Search results for " Soft"
showing 10 items of 1710 documents
Polydisperse hard spheres: crystallization kinetics in small systems and role of local structure
2016
We study numerically the crystallization of a hard-sphere mixture with 8\% polydispersity. Although often used as a model glass former, for small system sizes we observe crystallization in molecular dynamics simulations. This opens the possibility to study the competition between crystallization and structural relaxation of the melt, which typically is out of reach due to the disparate timescales. We quantify the dependence of relaxation and crystallization times on density and system size. For one density and system size we perform a detailed committor analysis to investigate the suitability of local structures as order parameters to describe the crystallization process. We find that local…
To make a glass—avoid the crystal
2016
Colloidal model systems allow for a flexible tuning of particle sizes, particle spacings and mutual interactions at constant temperature. Colloidal suspensions typically crystallize as soon as the interactions get sufficiently strong and long-ranged. Several strategies have been successfully applied to avoid crystallization and instead produce colloidal glasses. Most of these amorphous solids are formed at high particle concentrations. This paper shortly reviews experimental attempts to produce amorphous colloidal solids using strategies based on topological, thermodynamic and kinetic considerations. We complement this overview by introducing a (transient) amorphous solid forming in a thoro…
Mode-coupling theory for multiple decay channels
2013
We investigate the properties of a class of mode-coupling equations for the glass transition where the density mode decays into multiple relaxation channels. We prove the existence and uniqueness of the solutions for Newtonian as well as Brownian dynamics and demonstrate that they fulfill the requirements of correlation functions, in the latter case the solutions are purely relaxational. Furthermore, we construct an effective mode-coupling functional which allows to map the theory to the case of a single decay channel, such that the covariance principle found for the mode-coupling theory for simple liquids is properly generalized. This in turn allows establishing the maximum theorem stating…
Coupling theory for counterion distributions based in Tsallis statistics
2003
It is well known that the Poisson-Boltzmann (PB) equation yields the exact counterion density around charged objects in the weak coupling limit. In this paper we generalize the PB approach to account for coupling of arbitrary strength by making use of Tsallis q-exponential distributions. Both the weak coupling and the strong coupling limits are reproduced. For arbitrary coupling we also provide simple analytical expressions which are compared to recent Monte Carlo simulations by A. G. Moreira and R. R. Netz [Europhys. Lett. 52 (2000) 705]. Excellent agreement with these is obtained.
Using R via PHP for Teaching Purposes: R-php
2006
This paper deals with the R-php statistical software, that is an environment for statistical analysis, freely accessible and attainable through the World Wide Web, based on R. Indeed, this software uses, as "engine" for statistical analyses, R via PHP and its design has been inspired by a paper of de Leeuw (1997). R-php is based on two modules: a base module and a point-and-click module. R-php base allows the simple editing of R code in a form. R-php point-and-click allows some statistical analyses by means of a graphical user interface (GUI): then, to use this module it is not necessary for the user to know the R environment, but all the allowed analyses can be performed by using the compu…
The Power of Word-Frequency Based Alignment-Free Functions: a Comprehensive Large-Scale Experimental Analysis
2021
Abstract Motivation Alignment-free (AF) distance/similarity functions are a key tool for sequence analysis. Experimental studies on real datasets abound and, to some extent, there are also studies regarding their control of false positive rate (Type I error). However, assessment of their power, i.e. their ability to identify true similarity, has been limited to some members of the D2 family. The corresponding experimental studies have concentrated on short sequences, a scenario no longer adequate for current applications, where sequence lengths may vary considerably. Such a State of the Art is methodologically problematic, since information regarding a key feature such as power is either mi…
Estimating growth charts via nonparametric quantile regression: a practical framework with application in ecology.
2013
We discuss a practical and effective framework to estimate reference growth charts via regression quantiles. Inequality constraints are used to ensure both monotonicity and non-crossing of the estimated quantile curves and penalized splines are employed to model the nonlinear growth patterns with respect to age. A companion R package is presented and relevant code discussed to favour spreading and application of the proposed methods.
IndElec: A Software for Analyzing Party Systems and Electoral Systems
2011
IndElec is a software addressed to compute a wide range of indices from electoral data, which are intended to analyze both party systems and electoral systems in political studies. Further, IndElec can calculate such indices from electoral data at several levels of aggregation, even when the acronyms of some political parties change across districts. As the amount of information provided by IndElec may be considerable, this software also aids the user in the analysis of electoral data through three capabilities. First, IndElec automatically elaborates preliminary descriptive statistical reports of computed indices. Second, IndElec saves the computed information into text files in data matri…
Graphical User Interfaces for R
2012
Since R was first launched, it has managed to gain the support of an ever-increasing percentage of academic and professional statisticians. However, the spread of its use among novice and occasional users of statistics have not progressed at the same pace, which can be attributed partially to the lack of a graphical user interface (GUI). Nevertheless, this situation has changed in the last years and there is currently several projects that have added GUIs to R. This article discusses briefly the history of GUIs for data analysis and then introduces the papers submitted to an special issue of the Journal of Statistical Software on GUIs for R.
Glassy behavior of molecular crystals: A comparison between results from MD-simulation and mode coupling theory
2005
We have investigated the glassy behavior of a molecular crystal built up with chloroadamantane molecules. For a simple model of this molecule and a rigid fcc lattice a MD simulation was performed from which we obtained the dynamical orientational correlators $S_{\lambda \lambda '}({\bf{q}},t)$ and the ``self'' correlators $S_{\lambda \lambda '}^{(s)}(t)$, with $\lambda = (\ell, m)$, $\lambda' = (\ell', m')$. Our investigations are for the diagonal correlators $\lambda = \lambda'$. Since the lattice constant decreases with decreasing temperature which leads to an increase of the steric hindrance of the molecules, we find a strong slowing down of the relaxation. It has a high sensitivity on $…