Related papers: A coarse-grained model with implicit salt for RNAs…

We describe quantitatively a RNA molecule under the influence of an external force exerted at its two ends as in a typical single-molecule experiment. Our calculation incorporates the interactions between nucleotides by using the…

Background: MR-based subchondral bone effectively predicts knee osteoarthritis. However, its clinical application is limited by the cost and time of MR. Purpose: We aim to develop a novel distillation-learning-based method named SRRD for…

DNA bending is biologically important for genome regulation and is relevant to a range of nanotechnological systems. Recent results suggest that sharp bending is much easier than implied by the widely-used worm-like chain model; many of…

We introduce a novel fully convolutional neural network (FCN) architecture for predicting the secondary structure of ribonucleic acid (RNA) molecules. Interpreting RNA structures as weighted graphs, we employ deep learning to estimate the…

It has been well accepted that the RNA secondary structures of most functional non-coding RNAs (ncRNAs) are closely related to their functions and are conserved during evolution. Hence, prediction of conserved secondary structures from…

We aim to investigate relationships between select processing parameters or inputs (composition, temperature, annealing time) and two structural parameters, specifically, the mean radius and volume fraction of the Fe$_3$Si nanocrystals. To…

We present a panoramic view of the utility of coarse-grained (CG) models to study folding and functions of proteins and RNA. Drawing largely on the methods developed in our group over the last twenty years, we describe a number of key…

We investigate the impact of 3D hydrodynamical model atmospheres of red giant stars at different metallicities on the formation of spectral lines of a number of ions and molecules. We carry out realistic 3D simulations of surface convection…

The flexibility and stiffness of small DNA play a fundamental role ranging from several biophysical processes to nano-technological applications. Here, we estimate the mechanical properties of short double-stranded DNA (dsDNA) having length…

The kinetic folding of RNA sequences into secondary structures is modeled as a complex adaptive system, the components of which are possible RNA structural rearrangements (SRs) and their associated bases and base pairs. RNA bases and base…

Conformational entropy for atomic-level, three dimensional biomolecules is known experimentally to play an important role in protein-ligand discrimination, yet reliable computation of entropy remains a difficult problem. Here we describe…

Aims: We introduce a new deep-learning approach for the reconstruction of 3D dust density and temperature distributions from multi-wavelength dust emission observations on the scale of individual star-forming cloud cores (<0.2pc). Methods:…

The ongoing effort to detect and characterize physical entanglement in biopolymers has so far established that knots are present in many globular proteins and also abound in viral DNA packaged inside bacteriophages. RNA molecules, on the…

Given the importance of non-coding RNAs to cellular regulatory functions and rapid growth of RNA transcripts, computational prediction of RNA tertiary structure remains highly demanded yet significantly challenging. Even for a short RNA…

The graph neural network (GNN) has been a powerful deep-learning tool in chemistry domain, due to its close connection with molecular graphs. Most GNN models collect and update atom and molecule features from the fed atom (and, in some…

The observation by Ke et al. [Science 338, 1177 (2012)] that large numbers of short, pre-designed DNA strands can assemble into three-dimensional target structures came as a great surprise, as no colloidal self-assembling system has ever…

Predicting protein-ligand binding affinity is an essential part of computer-aided drug design. However, generalisable and performant global binding affinity models remain elusive, particularly in low data regimes. Despite the evolution of…

Recent single-molecule pulling experiments have shown how it is possible to manipulate RNA molecules using optical tweezers force microscopy. We investigate a minimal model for the experimental setup which includes a RNA molecule connected…

We study the effects of the shear force on the rupture mechanism on a double stranded DNA. Motivated by recent experiments, we perform the atomistic simulations with explicit solvent to obtain the distributions of extension in hydrogen and…

We use computer simulations to investigate the effect of salt on homogeneous ice nucleation. The melting point of the employed solution model was obtained both by direct coexistence simulations and by thermodynamic integration from previous…