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Understanding the mechanism of protein secondary structure formation is an essential part of protein-folding puzzle. Here we describe a simple model for the formation of the $\beta$-hairpin, motivated by the fact that folding of a…
The field of RNA secondary structure prediction has made significant progress with the adoption of deep learning techniques. In this work, we present the RNAformer, a lean deep learning model using axial attention and recycling in the…
Ordered protein layers are the subject of active biomedical research for their usually interesting physicochemical properties, e.g. permeability, stiffness and pours structure. In presented work, we focused on layers build of fibrinogen…
The atomistic characterization of the transition state is a fundamental step to improve the understanding of the folding mechanism and the function of proteins. From a computational point of view, the identification of the conformations…
A model to describe the mechanism of conformational dynamics in secondary protein based on matter interactions is proposed. The approach deploys the lagrangian method by imposing certain symmetry breaking. The protein backbone is initially…
The metastable T' phase in monolayer MoS2 exhibits remarkable persistence despite a strong thermodynamic driving force toward the stable H phase. Using machine learning-accelerated molecular dynamics and first-principles calculations, we…
Proteins work only if folded in their native state, but changes in temperature T and pressure P induce their unfolding. Therefore for each protein there is a stability region (SR) in the T-P thermodynamic plane outside which the biomolecule…
The interface between liquid water and the Pt(111) metal surface is characterized structurally and thermodynamically via reactive molecular dynamics (MD) simulations within the ReaxFF framework. The formation of a distinct buckled adsorbate…
Reactions at solid-water interfaces play a foundational role in water treatment systems, catalysis, chemical separations, and in predicting chemical fate and transport in the environment. Over the last century, experimental measurements and…
Several algorithms for RNA inverse folding have been used to design synthetic riboswitches, ribozymes and thermoswitches, whose activity has been experimentally validated. The RNAiFold software is unique among approaches for inverse folding…
A novel combination of discontinuous molecular dynamics and the Langevin equation, together with an intermediate-resolution model, are used to carry out long (several $\mu$s) simulation and study folding transition and transport of proteins…
The reentrant layering transitions found in rare gas adsorption on solid substrates have conflictually been explained either in terms of preroughening (PR), or of top layer melting-solidification phenomena. We obtain adsorption isotherms of…
Modern interfacial science is increasingly multi-disciplinary. Unique insight into interfacial interactions requires new multimodal techniques for interrogating surfaces with simultaneous complementary physical and chemical measurements. We…
We present a theory for the kinetics of surfactant adsorption at the interface between an aqueous solution and another fluid (air, oil) phase. The model relies on a free-energy formulation. It describes both the diffusive transport of…
We introduce a method for predicting RNA folding pathways, with an application to the most important RNA tetraloops. The method is based on the idea that ensembles of three-dimensional fragments extracted from high-resolution crystal…
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…
We investigate the competitive adsorption of a two-component gas on the surface of an adsorbent whose adsorption properties vary in adsorption due to the adsorbent deformation. The essential difference of adsorption isotherms for a…
Soft particles such as microgels and core-shell particles can undergo significant and anisotropic deformations when adsorbed to a liquid interface. This, in turn, leads to a complex phase behavior upon compression. Here we develop a…
Adsorption properties of chain fluids are of interest from both fundamental and industrial points of view. Density Functional Theory (DFT) based models are among the most appropriate techniques allowing to describe surface phenomena. At the…
Over the last few years, ReS2 has generated a myriad of unattended queries regarding its structure, the concomitant thickness dependent electronic properties and apparently contrasting experimental optical response. In this work, with…