Complexity of classical dynamics of molecular systems. I. Methodology

Methods for the calculation of complexity have been investigated as a possible alternative for the analysis of the dynamics of molecular systems. “Computational mechanics” is the approach chosen to describe emergent behavior in molecular systems that evolve in time. A novel algorithm has been developed for symbolization of a continuous physical trajectory of a dynamic system. A method for calculating statistical complexity has been implemented and tested on representative systems. It is shown that the computational mechanics approach is suitable for analyzing the dynamic complexity of molecular systems and offers new insight into the process.

Optimal Control of Heterogeneous Systems

Цветомир Цачев - В настоящия доклад се прави преглед на някои резултати от областта на оптималното управление на непрекъснатите хетерогенни системи, публикувани в периодичната научна литература в последните години. Една динамична система се нарича хетерогенна, ако всеки от нейните елементи има собствена динамиката. Тук разглеждаме оптимално управление на системи, чиято хетерогенност се описва с едномерен или двумерен параметър – на всяка стойност на параметъра отговаря съответен елемент на системата. Хетерогенните динамични системи се използват за моделиране на процеси в икономиката, епидемиологията, биологията, опазване на обществената сигурност (ограничаване на използването на наркотици) и др. Тук разглеждаме модел на оптимално инвестиране в образование на макроикономическо ниво [11], на ограничаване на последствията от разпространението на СПИН [9], на пазар на права за въглеродни емисии [3, 4] и на оптимален макроикономически растеж при повишаване на нивото на върховите технологии [1]. Ключови думи: оптимално управление, непрекъснати хетерогенни динамични системи, приложения в икономиката и епидемиолегията

Node centrality for continuous-time quantum walks

The study of complex networks has recently attracted increasing interest because of the large variety of systems that can be modeled using graphs. A fundamental operation in the analysis of complex networks is that of measuring the centrality of a vertex. In this paper, we propose to measure vertex centrality using a continuous-time quantum walk. More specifically, we relate the importance of a vertex to the influence that its initial phase has on the interference patterns that emerge during the quantum walk evolution. To this end, we make use of the quantum Jensen-Shannon divergence between two suitably defined quantum states. We investigate how the importance varies as we change the initial state of the walk and the Hamiltonian of the system. We find that, for a suitable combination of the two, the importance of a vertex is almost linearly correlated with its degree. Finally, we evaluate the proposed measure on two commonly used networks. © 2014 Springer-Verlag Berlin Heidelberg.

A continuous-time quantum walk kernel for unattributed graphs

Kernel methods provide a way to apply a wide range of learning techniques to complex and structured data by shifting the representational problem from one of finding an embedding of the data to that of defining a positive semidefinite kernel. In this paper, we propose a novel kernel on unattributed graphs where the structure is characterized through the evolution of a continuous-time quantum walk. More precisely, given a pair of graphs, we create a derived structure whose degree of symmetry is maximum when the original graphs are isomorphic. With this new graph to hand, we compute the density operators of the quantum systems representing the evolutions of two suitably defined quantum walks. Finally, we define the kernel between the two original graphs as the quantum Jensen-Shannon divergence between these two density operators. The experimental evaluation shows the effectiveness of the proposed approach. © 2013 Springer-Verlag.

Wave Operators for Defocusing Matrix Zakharov-Shabat Systems with Pnonvanishing at Infinity

2000 Mathematics Subject Classification: Primary: 34L25; secondary: 47A40, 81Q10.

Continuous property measurement techniques and physics based mathematical model for frost growth control

