Advances in reproductive biology and seed production systems of ...

African Journals Online (AJOL)

Eucalyptus globulus is the main eucalypt species grown in Australian plantations. The focus on seedling deployment systems, coupled with exploitation of large, open-pollinated base populations for breeding purposes over the last two decades, has required a detailed understanding of the reproductive biology of this ...

Mixed coherent states in coupled chaotic systems: Design of secure wireless communication

Science.gov (United States)

Vigneshwaran, M.; Dana, S. K.; Padmanaban, E.

2016-12-01

A general coupling design is proposed to realize a mixed coherent (MC) state: coexistence of complete synchronization, antisynchronization, and amplitude death in different pairs of similar state variables of the coupled chaotic system. The stability of coupled system is ensured by the Lyapunov function and a scaling of each variable is also separately taken care of. When heterogeneity as a parameter mismatch is introduced in the coupled system, the coupling function facilitates to retain its coherence and displays the global stability with renewed scaling factor. Robust synchronization features facilitated by a MC state enable to design a dual modulation scheme: binary phase shift key (BPSK) and parameter mismatch shift key (PMSK), for secure data transmission. Two classes of decoders (coherent and noncoherent) are discussed, the noncoherent decoder shows better performance over the coherent decoder, mostly a noncoherent demodulator is preferred in biological implant applications. Both the modulation schemes are demonstrated numerically by using the Lorenz oscillator and the BPSK scheme is demonstrated experimentally using radio signals.

Application of enriched stable isotopes as tracers in biological systems

DEFF Research Database (Denmark)

Stürup, Stefan; Hansen, Helle Rüsz; Gammelgaard, Bente

2008-01-01

The application of enriched stable isotopes of minerals and trace elements as tracers in biological systems is a rapidly growing research field that benefits from the many new developments in inorganic mass spectrometric instrumentation, primarily within inductively coupled plasma mass spectrometry...... (ICP-MS) instrumentation, such as reaction/collision cell ICP-MS and multicollector ICP-MS with improved isotope ratio measurement and interference removal capabilities. Adaptation and refinement of radioisotope tracer experiment methodologies for enriched stable isotope experiments......, and the development of new methodologies coupled with more advanced compartmental and mathematical models for the distribution of elements in living organisms has enabled a broader use of enriched stable isotope experiments in the biological sciences. This review discusses the current and future uses of enriched...

Using the Model Coupling Toolkit to couple earth system models

Science.gov (United States)

Warner, J.C.; Perlin, N.; Skyllingstad, E.D.

2008-01-01

Continued advances in computational resources are providing the opportunity to operate more sophisticated numerical models. Additionally, there is an increasing demand for multidisciplinary studies that include interactions between different physical processes. Therefore there is a strong desire to develop coupled modeling systems that utilize existing models and allow efficient data exchange and model control. The basic system would entail model "1" running on "M" processors and model "2" running on "N" processors, with efficient exchange of model fields at predetermined synchronization intervals. Here we demonstrate two coupled systems: the coupling of the ocean circulation model Regional Ocean Modeling System (ROMS) to the surface wave model Simulating WAves Nearshore (SWAN), and the coupling of ROMS to the atmospheric model Coupled Ocean Atmosphere Prediction System (COAMPS). Both coupled systems use the Model Coupling Toolkit (MCT) as a mechanism for operation control and inter-model distributed memory transfer of model variables. In this paper we describe requirements and other options for model coupling, explain the MCT library, ROMS, SWAN and COAMPS models, methods for grid decomposition and sparse matrix interpolation, and provide an example from each coupled system. Methods presented in this paper are clearly applicable for coupling of other types of models. ?? 2008 Elsevier Ltd. All rights reserved.

Feedback dynamics and cell function: Why systems biology is called Systems Biology.

Science.gov (United States)

Wolkenhauer, Olaf; Mesarovic, Mihajlo

2005-05-01

A new paradigm, like Systems Biology, should challenge the way research has been conducted previously. This Opinion article aims to present Systems Biology, not as the application of engineering principles to biology but as a merger of systems- and control theory with molecular- and cell biology. In our view, the central dogma of Systems Biology is that it is system dynamics that gives rise to the functioning and function of cells. The concepts of feedback regulation and control of pathways and the coordination of cell function are emphasized as an important area of Systems Biology research. The hurdles and risks for this area are discussed from the perspective of dynamic pathway modelling. Most of all, the aim of this article is to promote mathematical modelling and simulation as a part of molecular- and cell biology. Systems Biology is a success if it is widely accepted that there is nothing more practical than a good theory.

Effect of Topology Structures on Synchronization Transition in Coupled Neuron Cells System

International Nuclear Information System (INIS)

Liang Li-Si; Zhang Ji-Qian; Xu Gui-Xia; Liu Le-Zhu; Huang Shou-Fang

2013-01-01

In this paper, by the help of evolutionary algorithm and using Hindmarsh—Rose (HR) neuron model, we investigate the effect of topology structures on synchronization transition between different states in coupled neuron cells system. First, we build different coupling structure with N cells, and found the effect of synchronized transition contact not only closely with the topology of the system, but also with whether there exist the ring structures in the system. In particular, both the size and the number of rings have greater effects on such transition behavior. Secondly, we introduce synchronization error to qualitative analyze the effect of the topology structure. Furthermore, by fitting the simulation results, we find that with the increment of the neurons number, there always exist the optimization structures which have the minimum number of connecting edges in the coupling systems. Above results show that the topology structures have a very crucial role on synchronization transition in coupled neuron system. Biological system may gradually acquire such efficient topology structures through the long-term evolution, thus the systems' information process may be optimized by this scheme. (interdisciplinary physics and related areas of science and technology)

A MODELING AND SIMULATION LANGUAGE FOR BIOLOGICAL CELLS WITH COUPLED MECHANICAL AND CHEMICAL PROCESSES.

