Related papers: Structural and ultrametric properties of twenty(L-…
A minimal off-lattice model for alpha-helical proteins is presented. It is based on hydrophobicity forces and sequence independent local interactions. The latter are chosen so as to favor the formation of alpha-helical structure. They model…
The polyalanine-based peptide series Ac-Ala_n-LysH+ (n=5-20) is a prime example that a secondary structure motif which is well-known from the solution phase (here: helices) can be formed in vacuo. We here revisit this conclusion for…
Encoding the complex features of an energy landscape is a challenging task, and often chemists pursue the most salient features (minima and barriers) along a highly reduced space, i.e. 2- or 3-dimensions. Even though disconnectivity graphs…
Thermodynamics of helix-coil transitions in amino-acid homo-oligomers are studied by the recently proposed multicanonical algorithms. Homo-oligomers of length 10 are considered for three characteristic amino acids, alanine (helix former),…
A typical protein structure is a compact packing of connected alpha-helices and/or beta-strands. We have developed a method for generating the ensemble of compact structures a given set of helices and strands can form. The method is tested…
We investigate the formation of polycrystalline structures in a class of particle systems. The atomistic energy is modeled as a sum of particle energies that favor atoms being locally isometric to a reference lattice. The discrete frame…
Particles interacting through long-range attraction and short-range repulsion given by power-laws have been widely used to model physical and biological systems, and to predict or explain many of the patterns they display. Apart from rare…
We study equilibrium configurations of non-Euclidean plates, in which the reference metric is uniaxially periodic. This work is motivated by recent experiments on thin sheets of composite thermally responsive gels [1]. Such sheets bend…
Astrophysical tests of the stability of fundamental couplings, such as the fine-structure constant $\alpha$, are a powerful probe of new physics. Recently these measurements, combined with local atomic clock tests and Type Ia supernova and…
Helices are a key folding motif in protein structure. The question which factors determine helix stability for a given polypeptide or protein is an ongoing challenge. Here we use van der Waals corrected density-functional theory to address…
Persistent homology is a relatively new tool often used for \emph{qualitative} analysis of intrinsic topological features in images and data originated from scientific and engineering applications. In this paper, we report novel…
In this paper we characterise the equilibrium measure for a nonlocal and anisotropic weighted energy describing the interaction of positive dislocations in the plane. We prove that the minimum value of the energy is attained by a measure…
The flexibility of short DNA chains is investigated via computation of the average correlation function between dimers which defines the persistence length. Path integration techniques have been applied to confine the phase space available…
We study minimum energy configurations of $N$ particles in $\R^3$ of charge -1 (`electrons') in the potential of $M$ particles of charges $Z_\alpha>0$ (`atomic nuclei'). In a suitable large-N limit, we determine the asymptotic electron…
The formation/binding energetics and length scales associated with the interaction between He atoms and grain boundaries in BCC alpha-Fe was explored. Ten different low Sigma grain boundaries from the <100> and <110> symmetric tilt grain…
We present extensive calculations of the structure and the evolution of low-massstars in the range 0.07-0.8 $\msol$, for metallicities $-2.0\le \mh \le 0.0$. These calculations are based on the most recent description of the microphysics…
An atomic protein model with a minimalistic potential is developed and then tested on an alpha-helix and a beta-hairpin, using exactly the same parameters for both peptides. We find that melting curves for these sequences to a good…
Several commonly observed physical and biological systems are arranged in shapes that closely resemble an honeycomb cluster, that is, a tessellation of the plane by regular hexagons. Although these shapes are not always the direct product…
We investigate low energy structures of a lattice with dislocations in the context of nonlinear elasticity. We show that these low energy configurations exhibit in the limit a Cosserat-like behavior. Moreover, we give bounds from above and…
In this paper we consider nonlocal energies defined on probability measures in the plane, given by a convolution interaction term plus a quadratic confinement. The interaction kernel is $-\log|z|+\alpha\, x^2/|z|^2, \; z=x+iy,$ with $-1 <…