Related papers: Unravelling Mg$^{2+}$-RNA binding with atomistic m…
Defects intentionally introduced into magnetic materials often have a profound effect on the physical properties. Specifically tailored neutron spectroscopic experiments can provide detailed information on both the local exchange…
Computational prediction of RNA structures is an important problem in computational structural biology. Studies of RNA structure formation often assume that the process starts from a fully synthesized sequence. Experimental evidence,…
For the outcomes and phenotypes of complex diseases, multiple types of molecular (genetic, genomic, epigenetic, etc.) changes, environmental risk factors, and their interactions have been found to have important contributions. In each of…
Accurate identification of protein-nucleotide binding sites is fundamental to deciphering molecular mechanisms and accelerating drug discovery. However, current computational methods often struggle with suboptimal performance due to…
Charged particle and gamma decays in 24Mg* are investigated for excitation energies where quasimolecular resonances appear in 12C+12C collisions. Various theoretical predictions for the occurence of superdeformed and hyperdeformed bands…
We examine the adsorption of a single Ni atom on a monolayer of MgO on a Ag substrate using DFT and DFT+U computational approaches. We find that the electronic and magnetic properties vary considerably across the three binding sites of the…
Increasing interest in sustainable synthesis of ammonia, nitrates, and urea has led to an increase in studies of catalytic conversion between nitrogen-containing compounds using heterogeneous catalysts. Density functional theory (DFT) is…
The encapsulation of polyanions, whether single-stranded RNAs or synthetic polymers, is primarily driven by attractive electrostatic interactions between the positively charged, structurally disordered RNA-binding domains of virus coat…
Accurate prediction of protein-ligand binding affinities is an essential challenge in structure-based drug design. Despite recent advances in data-driven methods for affinity prediction, their accuracy is still limited, partially because…
RNA-binding proteins form biomolecular condensates with RNA through phase separation, playing crucial roles in various cellular processes. While intrinsically disordered regions (IDRs) are key drivers of phase separation, additional factors…
We study unbinding of multivalent cationic ligands from oppositely charged polymeric binding sites sparsely grafted on a flat neutral substrate. Our molecular dynamics (MD) simulations are suggested by single-molecule studies of protein-DNA…
We study a simple model of DNA divalent cationic surfactant complexation. We find that the combination of electrostatic and hydrophobic effects leads to a cooperative phenomenon in which as the amphiphile is added to the solution containing…
Structured RNA plays many functionally relevant roles in molecular life. Structural information, while required to understand the functional cycles in detail, is challenging to gather. Computational methods promise to complement…
Three-dimensional DNA networks, composed of tri- or higher valent nanostars with sticky, single-stranded DNA overhangs, have been previously studied in the context of designing thermally responsive, viscoelastic hydrogels. In this work, we…
When a highly charged globular macromolecule, such as a dendritic polyelectrolyte or charged nanogel, is immersed into a physiological electrolyte solution, monovalent and divalent counterions from the solution bind to the macromolecule in…
RNA binding proteins play a crucial role in post-transcriptional gene regulation by controlling the transport, processing, and translation of their target RNAs. Post-transcriptional gene regulation leads to the differential expression of…
Multivalent binding employs multiple simultaneous supramolecular interactions, increasing avidity and selectivity compared with monovalent binding. While equilibrium aspects of multivalency are well characterized, non-equilibrium behavior…
In this study we consider an idealization of a typical optical tweezers experiment involving a semiflexible double-knotted polymer, with steric hindrance and persistence length matching those of dsDNA in high salt concentration, under…
The nucleation of gas hydrates is of great interest in flow assurance, global energy demand, and carbon capture and storage. A complex molecular understanding is critical to control hydrate nucleation and growth in the context of potential…
Protein-RNA interactions are of vital importance to a variety of cellular activities. Both experimental and computational techniques have been developed to study the interactions. Due to the limitation of the previous database, especially…