Science.gov (United States)

Somogyi, Endre; Glazier, James A

2017-04-01

Biological cells are the prototypical example of active matter. Cells sense and respond to mechanical, chemical and electrical environmental stimuli with a range of behaviors, including dynamic changes in morphology and mechanical properties, chemical uptake and secretion, cell differentiation, proliferation, death, and migration. Modeling and simulation of such dynamic phenomena poses a number of computational challenges. A modeling language describing cellular dynamics must naturally represent complex intra and extra-cellular spatial structures and coupled mechanical, chemical and electrical processes. Domain experts will find a modeling language most useful when it is based on concepts, terms and principles native to the problem domain. A compiler must then be able to generate an executable model from this physically motivated description. Finally, an executable model must efficiently calculate the time evolution of such dynamic and inhomogeneous phenomena. We present a spatial hybrid systems modeling language, compiler and mesh-free Lagrangian based simulation engine which will enable domain experts to define models using natural, biologically motivated constructs and to simulate time evolution of coupled cellular, mechanical and chemical processes acting on a time varying number of cells and their environment.

Mapping biological systems to network systems

CERN Document Server

Rathore, Heena

2016-01-01

The book presents the challenges inherent in the paradigm shift of network systems from static to highly dynamic distributed systems – it proposes solutions that the symbiotic nature of biological systems can provide into altering networking systems to adapt to these changes. The author discuss how biological systems – which have the inherent capabilities of evolving, self-organizing, self-repairing and flourishing with time – are inspiring researchers to take opportunities from the biology domain and map them with the problems faced in network domain. The book revolves around the central idea of bio-inspired systems -- it begins by exploring why biology and computer network research are such a natural match. This is followed by presenting a broad overview of biologically inspired research in network systems -- it is classified by the biological field that inspired each topic and by the area of networking in which that topic lies. Each case elucidates how biological concepts have been most successfully ...

IVF, same-sex couples and the value of biological ties.

Science.gov (United States)

Di Nucci, Ezio

2016-12-01

Ought parents, in general, to value being biologically tied to their children? Is it important, in particular, that both parents be biologically tied to their children? I will address these fundamental questions by looking at a fairly new practice within IVF treatments, so-called IVF-with-ROPA (Reception of Oocytes from Partner), which allows lesbian couples to 'share motherhood', with one partner providing the eggs while the other becomes pregnant. I believe that IVF-with-ROPA is, just like other IVF treatments, morally permissible, but here I argue that the increased biological ties which IVF-with-ROPA allows for do not have any particular value beside the satisfaction of a legitimate wish, because there is no intrinsic value in a biological tie between parents and children; further, I argue that equality within parental projects cannot be achieved by redistributing biological ties. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Computational Systems Chemical Biology

OpenAIRE

Oprea, Tudor I.; May, Elebeoba E.; Leitão, Andrei; Tropsha, Alexander

2011-01-01

There is a critical need for improving the level of chemistry awareness in systems biology. The data and information related to modulation of genes and proteins by small molecules continue to accumulate at the same time as simulation tools in systems biology and whole body physiologically-based pharmacokinetics (PBPK) continue to evolve. We called this emerging area at the interface between chemical biology and systems biology systems chemical biology, SCB (Oprea et al., 2007).

Translation-coupling systems

Science.gov (United States)

Pfleger, Brian; Mendez-Perez, Daniel

2013-11-05

Disclosed are systems and methods for coupling translation of a target gene to a detectable response gene. A version of the invention includes a translation-coupling cassette. The translation-coupling cassette includes a target gene, a response gene, a response-gene translation control element, and a secondary structure-forming sequence that reversibly forms a secondary structure masking the response-gene translation control element. Masking of the response-gene translation control element inhibits translation of the response gene. Full translation of the target gene results in unfolding of the secondary structure and consequent translation of the response gene. Translation of the target gene is determined by detecting presence of the response-gene protein product. The invention further includes RNA transcripts of the translation-coupling cassettes, vectors comprising the translation-coupling cassettes, hosts comprising the translation-coupling cassettes, methods of using the translation-coupling cassettes, and gene products produced with the translation-coupling cassettes.

From systems biology to systems biomedicine.

Science.gov (United States)

Antony, Paul M A; Balling, Rudi; Vlassis, Nikos

2012-08-01

Systems Biology is about combining theory, technology, and targeted experiments in a way that drives not only data accumulation but knowledge as well. The challenge in Systems Biomedicine is to furthermore translate mechanistic insights in biological systems to clinical application, with the central aim of improving patients' quality of life. The challenge is to find theoretically well-chosen models for the contextually correct and intelligible representation of multi-scale biological systems. In this review, we discuss the current state of Systems Biology, highlight the emergence of Systems Biomedicine, and highlight some of the topics and views that we think are important for the efficient application of Systems Theory in Biomedicine. Copyright © 2011 Elsevier Ltd. All rights reserved.

Systems Biology and Health Systems Complexity in;

NARCIS (Netherlands)

Donald Combs, C.; Barham, S.R.; Sloot, P.M.A.

2016-01-01

Systems biology addresses interactions in biological systems at different scales of biological organization, from the molecular to the cellular, organ, organism, societal, and ecosystem levels. This chapter expands on the concept of systems biology, explores its implications for individual patients

Systems Biology-an interdisciplinary approach.

Science.gov (United States)

Friboulet, Alain; Thomas, Daniel

2005-06-15

System-level approaches in biology are not new but foundations of "Systems Biology" are achieved only now at the beginning of the 21st century [Kitano, H., 2001. Foundations of Systems Biology. MIT Press, Cambridge, MA]. The renewed interest for a system-level approach is linked to the progress in collecting experimental data and to the limits of the "reductionist" approach. System-level understanding of native biological and pathological systems is needed to provide potential therapeutic targets. Examples of interdisciplinary approach in Systems Biology are described in U.S., Japan and Europe. Robustness in biology, metabolic engineering and idiotypic networks are discussed in the framework of Systems Biology.

How noise and coupling influence leading indicators of population extinction in a spatially extended ecological system.

