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The conformation and the phase diagram of a membrane protein are investigated via grand canonical ensemble approach using a homopolymer model. We discuss the nature and pathway of $\alpha$-helix integration into the membrane that results…
Evolutionary models measure the probability of amino acid substitutions occurring over different evolutionary distances. We examine various evolutionary models based on empirically derived amino acid substitution matrices. The models are…
T cell receptors (TCRs) bind foreign or self-peptides attached to major histocompatibility complex (MHC) molecules, and the strength of this interaction determines T cell activation. Optimizing the ability of T cells to recognize a…
We present a comparative analysis of large-scale topological and evolutionary properties of transcription networks in three species, the two distant bacteria E. coli and B. subtilis, and the yeast S. cerevisiae. The study focuses on the…
We investigate membrane-mediated interactions between transmembrane proteins using coarse-grained models. We compare the effective potential of mean force (PMF) between two proteins, which are always aligned parallel to the z-axis of the…
Nuclear pore complexes (NPCs) are very selective filters that monitor the transport between the cytoplasm and the nucleoplasm. Two models have been suggested for the plug of the NPC. They are (i) it is a reversible hydrogel or (ii) it is a…
Cancer is a complex disease characterized by uncontrolled cell growth and proliferation. T cell receptors (TCRs) are essential proteins for the adaptive immune system, and their specific recognition of antigens plays a crucial role in the…
Proteins are complex biomolecules that play a central role in various biological processes, making them critical targets for breakthroughs in molecular biology, medical research, and drug discovery. Deciphering their intricate, hierarchical…
The self-organization of proteins into enriched compartments and the formation of complex patterns are crucial processes for life on the cellular level. Liquid-liquid phase separation is one mechanism for forming such enriched compartments.…
The in silico design of peptides and proteins as binders is useful for diagnosis and therapeutics due to their low adverse effects and major specificity. To select the most promising candidates, a key matter is to understand their…
The question of whether proteins originate from random sequences of amino acids is addressed. A statistical analysis is performed in terms of blocked and random walk values formed by binary hydrophobic assignments of the amino acids along…
It has been conjectured that evolution exerted pressure to preserve amino acids bearing thermodynamic, kinetic, and functional roles. In this letter we show that the physical requirement to maintain protein stability gives rise to a…
Proteins are the "work horses" in biological systems. In almost all functions specific proteins are involved. They control molecular transport processes, stabilize the cell structure, enzymatically catalyze chemical reactions; others act as…
We investigate the outflux of ions through the channels in a cell membrane. The channels undergo an open/close cycle according to a periodic schedule. Our study is based both on theoretical considerations relying on homogenization theory,…
The predominant structural protein in vertebrates is collagen, which plays a key role in extracellular matrix and connective tissue mechanics. Despite its prevalence and physical importance in biology, the mechanical properties of molecular…
Cellular membranes are elastic lipid bilayers that contain a variety of proteins, including ion channels, receptors, and scaffolding proteins. These proteins are known to diffuse in the plane of the membrane and to influence the bending of…
Interactions mediated by the cell membrane between inclusions, such as membrane proteins or antimicrobial peptides, play important roles in their biological activity. They also constitute a fascinating challenge for physicists, since they…
In the protein sequence space, natural proteins form clusters of families which are characterized by their unique native folds whereas the great majority of random polypeptides are neither clustered nor foldable to unique structures. Since…
An ensemble of LDPC convolutional codes with parity-check matrices composed of permutation matrices is considered. The convergence of the iterative belief propagation based decoder for terminated convolutional codes in the ensemble is…
Membrane phase behavior induced by the binding of curvature-inducing proteins is studied by a combination of analytical and numerical approaches. In thermal equilibrium under the detailed balance between binding and unbinding, the membrane…