Related papers: Sub-residue sharpness of protein helix-coil transi…
We provide a detailed analysis of the boundary layers for mixed hyperbolic-parabolic systems in one space dimension and small amplitude regimes. As an application of our results, we describe the solution of the so-called boundary Riemann…
We consider a noncompact lattice formulation of the three-dimensional electrodynamics with $N$-component complex scalar fields, i.e., the lattice Abelian-Higgs model with noncompact gauge fields. For any $N\ge 2$, the phase diagram shows…
The conformal boundary of a hyperbolic $3$-manifold $M$ is a union of Riemann surfaces. If any of these Riemann surfaces has a nontrivial Teichm\"uller space, then the hyperbolic metric of $M$ can be deformed quasi-isometrically. These…
The functionality of proteins is related to their structure in the native state. Protein structures are made up of emergent building blocks of helices and almost planar sheets. A simple coarse-grained geometrical model of a flexible tube…
Models of protein energetics which neglect interactions between amino acids that are not adjacent in the native state, such as the Go model, encode or underlie many influential ideas on protein folding. Implicit in this simplification is a…
We investigate nonequilibrium dynamics and weak ergodicity breaking in a harmonically trapped spin-$3/2$ Fermi gas by using the time-dependent Hartree-Fock equation. The Shannon entropy remains bounded and oscillatory throughout the…
The evolutionary trajectory of a protein through sequence space is constrained by function and three-dimensional (3D) structure. Residues in spatial proximity tend to co-evolve, yet attempts to invert the evolutionary record to identify…
We provide a statistical and correlational analysis of the spatial and energetic properties of equilibrium configurations of a few-body system of two to eight equally charged classical particles that are confined on a one-dimensional…
It is not merely the position of residues that are of utmost importance in protein function and stability, but the interactions between them. We illustrate, by using a network construction on a set of 595 non-homologous proteins, that…
Four-dimensional state space geometry is worked out for the exactly solved one-dimensional spin-3/2 lattice with a Blume-Emery-Griffiths (BEG) Hamiltonian as well as a more general one with a term containing a non-zero field coupling to the…
Biological information processing as implemented by regulatory and signaling networks in living cells requires sufficient specificity of molecular interaction to distinguish signals from one another, but much of regulation and signaling…
This paper builds upon the fundamental work of Niwa et al. [34], which provides the unique possibility to analyze the relative aggregation/folding propensity of the elements of the entire Escherichia coli (E. coli) proteome in a cell-free…
A microscopic theory of the free energy barriers and folding routes for minimally frustrated proteins is presented, greatly expanding on the presentation of the variational approach outlined previously [J. J. Portman, S. Takada, P. G.…
The mechanisms by which a protein's 3D structure can be determined based on its amino acid sequence have long been one of the key mysteries of biophysics. Often simplistic models, such as those derived from geometric constraints, capture…
The relation between dynamics and structure in systems of Brownian bidisperse 2D hard disks with arrested dynamics is examined using numerical simulations. Surprisingly, the suspensions show dynamic arrest at an area fraction of {\phi}…
Self-consistency based Kohn-Sham density functional theory (KS-DFT) electronic structure calculations with Gaussian basis sets are reported for a set of 17 protein-like molecules with geometries obtained from the protein data bank. It is…
The relation between cooperativity of protein folding and the Random-Field Ising Model (RFIM) is established. Generalization of the Imry-Ma argument predicts cooperative folding transition for small heterogeneity of the interactions…
We consider the low-energy particle-particle scattering properties in a periodic simple cubic crystal. In particular, we investigate the relation between the two-body scattering length and the energy shift experienced by the lowest-lying…
We derive a continuum model for incompatible elasticity as a variational limit of a family of discrete nearest-neighbor elastic models. The discrete models are based on discretizations of a smooth Riemannian manifold $(M,\mathfrak{g})$,…
One-dimensional Bose-Hubbard models are well known to obey a transition from regular to quantum-chaotic spectral statistics. We are extending this concept to relatively simple two-dimensional many-body models. Also in two dimensions a…