Dynamical hierarchy in transition states: Why and how does a system climb over the mountain?

How a reacting system climbs through a transition state during the course of a reaction has been an intriguing subject for decades. Here we present and quantify a technique to identify and characterize local invariances about the transition state of an N-particle Hamiltonian system, using Lie canonical perturbation theory combined with microcanonical molecular dynamics simulation. We show that at least three distinct energy regimes of dynamical behavior occur in the region of the transition state, distinguished by the extent of their local dynamical invariance and regularity. Isomerization of a six-atom Lennard–Jones cluster illustrates this: up to energies high enough to make the system manifestly chaotic, approximate invariants of motion associated with a reaction coordinate in phase space imply a many-body dividing hypersurface in phase space that is free of recrossings even in a sea of chaos. The method makes it possible to visualize the stable and unstable invariant manifolds leading to and from the transition state, i.e., the reaction path in phase space, and how this regularity turns to chaos with increasing total energy of the system. This, in turn, illuminates a new type of phase space bottleneck in the region of a transition state that emerges as the total energy and mode coupling increase, which keeps a reacting system increasingly trapped in that region.

Analysis of chaotic instabilities in a rotating body with internal energy dissipation

Melnikov's method is used to analytically predict the onset of chaotic instability in a rotating body with internal energy dissipation. The model has been found to exhibit chaotic instability when a harmonic disturbance torque is applied to the system for a range of forcing amplitude and frequency. Such a model may be considered to be representative of the dynamical behavior of a number of physical systems such as a spinning spacecraft. In spacecraft, disturbance torques may arise under malfunction of the control system, from an unbalanced rotor, from vibrations in appendages or from orbital variations. Chaotic instabilities arising from such disturbances could introduce uncertainties and irregularities into the motion of the multibody system and consequently could have disastrous effects on its intended operation. A comprehensive stability analysis is performed and regions of nonlinear behavior are identified. Subsequently, the closed form analytical solution for the unperturbed system is obtained in order to identify homoclinic orbits. Melnikov's method is then applied on the system once transformed into Hamiltonian form. The resulting analytical criterion for the onset of chaotic instability is obtained in terms of critical system parameters. The sufficient criterion is shown to be a useful predictor of the phenomenon via comparisons with numerical results. Finally, for the purposes of providing a complete, self-contained investigation of this fundamental system, the control of chaotic instability is demonstated using Lyapunov's method.

Prediction of chaotic instabilities in a dragline bucket swing

The occurrence of chaotic instabilities is investigated in the swing motion of a dragline bucket during operation cycles. A dragline is a large, powerful, rotating multibody system utilised in the mining industry for removal of overburden. A simplified representative model of the dragline is developed in the form of a fundamental non-linear rotating multibody system with energy dissipation. An analytical predictive criterion for the onset of chaotic instability is then obtained in terms of critical system parameters using Melnikov's method. The model is shown to exhibit chaotic instability due to a harmonic slew torque for a range of amplitudes and frequencies. These chaotic instabilities could introduce irregularities into the motion of the dragline system, rendering the system difficult to control by the operator and/or would have undesirable effects on dragline productivity and fatigue lifetime. The sufficient analytical criterion for the onset of chaotic instability is shown to be a useful predictor of the phenomenon under steady and unsteady slewing conditions via comparisons with numerical results. (c) 2005 Elsevier Ltd. All rights reserved.

Interference between propagating changes and its effect on system failure

Computer-based, socio-technical systems projects are frequently failures. In particular, computer-based information systems often fail to live up to their promise. Part of the problem lies in the uncertainty of the effect of combining the subsystems that comprise the complete system; i.e. the system's emergent behaviour cannot be predicted from a knowledge of the subsystems. This paper suggests uncertainty management is a fundamental unifying concept in analysis and design of complex systems and goes on to indicate that this is due to the co-evolutionary nature of the requirements and implementation of socio-technical systems. The paper shows a model of the propagation of a system change that indicates that the introduction of two or more changes over time can cause chaotic emergent behaviour.

Wave chaotic behaviour generated by linear systems

It is shown that regimes with dynamical chaos are inherent not only to nonlinear system but they can be generated by initially linear systems and the requirements for chaotic dynamics and characteristics need further elaboration. Three simplest physical models are considered as examples. In the first, dynamic chaos in the interaction of three linear oscillators is investigated. Analogous process is shown in the second model of electromagnetic wave scattering in a double periodical inhomogeneous medium occupying half-space. The third model is a linear parametric problem for the electromagnetic field in homogeneous dielectric medium which permittivity is modulated in time. © 2008 Springer Science+Business Media, LLC.

