Correlated electron-ion dynamics in metallic systems

In this paper we briefly discuss the problem of simulating non-adiabatic processes in systems that are usefully modelled using molecular dynamics. In particular we address the problems associated with metals, and describe two methods that can be applied: the Ehrenfest approximation and correlated electron-ion dynamics (CEID). The Ehrenfest approximation is used to successfully describe the friction force experienced by an energetic particle passing through a crystal, but is unable to describe the heating of a wire by an electric current. CEID restores the proper heating.

Generalized Langevin equation: An efficient approach to nonequilibrium molecular dynamics of open systems

The generalized Langevin equation (GLE) has been recently suggested to simulate the time evolution of classical solid and molecular systems when considering general nonequilibrium processes. In this approach, a part of the whole system (an open system), which interacts and exchanges energy with its dissipative environment, is studied. Because the GLE is derived by projecting out exactly the harmonic environment, the coupling to it is realistic, while the equations of motion are non-Markovian. Although the GLE formalism has already found promising applications, e. g., in nanotribology and as a powerful thermostat for equilibration in classical molecular dynamics simulations, efficient algorithms to solve the GLE for realistic memory kernels are highly nontrivial, especially if the memory kernels decay nonexponentially. This is due to the fact that one has to generate a colored noise and take account of the memory effects in a consistent manner. In this paper, we present a simple, yet efficient, algorithm for solving the GLE for practical memory kernels and we demonstrate its capability for the exactly solvable case of a harmonic oscillator coupled to a Debye bath.

Metal speciation dynamics in colloidal ligand dispersions. Part 3: Lability features of steady-state systems

A lability criterion is developed for dynamic metal binding by colloidal ligands with convective diffusion as the dominant mode of mass transport. Scanned stripping chronopotentiometric measurements of Pb(II) and Cd(II) binding by carboxylated latex core-shell particles were in good agreement with the predicted values. The dynamic features of metal ion binding by these particles illustrate that the conventional approach of assuming a smeared-out homogeneous ligand distribution overestimates the lability of a colloidal ligand system. Due to the nature of the spatial distribution of the binding sites, the change in lability of a metal species with changing ligand concentration depends on whether the ligand concentration is varied via manipulation of the pH (degree of protonation) or via the particle concentration. In the former case the local ligand density varies, whereas in the latter case it is constant. This feature provides a useful diagnostic tool for the presence of geometrically constrained binding sites.

Optimization of molecular dynamics simulation code and applications to biomolecular systems

Tese de doutoramento, Bioquimica, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2015

Studies on the Effect of Randomness on the Synchronization of Coupled Systems and on the Dynamics of Intermittently driven systems

Nonlinear dynamics has emerged into a prominent area of research in the past few Decades.Turbulence, Pattern formation,Multistability etc are some of the important areas of research in nonlinear dynamics apart from the study of chaos.Chaos refers to the complex evolution of a deterministic system, which is highly sensitive to initial conditions. The study of chaos theory started in the modern sense with the investigations of Edward Lorentz in mid 60's. Later developments in this subject provided systematic development of chaos theory as a science of deterministic but complex and unpredictable dynamical systems. This thesis deals with the effect of random fluctuations with its associated characteristic timescales on chaos and synchronization. Here we introduce the concept of noise, and two familiar types of noise are discussed. The classifications and representation of white and colored noise are introduced. Based on this we introduce the concept of randomness that we deal with as a variant of the familiar concept of noise. The dynamical systems introduced are the Rossler system, directly modulated semiconductor lasers and the Harmonic oscillator. The directly modulated semiconductor laser being not a much familiar dynamical system, we have included a detailed introduction to its relevance in Chaotic encryption based cryptography in communication. We show that the effect of a fluctuating parameter mismatch on synchronization is to destroy the synchronization. Further we show that the relation between synchronization error and timescales can be found empirically but there are also cases where this is not possible. Studies show that under the variation of the parameters, the system becomes chaotic, which appears to be the period doubling route to chaos.

Influence of the driving mechanism on the response of systems with athermal dynamics: The example of the random-field Ising model

We investigate the influence of the driving mechanism on the hysteretic response of systems with athermal dynamics. In the framework of local mean-field theory at finite temperature (but neglecting thermally activated processes), we compare the rate-independent hysteresis loops obtained in the random field Ising model when controlling either the external magnetic field H or the extensive magnetization M. Two distinct behaviors are observed, depending on disorder strength. At large disorder, the H-driven and M-driven protocols yield identical hysteresis loops in the thermodynamic limit. At low disorder, when the H-driven magnetization curve is discontinuous (due to the presence of a macroscopic avalanche), the M-driven loop is reentrant while the induced field exhibits strong intermittent fluctuations and is only weakly self-averaging. The relevance of these results to the experimental observations in ferromagnetic materials, shape memory alloys, and other disordered systems is discussed.