Science.gov (United States)

O'Regan, Suzanne M

2018-12-01

Anticipating critical transitions in spatially extended systems is a key topic of interest to ecologists. Gradually declining metapopulations are an important example of a spatially extended biological system that may exhibit a critical transition. Theory for spatially extended systems approaching extinction that accounts for environmental stochasticity and coupling is currently lacking. Here, we develop spatially implicit two-patch models with additive and multiplicative forms of environmental stochasticity that are slowly forced through population collapse, through changing environmental conditions. We derive patch-specific expressions for candidate indicators of extinction and test their performance via a simulation study. Coupling and spatial heterogeneities decrease the magnitude of the proposed indicators in coupled populations relative to isolated populations, and the noise regime and the degree of coupling together determine trends in summary statistics. This theory may be readily applied to other spatially extended ecological systems, such as coupled infectious disease systems on the verge of elimination.

Growing trend of CE at the omics level: the frontier of systems biology--an update.

Science.gov (United States)

Ban, Eunmi; Park, Soo Hyun; Kang, Min-Jung; Lee, Hyun-Jung; Song, Eun Joo; Yoo, Young Sook

2012-01-01

Omics is the study of proteins, peptides, genes, and metabolites in living organisms. Systems biology aims to understand the system through the study of the relationship between elements such as genes and proteins in biological system. Recently, systems biology emerged as the result of the advanced development of high-throughput analysis technologies such as DNA sequencers, DNA arrays, and mass spectrometry for omics studies. Among a number of analytical tools and technologies, CE and CE coupled to MS are promising and relatively rapidly developing tools with the potential to provide qualitative and quantitative analyses of biological molecules. With an emphasis on CE for systems biology, this review summarizes the method developments and applications of CE for the genomic, transcriptomic, proteomic, and metabolomic studies focusing on the drug discovery and disease diagnosis and therapies since 2009. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Communication: Biological applications of coupled-cluster frozen-density embedding

Science.gov (United States)

Heuser, Johannes; Höfener, Sebastian

2018-04-01

We report the implementation of the Laplace-transform scaled opposite-spin (LT-SOS) resolution-of-the-identity second-order approximate coupled-cluster singles and doubles (RICC2) combined with frozen-density embedding for excitation energies and molecular properties. In the present work, we furthermore employ the Hartree-Fock density for the interaction energy leading to a simplified Lagrangian which is linear in the Lagrangian multipliers. This approximation has the key advantage of a decoupling of the coupled-cluster amplitude and multipliers, leading also to a significant reduction in computation time. Using the new simplified Lagrangian in combination with efficient wavefunction models such as RICC2 or LT-SOS-RICC2 and density-functional theory (DFT) for the environment molecules (CC2-in-DFT) enables the efficient study of biological applications such as the rhodopsin and visual cone pigments using ab initio methods as routine applications.

Quantum Dynamics in Biological Systems

Science.gov (United States)

Shim, Sangwoo

In the first part of this dissertation, recent efforts to understand quantum mechanical effects in biological systems are discussed. Especially, long-lived quantum coherences observed during the electronic energy transfer process in the Fenna-Matthews-Olson complex at physiological condition are studied extensively using theories of open quantum systems. In addition to the usual master equation based approaches, the effect of the protein structure is investigated in atomistic detail through the combined application of quantum chemistry and molecular dynamics simulations. To evaluate the thermalized reduced density matrix, a path-integral Monte Carlo method with a novel importance sampling approach is developed for excitons coupled to an arbitrary phonon bath at a finite temperature. In the second part of the thesis, simulations of molecular systems and applications to vibrational spectra are discussed. First, the quantum dynamics of a molecule is simulated by combining semiclassical initial value representation and density funcitonal theory with analytic derivatives. A computationally-tractable approximation to the sum-of-states formalism of Raman spectra is subsequently discussed.

Biological conversion system

Science.gov (United States)

Scott, C.D.

A system for bioconversion of organic material comprises a primary bioreactor column wherein a biological active agent (zymomonas mobilis) converts the organic material (sugar) to a product (alcohol), a rejuvenator column wherein the biological activity of said biological active agent is enhanced, and means for circulating said biological active agent between said primary bioreactor column and said rejuvenator column.

Philosophical Basis and Some Historical Aspects of Systems Biology: From Hegel to Noble - Applications for Bioenergetic Research

Science.gov (United States)

Saks, Valdur; Monge, Claire; Guzun, Rita

2009-01-01

We live in times of paradigmatic changes for the biological sciences. Reductionism, that for the last six decades has been the philosophical basis of biochemistry and molecular biology, is being displaced by Systems Biology, which favors the study of integrated systems. Historically, Systems Biology - defined as the higher level analysis of complex biological systems - was pioneered by Claude Bernard in physiology, Norbert Wiener with the development of cybernetics, and Erwin Schrödinger in his thermodynamic approach to the living. Systems Biology applies methods inspired by cybernetics, network analysis, and non-equilibrium dynamics of open systems. These developments follow very precisely the dialectical principles of development from thesis to antithesis to synthesis discovered by Hegel. Systems Biology opens new perspectives for studies of the integrated processes of energy metabolism in different cells. These integrated systems acquire new, system-level properties due to interaction of cellular components, such as metabolic compartmentation, channeling and functional coupling mechanisms, which are central for regulation of the energy fluxes. State of the art of these studies in the new area of Molecular System Bioenergetics is analyzed. PMID:19399243

Development trend of radiation biology research-systems radiation biology

International Nuclear Information System (INIS)

Min Rui

2010-01-01

Radiation biology research has past 80 years. We have known much more about fundamentals, processes and results of biology effects induced by radiation and various factors that influence biology effects wide and deep, however many old and new scientific problems occurring in the field of radiation biology research remain to be illustrated. To explore and figure these scientific problems need systemic concept, methods and multi dimension view on the base of considerations of complexity of biology system, diversity of biology response, temporal and spatial process of biological effects during occurrence, and complex feed back network of biological regulations. (authors)

Systems biology: the reincarnation of systems theory applied in biology?