The development of a new set of frost property measurement techniques to be used in the control of frost growth and defrosting processes in refrigeration systems was investigated. Holographic interferometry and infrared thermometry were used to measure the temperature of the frost-air interface, while a beam element load sensor was used to obtain the weight of a deposited frost layer. The proposed measurement techniques were tested for the cases of natural and forced convection, and the characteristic charts were obtained for a set of operational conditions. ^ An improvement of existing frost growth mathematical models was also investigated. The early stage of frost nucleation was commonly not considered in these models and instead an initial value of layer thickness and porosity was regularly assumed. A nucleation model to obtain the droplet diameter and surface porosity at the end of the early frosting period was developed. The drop-wise early condensation in a cold flat plate under natural convection to a hot (room temperature) and humid air was modeled. A nucleation rate was found, and the relation of heat to mass transfer (Lewis number) was obtained. It was found that the Lewis number was much smaller than unity, which is the standard value usually assumed for most frosting numerical models. The nucleation model was validated against available experimental data for the early nucleation and full growth stages of the frosting process. ^ The combination of frost top temperature and weight variation signals can now be used to control the defrosting timing and the developed early nucleation model can now be used to simulate the entire process of frost growth in any surface material. ^

Power and thermal aware scheduling for real-time computing systems

Over the past few decades, we have been enjoying tremendous benefits thanks to the revolutionary advancement of computing systems, driven mainly by the remarkable semiconductor technology scaling and the increasingly complicated processor architecture. However, the exponentially increased transistor density has directly led to exponentially increased power consumption and dramatically elevated system temperature, which not only adversely impacts the system's cost, performance and reliability, but also increases the leakage and thus the overall power consumption. Today, the power and thermal issues have posed enormous challenges and threaten to slow down the continuous evolvement of computer technology. Effective power/thermal-aware design techniques are urgently demanded, at all design abstraction levels, from the circuit-level, the logic-level, to the architectural-level and the system-level. ^ In this dissertation, we present our research efforts to employ real-time scheduling techniques to solve the resource-constrained power/thermal-aware, design-optimization problems. In our research, we developed a set of simple yet accurate system-level models to capture the processor's thermal dynamic as well as the interdependency of leakage power consumption, temperature, and supply voltage. Based on these models, we investigated the fundamental principles in power/thermal-aware scheduling, and developed real-time scheduling techniques targeting at a variety of design objectives, including peak temperature minimization, overall energy reduction, and performance maximization. ^ The novelty of this work is that we integrate the cutting-edge research on power and thermal at the circuit and architectural-level into a set of accurate yet simplified system-level models, and are able to conduct system-level analysis and design based on these models. The theoretical study in this work serves as a solid foundation for the guidance of the power/thermal-aware scheduling algorithms development in practical computing systems.^

Turning Passive Detection Systems into Field Experiments: An Application Using Wetland Fishes and Enclosures to Track Fine-Scale Movement and Habitat Choice

Understanding habitat selection and movement remains a key question in behavioral ecology. Yet, obtaining a sufficiently high spatiotemporal resolution of the movement paths of organisms remains a major challenge, despite recent technological advances. Observing fine-scale movement and habitat choice decisions in the field can prove to be difficult and expensive, particularly in expansive habitats such as wetlands. We describe the application of passive integrated transponder (PIT) systems to field enclosures for tracking detailed fish behaviors in an experimental setting. PIT systems have been applied to habitats with clear passageways, at fixed locations or in controlled laboratory and mesocosm settings, but their use in unconfined habitats and field-based experimental setups remains limited. In an Everglades enclosure, we continuously tracked the movement and habitat use of PIT-tagged centrarchids across three habitats of varying depth and complexity using multiple flatbed antennas for 14 days. Fish used all three habitats, with marked species-specific diel movement patterns across habitats, and short-lived movements that would be likely missed by other tracking techniques. Findings suggest that the application of PIT systems to field enclosures can be an insightful approach for gaining continuous, undisturbed and detailed movement data in unconfined habitats, and for experimentally manipulating both internal and external drivers of these behaviors.