Studies on nonlinear dynamics of certain reaction systems

The nonlinear dynamics of certain important reaction systems are discussed and analysed in this thesis. The interest in the theoretical and the experimental studies of chemical reactions showing oscillatory dynamics and associated properties is increasing very rapidly. An attempt is made to study some nonlinear phenomena exhibited by the well known chemical oscillator, the BelousovZhabotinskii reaction whose mathematical properties are much in common with the properties of biological oscillators. While extremely complex, this reaction is still much simpler than biological systems at least from the modelling point of view. A suitable model [19] for the system is analysed and the researcher has studied the limit cycle behaviour of the system, for different values of the stoichiometric parameter f, by keeping the value of the reaction rate (k6) fixed at k6 = l. The more complicated three-variable model is stiff in nature.

Studies on the effect of randoniness on the synchronization of coupled systems and on the dynamics of intermittently driven systems

It has been shown recently that systems driven with random pulses show the signature of chaos ,even without non linear dynamics.This shows that the relation between randomness and chaos is much closer than it was understood earlier .The effect of random perturbations on synchronization can be also different. In some cases identical random perturbations acting on two different chaotic systems induce synchronizations. However most commonly ,the effect of random fluctuations on the synchronizations of chaotic system is to destroy synchronization. This thesis deals with the effect of random fluctuations with its associated characteristic timescales on chaos and synchronization. The author tries to unearth yet another manifestation of randomness on chaos and sychroniztion. This thesis is organized into six chapters.

Statistical dynamics of dislocation systems: The influence of dislocation-dislocation correlations.

During plastic deformation of crystalline materials, the collective dynamics of interacting dislocations gives rise to various patterning phenomena. A crucial and still open question is whether the long range dislocation-dislocation interactions which do not have an intrinsic range can lead to spatial patterns which may exhibit well-defined characteristic scales. It is demonstrated for a general model of two-dimensional dislocation systems that spontaneously emerging dislocation pair correlations introduce a length scale which is proportional to the mean dislocation spacing. General properties of the pair correlation functions are derived, and explicit calculations are performed for a simple special case, viz pair correlations in single-glide dislocation dynamics. It is shown that in this case the dislocation system exhibits a patterning instability leading to the formation of walls normal to the glide plane. The results are discussed in terms of their general implications for dislocation patterning.

W3233 -- Networks and Complexity in Social Systems (Collective Dynamics Group ISERP -- Columbia University) Course Syllabus

The Networks and Complexity in Social Systems course commences with an overview of the nascent field of complex networks, dividing it into three related but distinct strands: Statistical description of large scale networks, viewed as static objects; the dynamic evolution of networks, where now the structure of the network is understood in terms of a growth process; and dynamical processes that take place on fixed networks; that is, "networked dynamical systems". (A fourth area of potential research ties all the previous three strands together under the rubric of co-evolution of networks and dynamics, but very little research has been done in this vein and so it is omitted.) The remainder of the course treats each of the three strands in greater detail, introducing technical knowledge as required, summarizing the research papers that have introduced the principal ideas, and pointing out directions for future development. With regard to networked dynamical systems, the course treats in detail the more specific topic of information propagation in networks, in part because this topic is of great relevance to social science, and in part because it has received the most attention in the literature to date.

Robust Control of Systems Subjected to Uncertain Disturbances and Actuator Dynamics

Esta tesis está enfocada al diseño y validación de controladores robustos que pueden reducir de una manera efectiva las vibraciones structurales producidas por perturbaciones externas tales como terremotos, fuertes vientos o cargas pesadas. Los controladores están diseñados basados en teorías de control tradicionalamente usadas en esta area: Teoría de estabilidad de Lyapunov, control en modo deslizante y control clipped-optimal, una técnica reciente mente introducida : Control Backstepping y una que no había sido usada antes: Quantitative Feedback Theory. La principal contribución al usar las anteriores técnicas, es la solución de problemas de control estructural abiertos tales como dinámicas de actuador, perturbaciones desconocidas, parametros inciertos y acoplamientos dinámicos. Se utilizan estructuras típicas para validar numéricamente los controladores propuestos. Especificamente las estructuras son un edificio de base aislada, una plataforma estructural puente-camión y un puente de 2 tramos, cuya configuración de control es tal que uno o mas problemas abiertos están presentes. Se utilizan tres prototipos experimentales para implementar los controladores robustos propuestos, con el fin de validar experimentalmente su efectividad y viabilidad. El principal resultado obtenido con la presente tesis es el diseño e implementación de controladores estructurales robustos que resultan efectivos para resolver problemas abiertos en control estructural tales como dinámicas de actuador, parámetros inciertos, acoplamientos dinámicos, limitación de medidas y perturbaciones desconocidas.