Related papers: Atomic Scale Fractal Dimensionality in Proteins
A dynamic scaling of a diffusion process involving the Langmuir type adsorption is studied. We find dynamic scaling functions in one and two dimensions and compare them with direct numerical simulations, and we further study the dynamic…
Thermal unfolding of proteins is compared to folding and mechanical stretching in a simple topology-based dynamical model. We define the unfolding time and demonstrate its low-temperature divergence. Below a characteristic temperature,…
We use persistent homology in order to define a family of fractal dimensions, denoted $\mathrm{dim}_{\mathrm{PH}}^i(\mu)$ for each homological dimension $i\ge 0$, assigned to a probability measure $\mu$ on a metric space. The case of…
In this paper the amorphous/solid to disorder liquid structural phase transitions of an anomalous confined fluid is analyzed using their local fractal dimension. The model is a system of particles interacting through a two length scales…
The large values of the singlet and triplet scattering lengths locate the two-nucleon system close to the unitary limit, the limit in which these two values diverge. As a consequence, the system shows a continuous scale invariance which…
Atomic diffusion is usually understood as a succession of random, independent displacements of an adatom over the surface's potential energy landscape. Nevertheless, an analysis of Molecular Dynamics simulations of self-diffusion on Cu(111)…
Our first experience of dimension typically comes in the intuitive Euclidean sense: a line is one dimensional, a plane is two-dimensional, and a volume is three-dimensional. However, following the work of Mandelbrot \cite{mandelbrot},…
The folding and structure of biomacromolecules depend on the 3D distributions of their constituents, which ultimately controls their functionalities and interactions with other biomacromolecules. Atom probe tomography (APT) with its…
A contribution is presented to the study of hadron spectroscopy through the use of fractals and discrete scale invariance implying log-periodic corrections to continuous scaling. The masses of mesons and baryons, reported by the Particle…
For many biological applications of molecular dynamics (MD) the importance of good sampling in conformational space makes it necessary to eliminate the fastest motions from the system in order to increase the time step. An accurate…
In the dynamics of atoms and molecules at metal surfaces, electron-hole pair excitations can play a crucial role. In the case of hyperthermal hydrogen atom scattering, they lead to nonadiabatic energy loss and highly inelastic scattering.…
We show that in experimental atomic force microscopy studies of the lifetime distribution of mechanically stressed folded proteins the effects of externally applied fluctuations can not be distinguished from those of internally present…
We show how to localize and quantify the functional evolutionary constraints on natural proteins. The method compares the perturbations caused by local sequence variants to the energetics of the protein folding process and to the…
Precision spectroscopy of atoms and molecules allows one to search for and to put stringent limits on the variation of fundamental constants. These experiments are typically interpreted in terms of variations of the fine structure constant…
Using analytical calculations and computer simulations we consider both the lateral diffusion of a membrane protein and the fluctuation spectrum of the membrane in which the protein is embedded. The membrane protein interacts with the…
We establish a correspondence between Pavlovian conditioning processes and fractals. The association strength at a training trial corresponds to a point in a disconnected set at a given iteration level. In this way, one can represent a…
Jamming is a geometric phase transition occurring in dense particle systems in the absence of temperature. We use computer simulations to analyse the effect of thermal fluctuations on several signatures of the transition. We show that…
New definitions of the structural susceptibilities based on the fluctuations of distances to the native state of toy protein models are proposed. The calculation of such susceptibilities does not require the basin of native state and the…
The image fractal analysis is actively used in all science branches. In particular in materials science the fractal analysis is applied to study microstructure of deformed metals because its structure can be interpreted as the fractal…
A new thermometer based on fragment momentum fluctuations is presented. This thermometer exhibited residual contamination from the collective motion of the fragments along the beam axis. For this reason, the transverse direction has been…