Evaluating High-Resolution Aerial Photography Acquired by Unmanned Aerial Systems for Use in Mapping Everglades Wetland Plant Associations

Mapping of vegetation patterns over large extents using remote sensing methods requires field sample collections for two different purposes: (1) the establishment of plant association classification systems from samples of relative abundance estimates; and (2) training for supervised image classification and accuracy assessment of satellite data derived maps. One challenge for both procedures is the establishment of confidence in results and the analysis across multiple spatial scales. Continuous data sets that enable cross-scale studies are very time consuming and expensive to acquire and such extensive field sampling can be invasive. The use of high resolution aerial photography (hrAP) offers an alternative to extensive, invasive, field sampling and can provide large volume, spatially continuous, reference information that can meet the challenges of confidence building and multi-scale analysis.

Properties of seawater and particulate matter from a WETLabs AC-S spectrophotometer and a WETLabs chlorophyll fluorometer mounted on the continuous surface water sampling system during the Tara Oceans expedition 2009-2013

The Tara Oceans Expedition (2009-2013) was a global survey of ocean ecosystems aboard the Sailing Vessel Tara. It carried out extensive measurements of evironmental conditions and collected plankton (viruses, bacteria, protists and metazoans) for later analysis using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data publication provides permanent links to original and updated versions of validated data files containing measurements from the Continuous Surface Sampling System [CSSS]. Water was pumped at the front of the vessel from ~2m depth, then de-bubbled and circulated to a WETLabs AC-S spectrophotometer and a WETLabs chlorophyll fluorometer. Systems maintenance (instrument cleaning, flushing) was done approximately once a week and in port between successive legs. All data were stamped with a GPS.

Properties of seawater from a Sea-Bird TSG temperature and conductivity sensor mounted on the continuous surface water sampling system during the Tara Oceans expedition 2009-2013

The Tara Oceans Expedition (2009-2013) was a global survey of ocean ecosystems aboard the Sailing Vessel Tara. It carried out extensive measurements of evironmental conditions and collected plankton (viruses, bacteria, protists and metazoans) for later analysis using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data publication provides permanent links to original and updated versions of validated data files containing measurements from the Continuous Surface Sampling System [CSSS]. Water was pumped at the front of the vessel from ~2m depth, then de-bubbled and circulated to a Sea-Bird TSG temperature and conductivity sensor. Systems maintenance (instrument cleaning, flushing) was done approximately once a week and in port between successive legs. All data were stamped with a GPS.

Influence of alkyl chain length on sulfated zirconia catalysed batch and continuous esterification of carboxylic acids by light alcohols

The impact of alkyl chain length on the esterification of C2–C16 organic acids with C1–C4 alcohols has been systematically investigated over bulk and SBA-15 supported sulfated zirconias (SZs). Rates of catalytic esterification for methanol with acetic acid are directly proportional to the sulfur content for both SZ and SZ/SBA-15, with the high dispersion of SZ achievable in conformal coatings over mesoporous SBA-15 confering significant rate-enhancements. Esterification over the most active 0.24 mmol gcat−1 bulk SZ and 0.29 mmol gcat−1 SZ/SBA-15 materials was inversely proportional to the alkyl chain length of alcohol and acid reactants; being most sensitive to changes from methanol to ethanol and acetic to hexanoic acids respectively. Kinetic analyses reveal that these alkyl chain dependencies are in excellent accord with the Taft relationship for polar and steric effects in aliphatic systems and the enthalpy of alcohol adsorption, implicating a Langmuir–Hinshelwood mechanism. The first continuous production of methyl propionate over a SZ fixed-bed is also demonstrated.

On Provable Algorithms for Determination of Continuous Protein Interdomain Motions from Residual Dipolar Couplings

Dynamics of biomolecules over various spatial and time scales are essential for biological functions such as molecular recognition, catalysis and signaling. However, reconstruction of biomolecular dynamics from experimental observables requires the determination of a conformational probability distribution. Unfortunately, these distributions cannot be fully constrained by the limited information from experiments, making the problem an ill-posed one in the terminology of Hadamard. The ill-posed nature of the problem comes from the fact that it has no unique solution. Multiple or even an infinite number of solutions may exist. To avoid the ill-posed nature, the problem needs to be regularized by making assumptions, which inevitably introduce biases into the result.

