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Semiconductor heterostructures based on layered two-dimensional transition metal dichalcogenides (TMD) interfaced to gallium nitride (GaN) are excellent material systems to realize broadband light emitters and absorbers. The surface…
The melting of a homopolymer double-stranded (ds) deoxyribonucleic acid (DNA) in the dilute limit is studied numerically in the presence of an attractive and impenetrable surface on a simple cubic lattice. The two strands of the DNA are…
The computer-aided folding of biomolecules, particularly RNAs, is one of the most difficult challenges in computational structural biology. RNA tetraloops are fundamental RNA motifs playing key roles in RNA folding and RNA-RNA and…
We study using Monte Carlo simulations the finite-size scaling behavior of the interfacial adsorption of the two-dimensional square-lattice $q$-states Potts model. We consider the pure and random-bond versions of the Potts model for $q =…
An extension of the Random Sequential Adsorption (RSA) model has been proposed recently, motivated by the coverage of oil droplets by DNA-functionalized colloidal particles. Particles arrive to a flat substrate with a uniform flux F but…
This paper builds upon our previous work on the Reconciled Polynomial Network (RPN). The original RPN model was designed under the assumption of input data independence, presuming the independence among both individual instances within data…
Computational identification of unknown adsorption and desorption rates is discussed in conjunction with reactive flow considered at pore scale. The reactive transport is governed by incompressible Stokes equations, coupled with…
How do protein structure prediction models fold proteins? We investigate this question by tracing how ESMFold folds a beta hairpin, a prevalent structural motif. Through counterfactual interventions on model latents, we identify two…
Neuro-symbolic methods integrate neural architectures, knowledge representation and reasoning. However, they have been struggling at both dealing with the intrinsic uncertainty of the observations and scaling to real-world applications.…
Mechanical unfolding of RNA structures, ranging from hairpins to ribozymes, using laser optical tweezer (LOT) experiments have begun to reveal the features of the energy landscape that cannot be easily explored using conventional…
Capillarity-dominated two-phase displacement in porous media often continues beyond the initial invasion-percolation (IP) breakthrough, as surfactants alter interfacial properties and reopen pathways once sealed by capillary forces. This…
The assembly of banana-shaped rodlike proteins on membranes, and the associated membrane shape transformations, are investigated by analytical theory and coarse-grained simulations. The membrane-mediated interactions between two…
We investigate the conformation, position, and dynamics of core-shell nanoparticles (CSNPs) composed of a silica core encapsulated in a cross-linked poly-N-isopropylacrylamide shell at a water-oil interface for a systematic range of core…
The SARS-CoV-2 RNA pseudoknot is a promising target for antiviral intervention, as it regulates the efficiency of $-$1 programmed ribosomal frameshifting ($-$1 PRF), a mechanism that is essential for viral protein synthesis. The pseudoknot…
The determination of phase behavior and, in particular, the nature of phase transitions in two-dimensional systems is often clouded by finite size effects and by access to the appropriate thermodynamic regime. We address these issues using…
Accurately predicting complex protein-protein interactions (PPIs) is crucial for decoding biological processes, from cellular functioning to disease mechanisms. However, experimental methods for determining PPIs are computationally…
Protein translation is one of the most important processes in cell life but, despite being well understood biochemically, the implications of its intrinsic stochastic nature have not been fully elucidated. In this paper we develop a…
The OH-terminated self-assembled monolayers, as protein-resistant surfaces, have significant potential in biocompatible implant devices, which can avoid or reduce adverse reactions caused by protein adhesion to biomaterial surfaces, such as…
The ribosome flow model (RFM) is a phenomenological model for the unidirectional flow of particles along a 1D chain of $n$ sites. The RFM has been extensively used to study the dynamics of ribosome flow along a single mRNA molecule during…
We study the behavior of five proteins at the air-water and oil-water interfaces by all-atom molecular dynamics. The proteins are found to get distorted when pinned to the interface. This behavior is consistent with the phenomenological way…