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Recurrent Neural Networks (RNNs), which are a powerful scheme for modeling temporal and sequential data need to capture long-term dependencies on datasets and represent them in hidden layers with a powerful model to capture more information…
We introduce a solid-on-solid growth process which evolves by random deposition of dimers, surface diffusion, and evaporation of monomers from the edges of plateaus. It is shown that the model exhibits a robust transition from a smooth to a…
For a gas-solid interfacial system where chemical species undergo reversible adsorption, we develop a mesoscopic stochastic modeling method that simulates both gas-phase hydrodynamics and surface coverage dynamics by coupling the Langmuir…
The excess adsorption $\Gamma $ in two-dimensional Ising strips $(\infty \times L)$ subject to identical boundary fields, at both one-dimensional surfaces decaying in the orthogonal direction $j$ as $-h_1j^{-p}$, is studied for various…
These lectures will address two questions. Is there a simple variational principle underlying the existence of secondary motifs in the native state of proteins? Is there a general approach which can qualitatively capture the salient…
RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, experimental determination of RNA structures through X-ray…
The contact map of a protein fold is a graph that represents the patterns of contacts in the fold. It is known that the contact map can be decomposed into stacks and queues. RNA secondary structures are special stacks in which the degree of…
The adsorption behavior of ions at liquid-vapor interfaces exhibits several unexpected yet generic features. In particular, energy and entropy are both minimum when the solute resides near the surface, for a variety of ions in a range of…
Transport of ions and small molecules across the cell membrane against electrochemical gradients is catalyzed by integral membrane proteins that use a source of free energy to drive the energetically uphill flux of the transported…
Rhenium disulfide (ReS2) is a unique TMDC with a strong in-plane anisotropy and weak interlayer coupling. The pronounced anisotropy in the thermal conductivity observed in bulk ReS2 flakes (exceeding 60 nm) makes them valuable for…
The nucleation of gas hydrates is of great interest in flow assurance, global energy demand, and carbon capture and storage. A complex molecular understanding is critical to control hydrate nucleation and growth in the context of potential…
The overdamped thermal ratchet driven by an external (Orstein-Uhlenbeck) noise is revisited. The ratchet we consider is unbounded in space and not necessarily periodic . We briefly discuss the conditions under which current is obtained by…
SrHfO3 is a potential dielectric material for metal-oxide-semiconductor (MOS) devices. SrHfO3/GaAs interface has attracted attention due to its unique properties. In this paper, the interface properties of (001) SrHfO3/GaAs are investigated…
A reliable prediction of 3D protein structures from sequence data remains a big challenge due to both theoretical and computational difficulties. We have previously shown that our kinetostatic compliance method (KCM) implemented into the…
In this study, we tackle the challenging task of predicting secondary structures from protein primary sequences, a pivotal initial stride towards predicting tertiary structures, while yielding crucial insights into protein activity,…
The unique structural properties of interfacial water are at the heart of a vast range of important processes in electrochemistry, climate science, and biophysics. At interfaces, water molecules exhibit preferential orientations and an…
Understanding the principles of protein folding is a cornerstone of computational biology, with implications for drug design, bioengineering, and the understanding of fundamental biological processes. Lattice protein folding models offer a…
Transposable elements may acquire unrelated gene fragments into their sequences in a process called transduplication. Transduplication of protein-coding genes is common in plants, but is unknown of in animals. Here, we report that the…
The binding of a cationic surfactant (hexadecyltrimethylammonium bromide, CTAB) to a negatively charged natural polysaccharide (pectin) at air-solution interfaces, was investigated on single interfaces and in foams, versus the linear charge…
The air-water interface is a highly prevalent phase boundary with a far-reaching impact on natural and industrial processes. Water molecules behave differently at the interface compared to the bulk, exhibiting anisotropic orientational…