Related papers: Sub-residue sharpness of protein helix-coil transi…
In this study we evaluate, at full atomic detail, the folding processes of two small helical proteins, the B domain of protein A and the Villin headpiece. Folding kinetics are studied by performing a large number of ab initio Monte Carlo…
We consider a chain of $n$ coupled oscillators placed on a one-dimensional lattice with periodic boundary conditions. The interaction between particles is determined by a weakly anharmonic potential $V_n = r^2/2 + \sigma_nU(r)$, where $U$…
The biological function of a protein stems from its 3-dimensional structure, which is thermodynamically determined by the energetics of interatomic forces between its amino acid building blocks (the order of amino acids, known as the…
The tridimensional configuration and the twist density of helical rods with varying cross section radius are studied within the framework of the Kirchhoff rod model. It is shown that the twist density increases when the cross section radius…
The folding ability of a heteropolymer model for proteins subject to Monte Carlo dynamics on a simple cubic lattice is shown to be strongly correlated with the energy gap between the native state and the structurally dissimilar part of the…
Despite recent breakthroughs in understanding how protein sequence relates to structure and function, considerably less attention has been paid to the general features of protein surfaces beyond those regions involved in binding and…
The Spatial Convolution Model (SCM) analyzes allostery based on the spatial evolution of the docking protein elastic media, whereby convolution of the media in response to wave propagation is solved as a function of Z fluctuations and…
The two-dimensional nature of engineered transition-metal ultra-thin oxide films offers a large playground of yet to be fully understood physics. Here, we study pristine SrVO$_3$ monolayers that have recently been predicted to display a…
The sequence of a protein is not only constrained by its physical and biochemical properties under current selection, but also by features of its past evolutionary history. Understanding the extent and the form that these evolutionary…
We numerically study the problem of two fermions in a three dimensional optical lattice interacting via a zero-range Feshbach resonance, and display the dispersions of the bound states as a two-particle band structure with unique features…
This work examines the conformational ensemble involved in $\beta$-hairpin folding by means of advanced molecular dynamics simulations and dimensionality reduction. A fully atomistic description of the protein and the surrounding solvent…
Unraveling the relation between the chemical structure of small drug-like compounds and their rate of passive permeation across lipid membranes is of fundamental importance for pharmaceutical applications. The elucidation of a comprehensive…
We study the effect of varying the boundary condition on the spectral function of a finite 1D Hubbard chain, which we compute using direct (Lanczos) diagonalization of the Hamiltonian. By direct comparison with the two-body response…
In this paper we extend the Gaussian self-consistent method to permit study of the equilibrium and kinetics of conformational transitions for heteropolymers with any given primary sequence. The kinetic equations earlier derived by us are…
We study the indirect effects of new physics on the phenomenology of the "Higgs-like" particle. Assuming that the recently observed state belongs to a light electroweak doublet scalar and that the SU(2)_L x U(1)_Y symmetry is linearly…
We review the dual relationship between various compact U(1) lattice models and Abelian Higgs models, the latter being the disorder field theories of line-like topological excitations in the systems. We point out that the predicted…
Lattice models, for their coarse-grained nature, are best suited for the study of the ``designability problem'', the phenomenon in which most of the about 16,000 proteins of known structure have their native conformations concentrated in a…
Bound states and collisions of atoms with two-channel two-body interactions in harmonic waveguides are analyzed. The closed-channel contributions to two-atom bound states become dominant in the case of a weak resonance. At low energies and…
Geometrical properties of protein ground states are studied using an algebraic approach. It is shown that independent from inter-monomer interactions, the collection of ground state candidates for any folded protein is unexpectedly small:…
This paper develops the angular and static-channel component of Geometric and Spectral Alignment for residual Jacobian chains. Starting from Cartan-coordinate rigidity and fitted effective-rank windows, we study how dominant singular…