Related papers: Structural Stability and Immunogenicity of Peptide…
We study the effect of membrane proteins on the shape, composition and thermodynamic stability of the surrounding membrane. When the coupling between membrane composition and curvature is strong enough the nearby composition and shape both…
Self-assembly of polypeptides into fibrillar structures can be initiated by planar surfaces that interact favorably with certain residues. Using a coarse grained model, we systematically studied the folding and adsorption behavior of a…
Cell cell and cell matrix adhesions are fundamental in all multicellular organisms. They play a key role in cellular growth, differentiation, pattern formation and migration. Cell-cell adhesion is substantial in the immune response,…
In this paper we suggest that, under suitable conditions, supervised learning can provide the basis to formulate at the microscopic level quantitative questions on the phenotype structure of multicellular organisms. The problem of…
The concept of network immunity, i.e., the robustness of the network connectivity after a random deletion of edges or vertices, has been investigated in biological or communication networks. We apply this concept to a self-assembling,…
We study the stability of fragments using microscopic binding energy criteria in heavy-ion collisions.
We use ab initio density functional calculations to study the formation and structural as well as thermal stability of cellular foam-like carbon nanostructures. These systems with a mixed $sp^2/sp^3$ bonding character may be viewed as…
Monte Carlo simulations of a simple lattice model of protein folding show two distinct regimes depending on the chain length. The first regime well describes the folding of small protein sequences and its kinetic counterpart appears to be…
Here we develop an approach to bio-structural robustness integrated with structure-function relationship in a unified conceptual and methodological framework, and envision its study using adequate computational and experimental methods. To…
Analytical stability calculation is done to prove stability properties for systems with parameters that do not have explicit values. For systems with three components, the usual method of finding the characteristic polynomial as the…
The major histocompatibility complex (MHC) molecules, which bind peptides for presentation on the cell surface, play an important role in cell-mediated immunity. In light of developing databases and technologies over the years, significant…
We present a novel buckling instability relevant to membrane budding in eukaryotic cells. In this mechanism, curved filaments bind to a lipid bilayer without changing its intrinsic curvature. As more and more filaments adsorb, newly added…
We present a statistical mechanical study of stiff polymers, motivated by experiments on actin filaments and the considerable current interest in polymer networks. We obtain simple, approximate analytical forms for the force-extension…
We formulate a density functional theory that describes the phase behavior of hard rods and depleting polymers, as realized in recent experiments on suspensions of \emph{fd} virus and non-adsorbing polymer. The theory predicts the relative…
Understanding and manipulating the interactions between foreign bodies and cell membranes during endo- and phagocytosis is of paramount importance, not only for the fate of living cells but also for numerous biomedical applications. This…
This review reports some key results in theoretical investigations on configurations of lipid membranes and presents several challenges in this field which involve (i) exact solutions to the shape equation of lipid vesicles; (ii) exact…
Cyclic peptides offer inherent advantages in pharmaceuticals. For example, cyclic peptides are more resistant to enzymatic hydrolysis compared to linear peptides and usually exhibit excellent stability and affinity. Although deep generative…
We investigate the folding behavior of protein sequences by numerically studying all sequences with maximally compact lattice model through exhaustive enumeration. We get the prion-like behavior of protein folding. Individual proteins…
A new general algorithm for optimization of potential functions for protein folding is introduced. It is based upon gradient optimization of the thermodynamic stability of native folds of a training set of proteins with known structure. The…
A large family of deployable filamentary structures can be built by connecting two elastic rods along their length. The resulting structure has interesting shapes that can be stabilized by tuning the material properties of each rod. To…