Related papers: Sub-residue sharpness of protein helix-coil transi…
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…
To what extent do general features of folding/unfolding kinetics of small globular proteins follow from their thermodynamic properties? To address this question, we investigate a new simplifed protein chain model that embodies a cooperative…
Motivated by future collider proposals that aim to measure the Higgs properties precisely, we study the partial decay widths of the lightest Higgs boson in the minimal supersymmetric standard model with an emphasis on the parameter region…
We present a model, based on symmetry and geometry, for proteins. Using elementary ideas from mathematics and physics, we derive the geometries of discrete helices and sheets. We postulate a compatible solvent-mediated emergent pairwise…
Nearly a quarter of genomic sequences and almost half of all receptors that are likely to be targets for drug design are integral membrane proteins. Understanding the detailed mechanisms of the folding of membrane proteins is a largely…
A growing number of experimental evidence shows that it is general for a ligand binding protein to have a potential for allosteric regulation and for further evolution. In addition, such proteins generically change their conformation upon…
Elliptic partial differential equations arise in many fields of science and engineering such as steady state distribution of heat, fluid dynamics, structural/mechanical engineering, aerospace engineering and seismology etc. In three…
Understanding of the evolutionary origins of protein structures represents a key component of the understanding of molecular evolution as a whole. Here we seek to elucidate how the features of an underlying protein structural "space" might…
The electrical properties of a set of seven-helix transmembrane proteins, whose space arrangement (3D structure) is known, are investigated by using regular arrays of the amino acids. These structures, specifically cubes, have topological…
The discrete Efimov scaling behavior, well-known in the low-energy spectrum of three-body bound systems for large scattering lengths (unitary limit), is identified in the energy dependence of atom-molecule elastic cross-section in mass…
We exhibit simple lattice systems, motivated by recently proposed cold atom experiments, whose continuum limits interpolate between real and $p$-adic smoothness as a spectral exponent is varied. A real spatial dimension emerges in the…
A generalized computational method for folding proteins with a fully transferable potential and geometrically realistic all-atom model is presented and tested on seven different helix bundle proteins. The protocol, which includes…
We introduce a lattice model of protein conformations which is able to reproduce second structures of proteins (alpha--helices and beta--sheets). This model is based on the following two main ideas. First, we model backbone parts of amino…
Native protein folds often have a high degree of symmetry. We study the relationship between the symmetries of native proteins, and their designabilities -- how many different sequences encode a given native structure. Using a…
We carry out a theoretical study of the vibrational and relaxation properties of naturally-occurring proteins with the purpose of characterizing both the folding and equilibrium thermodynamics. By means of a suitable model we provide a full…
We isolate a geometric mechanism that complements the dynamical suppression of macroscopic interference: In a high-dimensional Hilbert space, almost all state vectors are nearly orthogonal, accommodating an exponentially large reservoir of…
What are the molecular mechanisms that dictate protein-protein binding stability and whether those are related to the ones behind protein fold stability are still largely open questions. Indeed, despite many past efforts, we still lack…
In this study, the distributions of protein structure classes (or folding types) of experimentally determined structures from a legacy dataset and a comprehensive database (SCOP) are modeled precisely with geometric constructs such as…
We investigate the impact of interactions between hidden sectors and the discovered Higgs boson $h_{125}$, allowing for additional invisible decay channels of $h_{125}$. We perform $\chi^2$-fits to the measurements of the Higgs-boson cross…
Protein folding processes are generally described statistically with the help of multidimensional free energy landscape, typically reduced to a 1-D free energy profile along good reaction co-ordinate. There are many physical parameters…