermodynamic…
By performing a comprehensive study on 1832 segments of 1212 complete genomes of viruses, we show that in viral genomes the hairpin structures of thermodynamically predicted RNA secondary structures are more abundant than expected under a…
Radiation damage in structural materials is a major challenge for advanced nuclear energy systems, and niobium is of particular interest due to its high melting point, mechanical strength, and corrosion resistance. To better understand its…
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…
Cosine-shaped bands that occur in DFT-based electronic band structures for MgB2 are further analyzed with calculations along reciprocal directions parallel to the high symmetry G-A direction at regular intervals along G-M. Band degeneracies…
A complex network approach to protein folding is proposed. The graph object is the network of shortcut edges present in a native-state protein (SCN0). Although SCN0s are found via an intuitive message passing algorithm (S. Milgram,…
Polymerization of RNA from a template DNA is carried out by a molecular machine called RNA polymerase (RNAP). It also uses the template as a track on which it moves as a motor utilizing chemical energy input. The time it spends at each…
Engineering and enhancing inversion symmetry breaking in solids is a major goal in condensed matter physics and materials science, as a route to advancing new physics and applications ranging from improved ferroelectrics for memory devices…
A major discovery of Parker Solar Probe (PSP) was the presence of large numbers of localized increases in the radial solar wind speed and associated sharp deflections of the magnetic field - switchbacks (SB). A possible generation mechanism…
The effect of polyvalent molecular cations, such as spermine, on the condensation of DNA into very well-defined toroidal shapes have been well studied and understood. However, a great effort has been made trying to obtain similar condensed…
DNA based nanostructures built on a long single stranded DNA scaffold, known as DNA origamis, offer the possibility to organize various molecules at the nanometer scale in one pot experiments. The folding of the scaffold is guaranteed by…
We investigate the mechanisms of histone sliding and detachment with a stochastic model that couples thermally-induced, passive histone sliding with active motor-driven histone unwrapping. Analysis of a passive loop or twist defect-mediated…
Membrane wrapping underlies nanoparticle uptake during endocytosis, whereas the reverse process of membrane unwrapping accompanies particle expulsion and membrane fusion events. Existing theoretical descriptions typically focus on adhesion…
Dynamics of nucleosomes, the building blocks of the chromatin, has crucial effects on expression, replication and repair of genomes in eukaryotes. Beside constant movements of nucleosomes by thermal fluctuations, ATP-dependent chromatin…
Context: We integrate the 2D MHD ideal equations of a straight slab to simulate observational results associated with fundamental sausage trapped modes. Aims: Starting from a non-equilibrium state with a dense chromospheric layer, we…
Many biological processes are supported by special molecules, called motor proteins or molecular motors, that transport cellular cargoes along linear protein filaments and can reversibly associate to their tracks. Stimulated by these…
The determination of the folding mechanisms of proteins is critical to understand the topological change that can propagate Alzheimer and Creutzfeld-Jakobs diseases, among others. The computational community has paid considerable attention…
Among the most intriguing features of non-Hermitian (NH) systems is the ability of complex energies to form braids under parametric variation. Several braiding behaviors, including link and knot formation, have been observed in experiments…