Investigation of chaotic mixing in laminar fluid systems by the use of computational fluid dynamics

This work presents significant development into chaotic mixing induced through periodic boundaries and twisting flows. Three-dimensional closed and throughput domains are shown to exhibit chaotic motion under both time periodic and time independent boundary motions, A property is developed originating from a signature of chaos, sensitive dependence to initial conditions, which successfully quantifies the degree of disorder withjn the mixing systems presented and enables comparisons of the disorder throughout ranges of operating parameters, This work omits physical experimental results but presents significant computational investigation into chaotic systems using commercial computational fluid dynamics techniques. Physical experiments with chaotic mixing systems are, by their very nature, difficult to extract information beyond the recognition that disorder does, does not of partially occurs. The initial aim of this work is to observe whether it is possible to accurately simulate previously published physical experimental results through using commercial CFD techniques. This is shown to be possible for simple two-dimensional systems with time periodic wall movements. From this, and subsequent macro and microscopic observations of flow regimes, a simple explanation is developed for how boundary operating parameters affect the system disorder. Consider the classic two-dimensional rectangular cavity with time periodic velocity of the upper and lower walls, causing two opposing streamline motions. The degree of disorder within the system is related to the magnitude of displacement of individual particles within these opposing streamlines. The rationale is then employed in this work to develop and investigate more complex three-dimensional mixing systems that exhibit throughputs and time independence and are therefore more realistic and a significant advance towards designing chaotic mixers for process industries. Domains inducing chaotic motion through twisting flows are also briefly considered. This work concludes by offering possible advancements to the property developed to quantify disorder and suggestions of domains and associated boundary conditions that are expected to produce chaotic mixing.

Dynamic complexity of chaotic transitions in high-dimensional classical dynamics:Leu-Enkephalin folding

Leu-Enkephalin in explicit water is simulated using classical molecular dynamics. A ß-turn transition is investigated by calculating the topological complexity (in the "computational mechanics" framework [J. P. Crutchfield and K. Young, Phys. Rev. Lett., 63, 105 (1989)]) of the dynamics of both the peptide and the neighbouring water molecules. The complexity of the atomic trajectories of the (relatively short) simulations used in this study reflect the degree of phase space mixing in the system. It is demonstrated that the dynamic complexity of the hydrogen atoms of the peptide and almost all of the hydrogens of the neighbouring waters exhibit a minimum precisely at the moment of the ß-turn transition. This indicates the appearance of simplified periodic patterns in the atomic motion, which could correspond to high-dimensional tori in the phase space. It is hypothesized that this behaviour is the manifestation of the effect described in the approach to molecular transitions by Komatsuzaki and Berry [T. Komatsuzaki and R.S. Berry, Adv. Chem. Phys., 123, 79 (2002)], where a "quasi-regular" dynamics at the transition is suggested. Therefore, for the first time, the less chaotic character of the folding transition in a realistic molecular system is demonstrated. © Springer-Verlag Berlin Heidelberg 2006.

Nonlinear dynamics and chaos simulation system analysis for improved design

Small errors proved catastrophic. Our purpose to remark that a very small cause which escapes our notice determined a considerable effect that we cannot fail to see, and then we say that the effect is due to chance. Small differences in the initial conditions produce very great ones in the final phenomena. A small error in the former will produce an enormous error in the latter. When dealing with any kind of electrical device specification, it is important to note that there exists a pair of test conditions that define a test: the forcing function and the limit. Forcing functions define the external operating constraints placed upon the device tested. The actual test defines how well the device responds to these constraints. Forcing inputs to threshold for example, represents the most difficult testing because this put those inputs as close as possible to the actual switching critical points and guarantees that the device will meet the Input-Output specifications. ^ Prediction becomes impossible by classical analytical analysis bounded by Newton and Euclides. We have found that non linear dynamics characteristics is the natural state of being in all circuits and devices. Opportunities exist for effective error detection in a nonlinear dynamics and chaos environment. ^ Nowadays there are a set of linear limits established around every aspect of a digital or analog circuits out of which devices are consider bad after failing the test. Deterministic chaos circuit is a fact not a possibility as it has been revived by our Ph.D. research. In practice for linear standard informational methodologies, this chaotic data product is usually undesirable and we are educated to be interested in obtaining a more regular stream of output data. ^ This Ph.D. research explored the possibilities of taking the foundation of a very well known simulation and modeling methodology, introducing nonlinear dynamics and chaos precepts, to produce a new error detector instrument able to put together streams of data scattered in space and time. Therefore, mastering deterministic chaos and changing the bad reputation of chaotic data as a potential risk for practical system status determination. ^

