Related papers: Two-dimensional chemical mapping for non-coding RN…
Cryogenic electron microscopy (cryo-EM) has transformed structural biology by allowing to reconstruct 3D biomolecular structures up to near-atomic resolution. However, the 3D reconstruction process remains challenging, as the 3D structures…
Cells receive signaling molecules by receptors and relay information via sensory networks so that they can respond properly depending on the type of signal. Recent studies have shown that cells can extract multi-dimensional information from…
RNA function is intimately related to its structural dynamics. Molecular dynamics simulations are useful for exploring biomolecular flexibility but are severely limited by the accessible timescale. Enhanced sampling methods allow this…
Dual graphs have been applied to model RNA secondary structures with pseudoknots, or intertwined base pairs. In previous works, a linear-time algorithm was introduced to partition dual graphs into maximally connected components called…
Due to the wide range of timescales that are present in macromolecular systems, hierarchical multiscale strategies are necessary for their computational study. Coarse-graining (CG) allows to establish a link between different system…
Motivation: Thanks to the recent advances in structural biology, nowadays three-dimensional structures of various proteins are solved on a routine basis. A large portion of these contain structural repetitions or internal symmetries. To…
The use of micro-Raman spectroscopy, through chemical bond nano-scale probes, allows the changes in conformations (alpha helix -> beta sheet), chain orientation, disconnection of disulfide bonds (-20%) and the increase of intra and…
Genetic mutations can disrupt protein structure, stability, and solubility, contributing to a wide range of diseases. Existing predictive models often lack interpretability and fail to integrate physical and chemical interactions critical…
Graphynes offer a chemically heterogeneous $sp/sp^{2}$ carbon framework with distinct electronic regimes and site-selective reactivity. Here, Density Functional Theory and Reactive Molecular Dynamics Simulations are combined to evaluate…
We discuss the ``soft-ratcheting'' algorithm which generates targeted stochastic trajectories in molecular systems with scores corresponding to their probabilities. The procedure, which requires no initial pathway guess, is capable of…
A cascade of phase transitions from square to hexagonal lattice is studied in 2D system of particles interacting via core-softened potential. Due to the presence of two length-scales of repulsion, different local configurations with four,…
A novel framework has recently been proposed for designing the molecular structure of chemical compounds with a desired chemical property using both artificial neural networks and mixed integer linear programming. In the framework, 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…
Many {\it ribosomes} simultaneously move on the same messenger RNA (mRNA), each synthesizing separately a copy of the same protein. In contrast to the earlier models, here {\it we develop a ``unified'' theoretical model} that not only…
We study neutrinoless double beta decay of several isotopes with state-of-the-art beyond self-consistent mean field methods to compute the nuclear matrix elements (NME). Generating coordinate method with particle number and angular momentum…
The calculation of chemical shifts in solids has enabled methods to determine crystal structures in powders. The dependence of chemical shifts on local atomic environments sets them among the most powerful tools for structure elucidation of…
In this paper, we study the interaction of an antisense RNA and its target mRNA, based on the model introduced by Alkan {\it et al.} (Alkan {\it et al.}, J. Comput. Biol., Vol:267--282, 2006). Our main results are the derivation of the…
Nonlinear optical effects have been studied extensively in microresonators as more photonics applications transition to integrated on-chip platforms. Due to low optical losses and small mode volumes, microresonators are demonstrably the…
Graphene has extraordinary mechanical and electronic properties, making it a promising material for membrane based nanoelectromechanical systems (NEMS). Here, chemical-vapor-deposited graphene is transferred onto target substrates to…
High-quality crystals without inversion symmetry are the conventional platform to achieve optical frequency conversion via three wave-mixing. In bulk crystals, efficient wave-mixing relies on phase-matching configurations, while at the…