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By means of extensive replica-exchange simulations of generic coarse-grained models for helical polymers, we systematically investigate the structural transitions into all possible helical phases for flexible and semiflexible elastic…
A new approximate method to calculate exchange-correlation contributions in the framework of first-principles tight-binding molecular dynamics methods has been developed. In the proposed scheme on-site (off-site) exchange-correlation matrix…
Liquid liquid phase separation (LLPS) of proteins is an intracellular process that is widely used by cells for many purposes. In living cells (in vivo), LLPS occurs in complex and crowded environments. Amino acids (AAs) are vital components…
We illuminate the many-body effects underlying the structure, formation, and dissolution of cellular adhesion domains in the presence and absence of forces. We consider mixed Glauber-Kawasaki dynamics of a two-dimensional model of…
Sex hormone-binding globulin (SHBG) is a binding protein that regulates availability of steroids hormones in the plasma. Although best known as steroid carrier, studies have associated SHBG in modulating behavioral aspects related to sexual…
Electrostatic interactions play a fundamental role in the structure and function of proteins. Due to ionizable amino acid residues present on the solvent-exposed surfaces of proteins, the protein charge is not constant but varies with the…
Aspartate carbamoyltransferase (ATCase) is a large dodecameric enzyme with six active sites that exhibits allostery: its catalytic rate is modulated by the binding of various substrates at distal points from the active sites. A recently…
The Histone-like Nucleoid Structuring protein (H-NS) is a nucleoid-associated protein, which is involved in both gene regulation and DNA compaction. Although it is a key player in genome organization by forming bridges between DNA duplexes,…
We present a systematic study of the high-pressure FeSe phase performed by means of the first-principle electronic structure calculations. Basing on available experimental information about the unit cell geometry we calculate the band…
Solid state quantum computing proposals rely on adiabatic operations of the exchange gate among localized spins in nanostructures. We study corrections to the Heisenberg interaction between lateral semiconductor quantum dots in an external…
The structural properties of liquid GeSe$_2$ are studied by using first-principles molecular dynamics in conjuncton with the Becke, Lee, Yang and Parr (BLYP) generalized gradient approximation for the exchange and correlation energy. The…
The spatiotemporal organisation of proteins and lipids on the cell surface has direct functional consequences for signaling, sorting and endocytosis. Earlier studies have shown that multiple types of membrane proteins including…
Bose-Fermi mixtures naturally appear in various physical systems. In semiconductor heterostructures, such mixtures can be realized, with bosons as excitons and fermions as dopant charges. However, the complexity of these hybrid systems…
We discuss the isoscalar $T=0, S=1$ pairing correlation in the low-lying states of $^{102}{\rm Sb}={}^{100}{\rm Sn}+p+n$ nucleus. To this end, we employ ${\rm core}+p+n$ three-body model with the model space constructed by self-consistent…
Ab-initio dynamical simulation is used to study the liquid Ga-Se system at the three concentrations Ga$_2$Se, GaSe and Ga$_2$Se$_3$ at the temperature 1300~K. The simulations are based on the density functional pseudopotential technique,…
We study the stability of solid- and supersolid (SS) phases of a three-dimensional spin- and a hardcore-Bose-Hubbard models on a body-centered cubic lattice. To see the quantum effects on the stability of the SS phase, we model the…
Availability of high-resolution crystal structures of ribosomal subunits of different species opens a route to investigate about molecular interactions between its constituents and stabilization strategy. Structural analysis of the small…
Adhesion between a T cell and an antigen presenting cell is achieved by TCR-pMHC and LFA1-ICAM1 protein complexes. These segregate to form a special pattern, known as the immunological synapse (IS), consisting of a central quasi-circular…
We show that a pair of overlapping Majorana bound states (MBSs) forming a partially-separated Andreev bound state (ps-ABS) represents a generic low-energy feature in spin-orbit coupled semiconductor-superconductor (SM-SC) hybrid nanowires…
Proline (Pro) is one kind of proteinogenic amino acid and an important signaling molecule in the process of metabolism. Hydroxyproline (Hyp) is a product on Pro oxygen sensing post-translational modification (PTM), which is efficiently…