Science.gov (United States)

Wolkenhauer, O

2001-09-01

With the availability of quantitative data on the transcriptome and proteome level, there is an increasing interest in formal mathematical models of gene expression and regulation. International conferences, research institutes and research groups concerned with systems biology have appeared in recent years and systems theory, the study of organisation and behaviour per se, is indeed a natural conceptual framework for such a task. This is, however, not the first time that systems theory has been applied in modelling cellular processes. Notably in the 1960s systems theory and biology enjoyed considerable interest among eminent scientists, mathematicians and engineers. Why did these early attempts vanish from research agendas? Here we shall review the domain of systems theory, its application to biology and the lessons that can be learned from the work of Robert Rosen. Rosen emerged from the early developments in the 1960s as a main critic but also developed a new alternative perspective to living systems, a concept that deserves a fresh look in the post-genome era of bioinformatics.

Efficient Integration of Coupled Electrical-chemical Systems in Multiscale Neuronal Simulations

Directory of Open Access Journals (Sweden)

Ekaterina Brocke

2016-09-01

Full Text Available Multiscale modeling and simulations in neuroscience is gaining scientific attention due to its growing importance and unexplored capabilities. For instance, it can help to acquire better understanding of biological phenomena that have important features at multiple scales of time and space. This includes synaptic plasticity, memory formation and modulation, homeostasis. There are several ways to organize multiscale simulations depending on the scientific problem and the system to be modeled. One of the possibilities is to simulate different components of a multiscale system simultaneously and exchange data when required. The latter may become a challenging task for several reasons. One of them is that the components of a multiscale system usually span different spatial and temporal scales, such that rigorous analysis of possible coupling solutions is required. For certain classes of problems a number of coupling mechanisms have been proposed and successfully used. However, a strict mathematical theory is missing in many cases. Recent work in the field has not so far investigated artifacts that may arise during coupled integration of different approximation methods. Moreover, the coupling of widely used numerical fixed step size solvers may lead to unexpected inefficiency. In this paper we address the question of possible numerical artifacts that can arise during the integration of a coupled system. We develop an efficient strategy to couple the components of a multiscale test system. We introduce an efficient coupling method based on the second-order backward differentiation formula numerical approximation. The method uses an adaptive step size integration with an error estimation proposed by Skelboe (2000. The method shows a significant advantage over conventional fixed step size solvers used for similar problems. We explore different coupling strategies that define the organization of computations between system components. We study the

Enzymes or redox couples? The kinetics of thioredoxin and glutaredoxin reactions in a systems biology context

NARCIS (Netherlands)

Pillay, Ché S.; Hofmeyr, Jan Hendrik S; Olivier, Brett G.; Snoep, Jacky L.; Rohwer, Johann M.

2009-01-01

Systems biology approaches, such as kinetic modelling, could provide valuable insights into how thioredoxins, glutaredoxins and peroxiredoxins (here collectively called redoxins), and the systems that reduce these molecules are regulated. However, it is not clear whether redoxins should be described

Growing trend of CE at the omics level: the frontier of systems biology.

Science.gov (United States)

Oh, Eulsik; Hasan, Md Nabiul; Jamshed, Muhammad; Park, Soo Hyun; Hong, Hye-Min; Song, Eun Joo; Yoo, Young Sook

2010-01-01

In a novel attempt to comprehend the complexity of life, systems biology has recently emerged as a state-of-the-art approach for biological research in contrast to the reductionist approaches that have been used in molecular cell biology since the 1950s. Because a massive amount of information is required in many systems biology studies of life processes, we have increasingly come to depend on techniques that provide high-throughput omics data. CE and CE coupled to MS have served as powerful analytical tools for providing qualitative and quantitative omics data. Recent systems biology studies have focused strongly on the diagnosis and treatment of diseases. The increasing number of clinical research papers on drug discovery and disease therapies reflects this growing interest among scientists. Since such clinical research reflects one of the ultimate purposes of bioscience, these trends will be sustained for a long time. Thus, this review mainly focuses on the application of CE and CE-MS in diagnosis as well as on the latest CE methods developed. Furthermore, we outline the new challenges that arose in 2008 and later in elucidating the system-level functions of the bioconstituents of living organisms.

Fostering synergy between cell biology and systems biology.

Science.gov (United States)

Eddy, James A; Funk, Cory C; Price, Nathan D

2015-08-01

In the shared pursuit of elucidating detailed mechanisms of cell function, systems biology presents a natural complement to ongoing efforts in cell biology. Systems biology aims to characterize biological systems through integrated and quantitative modeling of cellular information. The process of model building and analysis provides value through synthesizing and cataloging information about cells and molecules, predicting mechanisms and identifying generalizable themes, generating hypotheses and guiding experimental design, and highlighting knowledge gaps and refining understanding. In turn, incorporating domain expertise and experimental data is crucial for building towards whole cell models. An iterative cycle of interaction between cell and systems biologists advances the goals of both fields and establishes a framework for mechanistic understanding of the genome-to-phenome relationship. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

Imaging of Selenium by Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS) in 2-D Electrophoresis Gels and Biological Tissues.

Science.gov (United States)

Cruz, Elisa Castañeda Santa; Susanne Becker, J; Sabine Becker, J; Sussulini, Alessandra

2018-01-01

Selenium and selenoproteins are important components of living organisms that play a role in different biological processes. Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) is a powerful analytical technique that has been employed to obtain distribution maps of selenium in biological tissues in a direct manner, as well as in selenoproteins, previously separated by their molecular masses and isoelectric points using two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). In this chapter, we present the protocols to perform LA-ICP-MS imaging experiments, allowing the distribution visualization and determination of selenium and/or selenoproteins in biological systems.

ESPC Coupled Global Prediction System

Science.gov (United States)

2015-09-30

through an improvement to the sea ice albedo . Fig. 3: 2-m Temperature bias (deg C) of 120-h forecasts for the month of May 2014 for the Arctic...forecast system (NAVGEM) and ocean- sea ice forecast system (HYCOM/CICE) have never been coupled at high resolution. The coupled processes will be...winds and currents across the interface. The sea - ice component of this project requires modification of CICE versions 4 and 5 to run in the coupled

Synthetic and systems biology for microbial production of commodity chemicals.

