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Hypothesis:Diffusion in confinement is an important fundamental problem with significant implications for applications of supported liquid phases. However, resolving the spatially dependent diffusion coefficient, parallel and perpendicular…
When an ionic liquid adsorbs onto a porous electrode, its ionic arrangement is deeply modified due to a screening of the Coulombic interactions by the metallic surface and by the confinement imposed upon it by the electrode's morphology. In…
The field of nanofluidics has shown considerable progress over the past decade thanks to key instrumental advances, leading to the discovery of a number of exotic transport phenomena for fluids and ions under extreme confinement. Recently,…
Chemical reactions inside cells are typically subject to the effects both of the cell's confining surfaces and of the viscoelastic behavior of its contents. In this paper, we show how the outcome of one particular reaction of relevance to…
Molecular dynamics (MD) simulations were performed to investigate the influence of mechanical strain on irradiation-induced defect and dislocation evolution in nickel single crystals subjected to cumulative overlapping 5 keV collision…
We study the effect of spatial confinement on the strength of propulsive diffusiophoretic forces acting on a particle that generates density gradients by exploiting the chemical free energy of its environment. Using a recently proposed…
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…
The percentage and sequence of AT and GC base pairs and charges on the DNA backbone contribute significantly to the stiffness of DNA. This elastic property of DNA also changes with small interacting ligands. The single-molecule force…
Nano-clustering occurs in the monophasic "pre-Ouzo" region of ternary liquid mixtures without the use of surfactants. This study is proposed to elucidate the nucleation and stability of multiscale nanodomains in a surfactant-free…
We study the electron dynamics at a monocrystalline Pd(111) surface with stepped vicinal nanostructures modeled in a simple Kronig-Penney scheme. The unoccupied bands of the surface are resonantly excited \textit{via} the resonant charge…
Many studies have revealed that confined water chain flipping is closely related to the spatial size and even quantum effects of the confinement environment. Here, we show that these are not the only factors that affect the flipping process…
The growing significance of RNA engineering in diverse biological applications has spurred interest in developing AI methods for structure-based RNA design. While diffusion models have excelled in protein design, adapting them for RNA…
Recent biological experiments have shown that certain types of cells are able to move in structured and confined environment even without the activation of focal adhesion. Focusing on this particular phenomenon and based on previous works,…
Co-optimizing mRNA sequences for both codon optimality and secondary structure is crucial for producing stable and efficacious mRNA therapeutics. Codon optimization, which adjusts nucleotide sequences to enhance translational efficiency,…
Molecular clouds interacting with supernova remnants may be subject to a greatly enhanced irradiation by cosmic rays produced at the shocked interface between the ejecta and the molecular gas. Over the past decade, broad-band observations…
We introduce model folding, a novel data-free model compression technique that merges structurally similar neurons across layers, significantly reducing the model size without the need for fine-tuning or access to training data. Unlike…
We present two methods for characterization of motional-mode configurations that are generally applicable to the weak and strong-binding limit of single or multiple trapped atomic ions. Our methods are essential to realize control of the…
It has been shown that minimum free energy structure for RNAs and RNA-RNA interaction is often incorrect due to inaccuracies in the energy parameters and inherent limitations of the energy model. In contrast, ensemble based quantities such…
Using both theoretical modeling and computer simulations we study a model system for DNA interactions in the vicinity of charged membranes. We focus on the polarization of the mobile charges in the membranes due to the nearby charged rods…
We study how confining the equilibrium hard-sphere fluid to restrictive one- and two-dimensional channels with smooth interacting walls modifies its structure, dynamics, and entropy using molecular dynamics and transition-matrix Monte Carlo…