PHC Production Management System Based on RFID

At present, in large precast concrete enterprises, the management over precast concrete component has been chaotic. Most enterprises take labor-intensive manual input method, which is time consuming and laborious, and error-prone. Some other slightly better enterprises choose to manage through bar-code or printing serial number manually. However, on one hand, this is also labor-intensive, on the other hand, this method is limited by external environment, making the serial number blur or even lost, and also causes a big problem on production traceability and quality accountability. Therefore, to realize the enterprise’s own rapid development and cater to the needs of the time, to achieve the automated production management has been a big problem for a modern enterprise. In order to solve the problem, inefficiency in production and traceability of the products, this thesis try to introduce RFID technology into the production of PHC tubular pile. By designing a production management system of precast concrete components, the enterprise will achieve the control of the entire production process, and realize the informatization of enterprise production management. RFID technology has been widely used in many fields like entrance control, charge management, logistics and so on. RFID technology will adopt passive RFID tag, which is waterproof, shockproof, anti-interference, so it’s suitable for the actual working environment. The tag will be bound to the precast component steel cage (the structure of the PHC tubular pile before the concrete placement), which means each PHC tubular pile will have a unique ID number. Then according to the production procedure, the precast component will be performed with a series of actions, put the steel cage into the mold, mold clamping, pouring concrete (feed), stretching, centrifugalizing, maintenance, mold removing, welding splice. In every session of the procedure, the information of the precast components can be read through a RFID reader. Using a portable smart device connected to the database, the user can check, inquire and management the production information conveniently. Also, the system can trace the production parameter and the person in charge, realize the traceability of the information. This system can overcome the disadvantages in precast components manufacturers, like inefficiency, error-prone, time consuming, labor intensity, low information relevance and so on. This system can help to improve the production management efficiency, and can produce a good economic and social benefits, so, this system has a certain practical value.

A bistable reaction-diffusion system in a stretching flow

We examine the evolution of a bistable reaction in a one-dimensional stretching flow, as a model for chaotic advection. We derive two reduced systems of ordinary differential equations (ODEs) for the dynamics of the governing advection-reaction-diffusion partial differential equations (PDE), for pulse-like and for plateau-like solutions, based on a non-perturbative approach. This reduction allows us to study the dynamics in two cases: first, close to a saddle-node bifurcation at which a pair of nontrivial steady states are born as the dimensionless reaction rate (Damkoehler number) is increased, and, second, for large Damkoehler number, far away from the bifurcation. The main aim is to investigate the initial-value problem and to determine when an initial condition subject to chaotic stirring will decay to zero and when it will give rise to a nonzero final state. Comparisons with full PDE simulations show that the reduced pulse model accurately predicts the threshold amplitude for a pulse initial condition to give rise to a nontrivial final steady state, and that the reduced plateau model gives an accurate picture of the dynamics of the system at large Damkoehler number. Published in Physica D (2006)

Symbolic dynamics generated by a hybrid chaotic systems

We consider piecewise defined differential dynamical systems which can be analysed through symbolic dynamics and transition matrices. We have a continuous regime, where the time flow is characterized by an ordinary differential equation (ODE) which has explicit solutions, and the singular regime, where the time flow is characterized by an appropriate transformation. The symbolic codification is given through the association of a symbol for each distinct regular system and singular system. The transition matrices are then determined as linear approximations to the symbolic dynamics. We analyse the dependence on initial conditions, parameter variation and the occurrence of global strange attractors.

Obesity And Inflammation And The Effect On The Hematopoietic System.

Bone marrow is organized in specialized microenvironments known as 'marrow niches'. These are important for the maintenance of stem cells and their hematopoietic progenitors whose homeostasis also depends on other cell types present in the tissue. Extrinsic factors, such as infection and inflammatory states, may affect this system by causing cytokine dysregulation (imbalance in cytokine production) and changes in cell proliferation and self-renewal rates, and may also induce changes in the metabolism and cell cycle. Known to relate to chronic inflammation, obesity is responsible for systemic changes that are best studied in the cardiovascular system. Little is known regarding the changes in the hematopoietic system induced by the inflammatory state carried by obesity or the cell and molecular mechanisms involved. The understanding of the biological behavior of hematopoietic stem cells under obesity-induced chronic inflammation could help elucidate the pathophysiological mechanisms involved in other inflammatory processes, such as neoplastic diseases and bone marrow failure syndromes.