Science.gov (United States)

Chubukov, Victor; Mukhopadhyay, Aindrila; Petzold, Christopher J; Keasling, Jay D; Martín, Héctor García

2016-01-01

The combination of synthetic and systems biology is a powerful framework to study fundamental questions in biology and produce chemicals of immediate practical application such as biofuels, polymers, or therapeutics. However, we cannot yet engineer biological systems as easily and precisely as we engineer physical systems. In this review, we describe the path from the choice of target molecule to scaling production up to commercial volumes. We present and explain some of the current challenges and gaps in our knowledge that must be overcome in order to bring our bioengineering capabilities to the level of other engineering disciplines. Challenges start at molecule selection, where a difficult balance between economic potential and biological feasibility must be struck. Pathway design and construction have recently been revolutionized by next-generation sequencing and exponentially improving DNA synthesis capabilities. Although pathway optimization can be significantly aided by enzyme expression characterization through proteomics, choosing optimal relative protein expression levels for maximum production is still the subject of heuristic, non-systematic approaches. Toxic metabolic intermediates and proteins can significantly affect production, and dynamic pathway regulation emerges as a powerful but yet immature tool to prevent it. Host engineering arises as a much needed complement to pathway engineering for high bioproduct yields; and systems biology approaches such as stoichiometric modeling or growth coupling strategies are required. A final, and often underestimated, challenge is the successful scale up of processes to commercial volumes. Sustained efforts in improving reproducibility and predictability are needed for further development of bioengineering.

Philosophical Basis and Some Historical Aspects of Systems Biology: From Hegel to Noble - Applications for Bioenergetic Research

Directory of Open Access Journals (Sweden)

Valdur Saks

2009-03-01

Full Text Available We live in times of paradigmatic changes for the biological sciences. Reductionism, that for the last six decades has been the philosophical basis of biochemistry and molecular biology, is being displaced by Systems Biology, which favors the study of integrated systems. Historically, Systems Biology - defined as the higher level analysis of complex biological systems - was pioneered by Claude Bernard in physiology, Norbert Wiener with the development of cybernetics, and Erwin Schrödinger in his thermodynamic approach to the living. Systems Biology applies methods inspired by cybernetics, network analysis, and non-equilibrium dynamics of open systems. These developments follow very precisely the dialectical principles of development from thesis to antithesis to synthesis discovered by Hegel. Systems Biology opens new perspectives for studies of the integrated processes of energy metabolism in different cells. These integrated systems acquire new, system-level properties due to interaction of cellular components, such as metabolic compartmentation, channeling and functional coupling mechanisms, which are central for regulation of the energy fluxes. State of the art of these studies in the new area of Molecular System Bioenergetics is analyzed.

Coupling Strength and System Size Induce Firing Activity of Globally Coupled Neural Network

International Nuclear Information System (INIS)

Wei Duqu; Luo Xiaoshu; Zou Yanli

2008-01-01

We investigate how firing activity of globally coupled neural network depends on the coupling strength C and system size N. Network elements are described by space-clamped FitzHugh-Nagumo (SCFHN) neurons with the values of parameters at which no firing activity occurs. It is found that for a given appropriate coupling strength, there is an intermediate range of system size where the firing activity of globally coupled SCFHN neural network is induced and enhanced. On the other hand, for a given intermediate system size level, there exists an optimal value of coupling strength such that the intensity of firing activity reaches its maximum. These phenomena imply that the coupling strength and system size play a vital role in firing activity of neural network

Coupling chemical and biological catalysis: a flexible paradigm for producing biobased chemicals.

Science.gov (United States)

Schwartz, Thomas J; Shanks, Brent H; Dumesic, James A

2016-04-01

Advances in metabolic engineering have allowed for the development of new biological catalysts capable of selectively de-functionalizing biomass to yield platform molecules that can be upgraded to biobased chemicals using high efficiency continuous processing allowed by heterogeneous chemical catalysis. Coupling these disciplines overcomes the difficulties of selectively activating COH bonds by heterogeneous chemical catalysis and producing petroleum analogues by biological catalysis. We show that carboxylic acids, pyrones, and alcohols are highly flexible platforms that can be used to produce biobased chemicals by this approach. More generally, we suggest that molecules with three distinct functionalities may represent a practical upper limit on the extent of functionality present in the platform molecules that serve as the bridge between biological and chemical catalysis. Copyright © 2016 Elsevier Ltd. All rights reserved.

Wearable System for Acquisition and Monitoring of Biological Signals

Science.gov (United States)

Piccinini, D. J.; Andino, N. B.; Ponce, S. D.; Roberti, MA; López, y. N.

2016-04-01

This paper presents a modular, wearable system for acquisition and wireless transmission of biological signals. Configurable slaves for different signals (such as ECG, EMG, inertial sensors, and temperature) based in the ADS1294 Medical Analog Front End are connected to a Master, based in the CC3200 microcontroller, both from Texas Instruments. The slaves are configurable according to the specific application, providing versatility to the wearable system. The battery consumption is reduced, through a couple of Li-ion batteries and the circuit has also a battery charger. A custom made box was designed and fabricated in a 3D printer, preserving the requirements of low cost, low weight and safety recommendations.

Robustness leads close to the edge of chaos in coupled map networks: toward the understanding of biological networks

International Nuclear Information System (INIS)

Saito, Nen; Kikuchi, Macoto

2013-01-01

Dynamics in biological networks are, in general, robust against several perturbations. We investigate a coupled map network as a model motivated by gene regulatory networks and design systems that are robust against phenotypic perturbations (perturbations in dynamics), as well as systems that are robust against mutation (perturbations in network structure). To achieve such a design, we apply a multicanonical Monte Carlo method. Analysis based on the maximum Lyapunov exponent and parameter sensitivity shows that systems with marginal stability, which are regarded as systems at the edge of chaos, emerge when robustness against network perturbations is required. This emergence of the edge of chaos is a self-organization phenomenon and does not need a fine tuning of parameters. (paper)

Micro-separation toward systems biology.

