Related papers: Unravelling Mg$^{2+}$-RNA binding with atomistic m…
This work investigates the interactions of H-NS proteins and bacterial genomic DNA through computer simulations performed with a coarse-grained model. The model was developed specifically to study the switch of H-NS proteins from the…
Mn doped semiconductors are extremely interesting systems due to their novel magnetic properties suitable for the spintronics applications. It has been shown recently by both theory and experiment that Mn doped GaN systems have a very high…
Recently several minimum free energy (MFE) folding algorithms for predicting the joint structure of two interacting RNA molecules have been proposed. Their folding targets are interaction structures, that can be represented as diagrams with…
The intricate network of interactions observed in RNA three-dimensional structures is often described in terms of a multitude of geometrical properties, including helical parameters, base pairing/stacking, hydrogen bonding and backbone…
Annealing Mg-implanted homoepitaxial GaN at temperatures at or above 1400 {\deg}C eliminates the formation of inversion domains and leads to improved dopant activation efficiency. Extended defects in the form of inversion domains contain…
We analyze a series of publicly available controlled experiments (Latin square) on Affymetrix high density oligonucleotide microarrays using a simple physical model of the hybridization process. We plot for each gene the signal intensity…
We study numerically the mechanical stability and elasticity properties of duplex DNA molecules within the frame of a network model incorporating microscopic degrees of freedom related with the arrangement of the base pairs. We pay special…
This research paper delves into the dynamics of a novel ecology model that describes the intricate interplay between radioactivity and cancer cases. Organized into three main sections, the study covers numerical analysis using advanced…
By the theory based on the equilibrium binding model, phase diagrams have been calculated for the poly rA poly rU system in the presence of Mg2+, Ni2+, Cd2+, with Na+ 0.1 M. Binding constants (KA, KU, KAU, KA2U) have been determined, the…
Atomically detailed simulations of RNA folding have proven very challenging in view of the difficulties of developing realistic force fields and the intrinsic computational complexity of sampling rare conformational transitions. To tackle…
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…
G-quadruplexes represent a novelty for molecular biology. Their role inside the cell remains mysterious. We investigate a possible correlation with mRNA localization. In particular, we hypothesize that Gquadruplexes influence fluid…
Multivalent interactions between deformable mesoscopic units are ubiquitous in biology, where membrane macromolecules mediate the interactions between neighbouring living cells and between cells and solid substrates. Lately, analogous…
The crystal structure of MoS$_2$ with strong covalent bonds in plane and weak Van der Waals interactions out of plane gives rise to interesting properties for applications such as solid lubrication, optoelectronics, and catalysis, which can…
A quantitative understanding of how cells interact with their extracellular matrix via molecular bonds is fundamental for many important processes in cell biology and engineering. In these interactions, the deformability of cells and matrix…
Multi-valent (MV) battery architectures based on pairing a Mg metal anode with a high-voltage ($\sim$ 3 V) intercalation cathode offer a realistic design pathway toward significantly surpassing the energy storage performance of traditional…
In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is…
We use the ab initio local-density approximation (LDA) to study of exchange interactions and Tc of Ga1−xMnxAs grown in digitally doped structures. We analyze the crystallographic dependence of exchange interactions predicted by the…
Much of the complexity observed in gene regulation originates from cooperative protein-DNA binding. While studies of the target search of proteins for their specific binding sites on the DNA have revealed design principles for the…
Background: Magnetic quadrupole (M2) excitation represents a fundamental feature in atomic nucleus associated to nuclear magnetism induced by spin and orbital transition operator. So far it has only been investigated within the…