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We study an interacting two-flavor fermionic system via field-theoretical functional renormalization group (RG). Each flavor, labeled by $\pm$, has a dispersion of $E^{\pm}=c k^{2\alpha}-\mu^\pm$ with tunable real exponent $\alpha>0$. The…
Proteins are essential for life, and their structure determines their function. The protein secondary structure is formed by the folding of the protein primary structure, and the protein tertiary structure is formed by the bending and…
Wang-Landau sampling has been applied to investigate the thermodynamics and structural properties of a lattice hydrophobic-polar heteropolymer (the HP protein model) interacting with an attractive substrate. For simplicity, we consider a…
Protein language models such as ESM-2 learn rich residue representations that achieve strong performance on protein function prediction, but their features remain difficult to interpret as structural $\&$ evolutionary signals are encoded in…
Recent studies attracted the attention on the inherent structure landscape (ISL) approach as a reduced description of proteins allowing to map their full thermodynamic properties. However, the analysis has been so far limited to a single…
Protein folding cooperativity is defined by the nature of the finite-size thermodynamic transition exhibited upon folding: two-state transitions show a free energy barrier between the folded and unfolded ensembles, while downhill folding is…
We modify and extend the recently developed statistical mechanical model for predicting the thermodynamic properties of chain molecules having noncovalent double-stranded conformations, as in RNA or ssDNA, and $\beta-$sheets in protein, by…
Under the most common experimental conditions, the adsorption of proteins to solid surfaces is an spontaneous process that leads to a rather compact layer of randomly oriented molecules. Due to the importance of this process for the…
The dynamics of gene transcription is tightly regulated in eukaryotes. Recent experiments have revealed various kinds of transcriptional dynamics, such as RNA polymerase II pausing, that involves regulation at the transcription initiation…
As a consequence of the rugged landscape of RNA molecules their folding is described by the kinetic partitioning mechanism according to which only a small fraction ($\phi_F$) reaches the folded state while the remaining fraction of…
Peptide surfactants (PEPS) are studied to capture and retain rare earth elements (REEs) at air-water interfaces to enable REE separations. Peptide sequences, designed to selectively bind REEs, depend crucially on the position of ligands…
The present paper is dedicated to the 2-dimensional Interacting Partially Directed Self Avoiding Walk constrained to remain in the upper-half plan and interacting with the horizontal axis. The model has been introduced in \cite{F90} to…
The most important function of proteins may well be to bind to other biomolecules. It has long been felt that kinetic rates of bond formation and dissociation between soluble receptors and ligands might account for most features of the…
Two-dimensional transition metal dichalcogenides (TMDCs) have been extensively investigated due to their tunable properties. In this work, density functional theory (DFT) is employed to investigate the adsorption behavior and sensing…
The ribosome flow model (RFM) is a phenomenological model for the flow of particles along a 1D chain of $n$ sites. It has been extensively used to study ribosome flow along the mRNA molecule during translation. When the transition rates…
Based on a newly developed contact-density chain-growth algorithm, we have simulated a nongrafted peptide in the vicinity of different attractive substrates. We analyzed the specificity of the peptide adsorption by focussing on the…
A solid-on-solid growth model for dimer adsorption and desorption is introduced and studied numerically. The special property of the model is that dimers can only desorb at the edges of terraces. It is shown that the model exhibits a…
We investigate the interplay between post-translational folding and escape of two small single-domain proteins at the ribosomal exit tunnel by using Langevin dynamics with coarse-grained models. It is shown that at temperatures lower or…
Designing protein sequences that fold into a target 3-D structure, termed as the inverse folding problem, is central to protein engineering. However, it remains challenging due to the vast sequence space and the importance of local…
Although the immobilization of oligonucleotides (nucleic acid) on mineral surfaces is at the basis of different biotechnological applications, an atomistic understanding of the interaction of the nucleic acid components with the titanium…