The Value Of The 2005 International Society Of Urological Pathology (isup) Modified Gleason Grading System As A Predictor Of Biochemical Recurrence After Radical Prostatectomy.

To compare time and risk to biochemical recurrence (BR) after radical prostatectomy of two chronologically different groups of patients using the standard and the modified Gleason system (MGS). Cohort 1 comprised biopsies of 197 patients graded according to the standard Gleason system (SGS) in the period 1997/2004, and cohort 2, 176 biopsies graded according to the modified system in the period 2005/2011. Time to BR was analyzed with the Kaplan-Meier product-limit analysis and prediction of shorter time to recurrence using univariate and multivariate Cox proportional hazards model. Patients in cohort 2 reflected time-related changes: striking increase in clinical stage T1c, systematic use of extended biopsies, and lower percentage of total length of cancer in millimeter in all cores. The MGS used in cohort 2 showed fewer biopsies with Gleason score ≤ 6 and more biopsies of the intermediate Gleason score 7. Time to BR using the Kaplan-Meier curves showed statistical significance using the MGS in cohort 2, but not the SGS in cohort 1. Only the MGS predicted shorter time to BR on univariate analysis and on multivariate analysis was an independent predictor. The results favor that the 2005 International Society of Urological Pathology modified system is a refinement of the Gleason grading and valuable for contemporary clinical practice.

The Applicability Of Ordered Mesoporous Sba-15 And Its Hydrophobic Glutaraldehyde-bridge Derivative To Improve Ibuprofen-loading In Releasing System.

The mesoporous SBA-15 silica with uniform hexagonal pore, narrow pore size distribution and tuneable pore diameter was organofunctionalized with glutaraldehyde-bridged silylating agent. The precursor and its derivative silicas were ibuprofen-loaded for controlled delivery in simulated biological fluids. The synthesized silicas were characterized by elemental analysis, infrared spectroscopy, (13)C and (29)Si solid state NMR spectroscopy, nitrogen adsorption, X-ray diffractometry, thermogravimetry and scanning electron microscopy. Surface functionalization with amine containing bridged hydrophobic structure resulted in significantly decreased surface area from 802.4 to 63.0 m(2) g(-1) and pore diameter 8.0-6.0 nm, which ultimately increased the drug-loading capacity from 18.0% up to 28.3% and a very slow release rate of ibuprofen over the period of 72.5h. The in vitro drug release demonstrated that SBA-15 presented the fastest release from 25% to 27% and SBA-15GA gave near 10% of drug release in all fluids during 72.5 h. The Korsmeyer-Peppas model better fits the release data with the Fickian diffusion mechanism and zero order kinetics for synthesized mesoporous silicas. Both pore sizes and hydrophobicity influenced the rate of the release process, indicating that the chemically modified silica can be suggested to design formulation of slow and constant release over a defined period, to avoid repeated administration.

Electronic And Structural Study Of Pt-modified Au Vicinal Surfaces: A Model System For Pt-au Catalysts.

Two single crystalline surfaces of Au vicinal to the (111) plane were modified with Pt and studied using scanning tunneling microscopy (STM) and X-ray photoemission spectroscopy (XPS) in ultra-high vacuum environment. The vicinal surfaces studied are Au(332) and Au(887) and different Pt coverage (θPt) were deposited on each surface. From STM images we determine that Pt deposits on both surfaces as nanoislands with heights ranging from 1 ML to 3 ML depending on θPt. On both surfaces the early growth of Pt ad-islands occurs at the lower part of the step edge, with Pt ad-atoms being incorporated into the steps in some cases. XPS results indicate that partial alloying of Pt occurs at the interface at room temperature and at all coverage, as suggested by the negative chemical shift of Pt 4f core line, indicating an upward shift of the d-band center of the alloyed Pt. Also, the existence of a segregated Pt phase especially at higher coverage is detected by XPS. Sample annealing indicates that the temperature rise promotes a further incorporation of Pt atoms into the Au substrate as supported by STM and XPS results. Additionally, the catalytic activity of different PtAu systems reported in the literature for some electrochemical reactions is discussed considering our findings.