Related papers: Unravelling Mg$^{2+}$-RNA binding with atomistic m…
[Background] Several studies have mentioned network modularity -- that a network can easily be decomposed into subgraphs that are densely connected within and weakly connected between each other -- as a factor affecting metabolic…
Metrics for indirectly predicting the folding rates of RNA sequences are of interest. In this letter, we introduce a simple metric of RNA structural complexity, which accounts for differences in the energetic contributions of RNA base…
Hydrogen bonding between nucleobases produces diverse DNA structural motifs, including canonical duplexes, guanine (G) quadruplexes and cytosine (C) i-motifs. Incorporating metal-mediated base pairs into nucleic acid structures can…
The issue of the nucleation and slow closure mechanisms of non superhelical stress-induced denaturation bubbles in DNA is tackled using coarse-grained MetaDynamics and Brownian simulations. A minimal mesoscopic model is used where the…
Many variants of RNA, DNA, and even proteins can be considered semiflexible polymers, where bending stiffness, as a type of energetic penalty, competes with attractive van der Waals forces in structure formation processes. Here, we…
First principles density functional theory calculations within the GGA+U approximation were performed for LiMn$_{1-x}$M$_x$O$_{2}$, a candidate cathode material for lithium-ion batteries, with ($x=0.25$, M=Ni, Fe, Co, Mg), to investigate…
The metallic oxide RuO$_2$ hosts a fascinating edge case of magnetism: while nonmagnetic in ideal bulk material, density functional theory (DFT) predicts an altermagnetic ground state within the DFT$+U$ method. The magnetic state of…
RuO$_2$ has been regarded as a prototypical candidate for metallic altermagnet, offering a potential platform for high-speed and high-efficiency spintronics. However, the magnetic ground state of RuO$_2$ remains a topic of active debate due…
Deformation twinning is an important deformation mechanism in a variety of materials, including metals and ceramics. This deformation mechanism is particularly important in low-symmetry hexagonal close-packed (hcp) metals such as Magnesium…
Predicting how protein mutations affect drug binding remains a major challenge, particularly when the mutations are distal from the binding site. In this study, we introduce a coupled simulation workflow that combines long-time-scale…
The SCAN meta-GGA exchange-correlation functional [Phys. Rev. Lett. 115, 036402 (2015)] is constructed as a chemical environment-determined interpolation between two separate energy densities: one describes single orbital electron densities…
Protein dynamics play a crucial role in many biological processes and drug interactions. However, measuring, and simulating protein dynamics is challenging and time-consuming. While machine learning holds promise in deciphering the…
We present a semi-quantitative model of condensation of short nucleic acid (NA) duplexes induced by tri-valent cobalt(III) hexammine (CoHex) ions. The model is based on partitioning of bound counterion distribution around singleNA duplex…
Synthesis and efficient implementation mRNA strands has been shown to have wide utility, especially recently in the development of COVID vaccines. However, the intrinsic chemical stability of mRNA poses a challenge due to the presence of…
Large-scale simultaneous mRNA translation and the resulting competition for the available ribosomes has important implications to the cell's functioning and evolution. Developing a better understanding of the intricate correlations between…
An analysis of the stability of a duplex containing G.A mispairs or G.A/A.G tandem during DNA melting has revealed that duplex stability depends on both DNA sequences and on the conformations of the G.A mispairs. The thermodynamics of…
Nonequilibrium experiments of single biomolecules such as force-induced unfolding reveal details about a few degrees of freedom of a complex system. Molecular dynamics simulations can provide complementary information, but exploration of…
This letter gives results on improving protein-ligand binding affinity predictions based on molecular dynamics simulations using machine learning potentials with a hybrid neural network potential and molecular mechanics methodology…
The ongoing search for high voltage positive electrode materials for Mg batteries has been primarily hampered by poor Mg mobility in bulk oxide frameworks. Motivated by the presence of Mo$_3$ clusters that can facilitate charge…
We analyze the possible phase diagrams of a simple model for an associating liquid proposed previously. Our two-dimensional lattice model combines oreintati onal ice-like interactions and \"{}Van der Waals\"{} interactions which may be…