Science.gov (United States)

Liu, Bi-Feng; Xu, Bo; Zhang, Guisen; Du, Wei; Luo, Qingming

2006-02-17

Current biology is experiencing transformation in logic or philosophy that forces us to reevaluate the concept of cell, tissue or entire organism as a collection of individual components. Systems biology that aims at understanding biological system at the systems level is an emerging research area, which involves interdisciplinary collaborations of life sciences, computational and mathematical sciences, systems engineering, and analytical technology, etc. For analytical chemistry, developing innovative methods to meet the requirement of systems biology represents new challenges as also opportunities and responsibility. In this review, systems biology-oriented micro-separation technologies are introduced for comprehensive profiling of genome, proteome and metabolome, characterization of biomolecules interaction and single cell analysis such as capillary electrophoresis, ultra-thin layer gel electrophoresis, micro-column liquid chromatography, and their multidimensional combinations, parallel integrations, microfabricated formats, and nano technology involvement. Future challenges and directions are also suggested.

Controllable nonlinearity in a dual-coupling optomechanical system under a weak-coupling regime

Science.gov (United States)

Zhu, Gui-Lei; Lü, Xin-You; Wan, Liang-Liang; Yin, Tai-Shuang; Bin, Qian; Wu, Ying

2018-03-01

Strong quantum nonlinearity gives rise to many interesting quantum effects and has wide applications in quantum physics. Here we investigate the quantum nonlinear effect of an optomechanical system (OMS) consisting of both linear and quadratic coupling. Interestingly, a controllable optomechanical nonlinearity is obtained by applying a driving laser into the cavity. This controllable optomechanical nonlinearity can be enhanced into a strong coupling regime, even if the system is initially in the weak-coupling regime. Moreover, the system dissipation can be suppressed effectively, which allows the appearance of phonon sideband and photon blockade effects in the weak-coupling regime. This work may inspire the exploration of a dual-coupling optomechanical system as well as its applications in modern quantum science.

Nutritional Systems Biology

DEFF Research Database (Denmark)

Jensen, Kasper

and network biology has the potential to increase our understanding of how small molecules affect metabolic pathways and homeostasis, how this perturbation changes at the disease state, and to what extent individual genotypes contribute to this. A fruitful strategy in approaching and exploring the field...... biology research. The paper also shows as a proof-of-concept that a systems biology approach to diet is meaningful and demonstrates some basic principles on how to work with diet systematic. The second chapter of this thesis we developed the resource NutriChem v1.0. A foodchemical database linking...... sites of diet on the disease pathway. We propose a framework for interrogating the critical targets in colon cancer process and identifying plant-based dietary interventions as important modifiers using a systems chemical biology approach. The fifth chapter of the thesis is on discovering of novel anti...

Informing biological design by integration of systems and synthetic biology.

Science.gov (United States)

Smolke, Christina D; Silver, Pamela A

2011-03-18

Synthetic biology aims to make the engineering of biology faster and more predictable. In contrast, systems biology focuses on the interaction of myriad components and how these give rise to the dynamic and complex behavior of biological systems. Here, we examine the synergies between these two fields. Copyright © 2011 Elsevier Inc. All rights reserved.

Thermodynamic Optimality criteria for biological systems in linear irreversible thermodynamics

International Nuclear Information System (INIS)

Chimal, J C; Sánchez, N; Ramírez, PR

2017-01-01

In this paper the methodology of the so-called Linear Irreversible Thermodynamics (LIT) is applied; although traditionally used locally to study general systems in non-equilibrium states in which it is consider both internal and external contributions to the entropy increments in order to analyze the efficiency of two coupled processes with generalized fluxes J 1 , J 2 and their corresponding forces X 1 , X 2 . We extend the former analysis to takes into account two different operating regimes namely: Omega Function and Efficient Power criterion, respectively. Results show analogies in the optimal performance between and we can say that there exist a criteria of optimization which can be used specially for biological systems where a good design of the biological parameters made by nature at maximum efficient power conditions lead to more efficient engines than those at the maximum power conditions or ecological conditions. (paper)

Phenol wastewater remediation: advanced oxidation processes coupled to a biological treatment.

Science.gov (United States)

Rubalcaba, A; Suárez-Ojeda, M E; Stüber, F; Fortuny, A; Bengoa, C; Metcalfe, I; Font, J; Carrera, J; Fabregat, A

2007-01-01

Nowadays, there are increasingly stringent regulations requiring more and more treatment of industrial effluents to generate product waters which could be easily reused or disposed of to the environment without any harmful effects. Therefore, different advanced oxidation processes were investigated as suitable precursors for the biological treatment of industrial effluents containing phenol. Wet air oxidation and Fenton process were tested batch wise, while catalytic wet air oxidation and H2O2-promoted catalytic wet air oxidation processes were studied in a trickle bed reactor, the last two using over activated carbon as catalyst. Effluent characterisation was made by means of substrate conversion (using high liquid performance chromatography), chemical oxygen demand and total organic carbon. Biodegradation parameters (i.e. maximum oxygen uptake rate and oxygen consumption) were obtained from respirometric tests using activated sludge from an urban biological wastewater treatment plant (WWTP). The main goal was to find the proper conditions in terms of biodegradability enhancement, so that these phenolic effluents could be successfully treated in an urban biological WWTP. Results show promising research ways for the development of efficient coupled processes for the treatment of wastewater containing toxic or biologically non-degradable compounds.

Spatial Structures and Regulation in Biological Systems

DEFF Research Database (Denmark)

Yde, Pernille

, and the other is the spatial regulation of biological systems, here related to different aspects of the inflammatory response. All systems are studied using computational modelling and mathematical analysis. The first part of the thesis explores different protein aggregation scenarios. In Chapter 1, we consider...... a previously studied and very general aggregation model describing frangible linear filaments. This model is especially relevant for the growth of amyloid fibres, that have been related to a number of serious human diseases, and which are known to grow in an accelerated self-enhanced manner.We derive...... model of the tissue and show how coupled cells are able to function as an excitable medium and propagate waves of high cytokine concentration through the tissue. If the internal regulation in the cells is over-productive, the model predicts a continuous amplification of cytokines, which spans the entire...

