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We investigate the ultralow-frequency Raman response of atomically thin ReS2, a special type of two-dimensional (2D) semiconductors with unique distorted 1T structure. Bilayer and few-layer ReS2 exhibit rich Raman spectra at frequencies…
DNA adsorption on solid or liquid surfaces is a topic of broad fundamental and applied interest. Here we study by x-ray reflectivity the adsorption of monodisperse double-stranded DNA molecules a positively-charged surface, obtained through…
Integrative biomolecular modeling of RNA relies on structural refined collections and accurate experimental data that reflect binding and folding behavior. However, the prediction of such collections remains challenging due to the rugged…
We study the statistical mechanics of RNA secondary structures designed to have an attraction between two different types of structures as a model system for heteropolymer aggregation. The competition between the branching entropy of the…
A theoretical model for the folding of proteins containing disulfide bonds is introduced. The model exploits the knowledge of the native state to favour the progressive establishment of native interactions. At variance with traditional…
In this paper, we present an approach for combining non-rigid structure-from-motion (NRSfM) with deep generative models,and propose an efficient framework for discovering trajectories in the latent space of 2D GANs corresponding to changes…
Protein inverse folding, the task of predicting amino acid sequences for desired structures, is pivotal for de novo protein design. However, existing GNN-based methods typically suffer from restricted receptive fields that miss long-range…
In this work, we propose a novel transport model for soluble surfactants in two-phase flows. In a two-phase flow, the soluble surfactants can adsorb/desorb from/into the bulk of any of the phases to the interface and can modify the…
For cellular functions like division and polarization, protein pattern formation driven by NTPase cycles is a central spatial control strategy. Operating far from equilibrium, no general theory links microscopic reaction networks and…
The structure of the self-cleaving hairpin ribozyme is well characterized, and its folding has been examined in bulk and by single-molecule fluorescence, establishing the importance of cations, especially magnesium in the stability of the…
The well known phenomenon of phase separation in synthetic polymers and proteins has become a major topic in biophysics because it has been invoked as a mechanism of compartment formation in cells, without the need for membranes. Most of…
The folding of RNA and DNA strands plays crucial roles in biological systems and bionanotechnology. However, studying these processes with high-resolution numerical models is beyond current computational capabilities due to the timescales…
A complex network approach to protein folding is proposed. The graph object is the network of shortcut edges present in a native-state protein (SCN0). Although SCN0s are found via an intuitive message passing algorithm (S. Milgram,…
Among the family of TMDs, ReS2 takes a special position, which crystalizes in a unique distorted low-symmetry structure at ambient conditions. The interlayer interaction in ReS2 is rather weak, thus its bulk properties are similar to that…
Capturing molecular dynamics in nanoconfined channels with high spatiotemporal resolution is a key challenge in nanoscience, crucial for advancing catalysis, energy conversion, and molecular sensing. Bottom-up ultrathin plasmonic nanogaps,…
We study theoretically the denaturation of single RNA molecules by mechanical stretching, focusing on signatures of the (un)folding pathway in molecular fluctuations. Our model describes the interactions between nucleotides by incorporating…
Crystalline CaF2 is drawing huge attentions due to its great potential of being the gate dielectric of two-dimensional (2D) material MOSFETs. It is deemed to be much superior than boron nitride and traditional SiO2 because of its larger…
Using force as a probe to map the folding landscapes of RNA molecules has become a reality thanks to major advances in single molecule pulling experiments. Although the unfolding pathways under tension are complicated to predict studies in…
It is the first step for understanding how RNA structure folds from base sequences that to know how its secondary structure is formed. Traditional energy-based algorithms are short of precision, particularly for non-nested sequences, while…
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,…