Related papers: Recurrence quantification analysis as a tool for t…
Observables of out-of-equilibrium quantum many-body systems display complex temporal behavior that encodes the underlying physical mechanisms but typically resists straightforward interpretations. We introduce recurrence analysis - a…
We present the statistical method to study the interaction between a chosen protein and another molecule (e.g., both being components of lubricin found in synovial fluid) in a water environment. The research is performed on the example of…
We propose lacunarity as a novel recurrence quantification measure and illustrate its efficacy to detect dynamical regime transitions which are exhibited by many complex real-world systems. We carry out a recurrence plot based analysis for…
The growing study of time series, especially those related to nonlinear systems, has challenged the methodologies to characterize and classify dynamical structures of a signal. Here we conceive a new diagnostic tool for time series based on…
We simulate the compression of a two-component Lennard-Jones liquid at a variety of constant temperatures using a molecular dynamics algorithm in an isobaric-isothermal ensemble. The viscosity of the liquid increases with pressure,…
Recurrence plots and their associated quantifiers provide a robust framework for detecting and characterising complex patterns in non-linear time-series. In this paper, we employ recurrence quantification analysis to investigate the…
Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a…
Recently there has been great interest in Glycol-Water chemistry and solubility and temperature dependent phase dynamics. The Glycol-Water biochemistry of interactions is present in plant biology and chemistry, is of great interest to…
We use Monte Carlo and molecular dynamics simulations to study phase behavior and transport properties in a symmetric binary fluid where particles interact via Lennard-Jones potential. Our results for the critical behavior of collective…
Recurrence quantification analysis is a widely used method for characterizing patterns in time series. This article presents a comprehensive survey for conducting a wide range of recurrence-based analyses to quantify the dynamical structure…
We have investigated by molecular dynamics method the influence of a finite number of particles used in computer simulations on fluctuations of thermodynamic properties. As a case study, we used the two-dimensional Lennard-Jones system. 2D…
Recurrence plot based time series analysis is widely used to study changes and transitions in the dynamics of a system or temporal deviations from its overall dynamical regime. However, most studies do not discuss the significance of the…
At the fundamental level, our understanding of water hydrogen-bond dynamics has been largely built on the detailed analysis of classical molecular simulations. The latter served to develop a plethora of hydrogen bond definitions based on…
Kinetics of phase separation in a three dimensional single-component Lennard-Jones fluid, that exhibits vapor-liquid transition, is studied via molecular dynamics simulations after quenching homogeneous systems, of different overall…
We use molecular dynamics simulations to study the behavior of a compressible Lennard-Jones fluid in simple shear flow in a two-dimensional nanochannel. The system is equilibrated in the fluid phase close to the triple point at which gas,…
We present a method to sample reactive pathways via biased molecular dynamics simulations in trajectory space. We show that the use of enhanced sampling techniques enables unconstrained exploration of multiple reaction routes. Time…
The length-scale dependence of the dynamic entropy is studied in a molecular dynamics simulation of a binary Lennard-Jones liquid above the mode-coupling critical temperature $T_c$. A number of methods exist for estimating the entropy of…
We find that a Lennard-Jones mixture displays a dynamic phase transition between an active regime and an inactive one. By means of molecular dynamics simulations and of a finite-size study, we show that the space time dynamics in the…
Recurrence plot is a quite easy tool to be used in time series analysis,in particular for measuring unstable periodic orbits embedded in a chaotic dynamical system. Recurrence quantified analysis (RQA) is an advance tool that allows the…
Recurrence is a fundamental property of dynamical systems, which can be exploited to characterise the system's behaviour in phase space. A powerful tool for their visualisation and analysis called recurrence plot was introduced in the late…