Nonequilibrium thermodynamics transport and rate processes in physical, chemical and biological systems

CERN Document Server

Demirel, Yasar

2014-01-01

Natural phenomena consist of simultaneously occurring transport processes and chemical reactions. These processes may interact with each other and may lead to self-organized structures, fluctuations, instabilities, and evolutionary systems. Nonequilibrium Thermodynamics, 3rd edition emphasizes the unifying role of thermodynamics in analyzing the natural phenomena. This third edition updates and expands on the first and second editions by focusing on the general balance equations for coupled processes of physical, chemical, and biological systems. The new edition contains a new chapte

Feedback coupling in dynamical systems

Science.gov (United States)

Trimper, Steffen; Zabrocki, Knud

2003-05-01

Different evolution models are considered with feedback-couplings. In particular, we study the Lotka-Volterra system under the influence of a cumulative term, the Ginzburg-Landau model with a convolution memory term and chemical rate equations with time delay. The memory leads to a modified dynamical behavior. In case of a positive coupling the generalized Lotka-Volterra system exhibits a maximum gain achieved after a finite time, but the population will die out in the long time limit. In the opposite case, the time evolution is terminated in a crash. Due to the nonlinear feedback coupling the two branches of a bistable model are controlled by the the strength and the sign of the memory. For a negative coupling the system is able to switch over between both branches of the stationary solution. The dynamics of the system is further controlled by the initial condition. The diffusion-limited reaction is likewise studied in case the reacting entities are not available simultaneously. Whereas for an external feedback the dynamics is altered, but the stationary solution remain unchanged, a self-organized internal feedback leads to a time persistent solution.

A short comparison of electron and proton transfer processes in biological systems

International Nuclear Information System (INIS)

Bertrand, Patrick

2005-01-01

The main differences between electron and proton transfers that take place in biological systems are examined. The relation between the distance dependence of the rate constant and the mass of the transferred particle is analyzed in detail. Differences between the two processes have important consequences at the experimental level, which are discussed. The various mechanisms that ensure the coupling between electron and proton transfers are briefly described

Achieving Synchronization in Arrays of Coupled Differential Systems with Time-Varying Couplings

Directory of Open Access Journals (Sweden)

Xinlei Yi

2013-01-01

Full Text Available We study complete synchronization of the complex dynamical networks described by linearly coupled ordinary differential equation systems (LCODEs. Here, the coupling is timevarying in both network structure and reaction dynamics. Inspired by our previous paper (Lu et al. (2007-2008, the extended Hajnal diameter is introduced and used to measure the synchronization in a general differential system. Then we find that the Hajnal diameter of the linear system induced by the time-varying coupling matrix and the largest Lyapunov exponent of the synchronized system play the key roles in synchronization analysis of LCODEs with identity inner coupling matrix. As an application, we obtain a general sufficient condition guaranteeing directed time-varying graph to reach consensus. Example with numerical simulation is provided to show the effectiveness of the theoretical results.

Excited states in biological systems

International Nuclear Information System (INIS)

Cilento, G.; Zinner, K.; Bechara, E.J.H.; Duran, N.; Baptista, R.C. de; Shimizu, Y.; Augusto, O.; Faljoni-Alario, A.; Vidigal, C.C.C.; Oliveira, O.M.M.F.; Haun, M.

1979-01-01

Some aspects of bioluminescence related to bioenergetics are discussed: 1. chemical generation of excited species, by means of two general processes: electron transference and cyclic - and linear peroxide cleavage; 2. biological systems capable of generating excited states and 3. biological functions of these states, specially the non-emissive ones (tripletes). The production and the role of non-emissive excited states in biological systems are analysed, the main purpose of the study being the search for non-emissive states. Experiences carried out in biological systems are described; results and conclusions are given. (M.A.) [pt

Dynamics and thermodynamics in hierarchically organized systems applications in physics, biology and economics

CERN Document Server

Auger, P

2013-01-01

One of the most fundamental and efficient ways of conceptualizing complex systems is to organize them hierarchically. A hierarchically organized system is represented by a network of interconnected subsystems, each of which has its own network of subsystems, and so on, until some elementary subsystems are reached that are not further decomposed. This original and important book proposes a general mathematical theory of a hierarchical system and shows how it can be applied to very different topics such as physics (Hamiltonian systems), biology (coupling the molecular and the cellular levels), e

Telemetry System of Biological Parameters

Directory of Open Access Journals (Sweden)

Jan Spisak

2005-01-01

Full Text Available The mobile telemetry system of biological parameters serves for reading and wireless data transfer of measured values of selected biological parameters to an outlying computer. It concerns basically long time monitoring of vital function of car pilot.The goal of this projects is to propose mobile telemetry system for reading, wireless transfer and processing of biological parameters of car pilot during physical and psychical stress. It has to be made with respect to minimal consumption, weight and maximal device mobility. This system has to eliminate signal noise, which is created by biological artifacts and disturbances during the data transfer.

Enhanced Electron-Phonon Coupling at Metal Surfaces

Energy Technology Data Exchange (ETDEWEB)

Plummer, Ward E.

2010-08-04

The Born-Oppenheimer approximation (BOA) decouples electronic from nuclear motion, providing a focal point for most quantum mechanics textbooks. However, a multitude of important chemical, physical and biological phenomena are driven by violations of this approximation. Vibronic interactions are a necessary ingredient in any process that makes or breaks a covalent bond, for example, conventional catalysis or enzymatically delivered biological reactions. Metastable phenomena associated with defects and dopants in semiconductors, oxides, and glasses entail violation of the BOA. Charge exchange in inorganic polymers, organic slats and biological systems involves charge- induced distortions of the local structure. A classic example is conventional superconductivity, which is driven by the electron-lattice interaction. High-resolution angle-resolved photoemission experiments are yielding new insight into the microscopic origin of electron-phonon coupling (EPC) in anisotropic two-dimensional systems. Our recent surface phonon measurement on the surface of a high-Tc material clearly indicates an important momentum dependent EPC in these materials. In the last few years we have shifted our research focus from solely looking at electron phonon coupling to examining the structure/functionality relationship at the surface of complex transition metal compounds. The investigation on electron phonon coupling has allowed us to move to systems where there is coupling between the lattice, the electrons and the spin.