Here, I present two continuous probability density function approaches to solve an important inverse problem called the RDC trigonometric moment problem. By focusing on interdomain orientations we reduced the problem to determination of a distribution on the 3D rotational space from residual dipolar couplings (RDCs). We derived an analytical equation that relates alignment tensors of adjacent domains, which serves as the foundation of the two methods. In the first approach, the ill-posed nature of the problem was avoided by introducing a continuous distribution model, which enjoys a smoothness assumption. To find the optimal solution for the distribution, we also designed an efficient branch-and-bound algorithm that exploits the mathematical structure of the analytical solutions. The algorithm is guaranteed to find the distribution that best satisfies the analytical relationship. We observed good performance of the method when tested under various levels of experimental noise and when applied to two protein systems. The second approach avoids the use of any model by employing maximum entropy principles. This 'model-free' approach delivers the least biased result which presents our state of knowledge. In this approach, the solution is an exponential function of Lagrange multipliers. To determine the multipliers, a convex objective function is constructed. Consequently, the maximum entropy solution can be found easily by gradient descent methods. Both algorithms can be applied to biomolecular RDC data in general, including data from RNA and DNA molecules.

Research in information systems: A study of diversity and inter-disciplinary discourse in the AIS basket journals between 1995 and 2011

The paper investigates how Information Systems (IS) has emerged as the product of inter-disciplinary discourses. The research aim in this study is to better understand diversity in IS research, and the extent to which the diversity of discourse expanded and contracted from 1995 to 2011. Methodologically, we apply a combined citations/co-citations analysis based on the eight Association for Information Systems basket journals and the 22 subject-field classification framework provided by the Association of Business Schools. Our findings suggest that IS is in a state of continuous interaction and competition with other disciplines. General Management was reduced from a dominant position as a reference discipline in IS at the expense of a growing variety of other discourses including Business Strategy, Marketing, and Ethics and Governance, among others. Over time, IS as a field moved from the periphery to a central position during its discursive formation. This supports the notion of IS as a fluid discipline dynamically embracing a diverse range of adjacent reference disciplines, while keeping a degree of continuing interaction with them. Understanding where IS is currently at allows us to better understand and propose fruitful avenues for its development in both academia and practice. © 2013 JIT Palgrave Macmillan All rights reserved.

A review of the welfare of dairy cows in continuously housed and pasture-based production systems.

There is increasing interest in the use of continuous housing systems for dairy cows, with various reasons put forward to advocate such systems. However, the welfare of dairy cows is typically perceived to be better within pasture-based systems, although such judgements are often not scientifically based. The aim of this review was to interrogate the existing scientific literature to compare the welfare, including health, of dairy cows in continuously housed and pasture-based systems. While summarising existing work, knowledge gaps and directions for future research are also identified. The scope of the review is broad, examining relevant topics under three main headings; health, behaviour, and physiology. Regarding health, cows on pasture-based systems had lower levels of lameness, hoof pathologies, hock lesions, mastitis, uterine disease, and mortality compared to cows on continuously housed systems. Pasture access also had benefits for dairy cow behaviour, in terms of grazing, improved lying / resting times, and lower levels of aggression. Moreover, when given the choice between pasture and indoor housing, cows showed an overall preference for pasture, particularly at night. However, the review highlighted the need for a deeper understanding of cow preference and behaviour. Potential areas for concern within pasture-based systems included physiological indicators of more severe negative energy balance, and in some situations, the potential for compromised welfare with exposure to unpredictable weather conditions. In summary, the results from this review highlight that there remain considerable animal welfare benefits from incorporating pasture access into dairy production systems.