Logical analysis of biological systems

DEFF Research Database (Denmark)

Mardare, Radu Iulian

2005-01-01

R. Mardare, Logical analysis of biological systems. Fundamenta Informaticae, N 64:271-285, 2005.......R. Mardare, Logical analysis of biological systems. Fundamenta Informaticae, N 64:271-285, 2005....

Linearly and nonlinearly bidirectionally coupled synchronization of hyperchaotic systems

International Nuclear Information System (INIS)

Zhou Jin; Lu Junan; Wu Xiaoqun

2007-01-01

To date, there have been many results about unidirectionally coupled synchronization of chaotic systems. However, much less work is reported on bidirectionally-coupled synchronization. In this paper, we investigate the synchronization of two bidirectionally coupled Chen hyperchaotic systems, which are coupled linearly and nonlinearly respectively. Firstly, linearly coupled synchronization of two hyperchaotic Chen systems is investigated, and a theorem on how to choose the coupling coefficients are developed to guarantee the global asymptotical synchronization of two coupled hyperchaotic systems. Analysis shows that the choice of the coupling coefficients relies on the bound of the chaotic system. Secondly, the nonlinearly coupled synchronization is studied; a sufficient condition for the locally asymptotical synchronization is derived, which is independent of the bound of the hyperchaotic system. Finally, numerical simulations are included to verify the effectiveness and feasibility of the developed theorems

Institute for Genomics and Systems Biology

Science.gov (United States)

Institute for Genomics and Systems Biology Discover. Predict. Improve. Advancing Human and , 2015 See all Research Papers Featured Video Introduction to Systems Biology Video: Introduction to Systems Biology News Jack Gilbert Heading UChicago Startup that Aims to Predict Behavior of Trillions of

Degradation alternatives for a commercial fungicide in water: biological, photo-Fenton, and coupled biological photo-Fenton processes.

Science.gov (United States)

López-Loveira, Elsa; Ariganello, Federico; Medina, María Sara; Centrón, Daniela; Candal, Roberto; Curutchet, Gustavo

2017-11-01

Imazalil (IMZ) is a widely used fungicide for the post-harvest treatment of citrus, classified as "likely to be carcinogenic in humans" for EPA, that can be only partially removed by conventional biological treatment. Consequently, specific or combined processes should be applied to prevent its release to the environment. Biological treatment with adapted microorganism consortium, photo-Fenton, and coupled biological photo-Fenton processes were tested as alternatives for the purification of water containing high concentration of the fungicide and the coadjutants present in the commercial formulation. IMZ-resistant consortium with the capacity to degrade IMZ in the presence of a C-rich co-substrate was isolated from sludge coming from a fruit packaging company wastewater treatment plant. This consortium was adapted to resist and degrade the organics present in photo-Fenton-oxidized IMZ water solution. Bacteria colonies from the consortia were isolated and identified. The effect of H 2 O 2 initial concentration and dosage on IMZ degradation rate, average oxidation state (AOS), organic acid concentration, oxidation, and mineralization percentage after photo-Fenton process was determined. The application of biological treatment to the oxidized solutions notably decreased the total organic carbon (TOC) in solution. The effect of the oxidation degree, limited by H 2 O 2 concentration and dosage, on the percentage of mineralization obtained after the biological treatment was determined and explained in terms of changes in AOS. The concentration of H 2 O 2 necessary to eliminate IMZ by photo-Fenton and to reduce TOC and chemical oxygen demand (COD) by biological treatment, in order to allow the release of the effluents to rivers with different flows, was estimated.

Physics and biology

International Nuclear Information System (INIS)

Frauenfelder, H.

1988-01-01

The author points out that the coupling between physics and biology is becoming closer as time goes on. He tries to show that physical studies on biological systems not only yield insight into biology but also provide results of interest to physics. Biological systems are extremly complex system. Ideally one would like to understand the behavior of such systems in terms of the behavior of its constituent atoms. Since in small organisms this may be 10 20 atoms, it is clear these are not simple many-body systems. He reviews the basic elements of cells and then considers the broader questions of structure, complexity, and function, which must be looked at on levels from the cell to the organism. Despite the vast amount of observational material already in existence, biophysics and biological physics are only at a beginning. We can expect that physics will continue to interact strongly with biology. Actually, the connection also includes chemistry and mathematics. New tools that become available in physics will continue to be applied to biological problems. We can expect that the flow of information will not be one way; biological systems will provide new information on many old and new parts of physics, from reaction theory and transport phenomena to complexity, cooperativity, and nonlinear processes

Biophysics and systems biology.

Science.gov (United States)

Noble, Denis

2010-03-13

Biophysics at the systems level, as distinct from molecular biophysics, acquired its most famous paradigm in the work of Hodgkin and Huxley, who integrated their equations for the nerve impulse in 1952. Their approach has since been extended to other organs of the body, notably including the heart. The modern field of computational biology has expanded rapidly during the first decade of the twenty-first century and, through its contribution to what is now called systems biology, it is set to revise many of the fundamental principles of biology, including the relations between genotypes and phenotypes. Evolutionary theory, in particular, will require re-assessment. To succeed in this, computational and systems biology will need to develop the theoretical framework required to deal with multilevel interactions. While computational power is necessary, and is forthcoming, it is not sufficient. We will also require mathematical insight, perhaps of a nature we have not yet identified. This article is therefore also a challenge to mathematicians to develop such insights.

Inverse problems in systems biology

International Nuclear Information System (INIS)

Engl, Heinz W; Lu, James; Müller, Stefan; Flamm, Christoph; Schuster, Peter; Kügler, Philipp

2009-01-01

Systems biology is a new discipline built upon the premise that an understanding of how cells and organisms carry out their functions cannot be gained by looking at cellular components in isolation. Instead, consideration of the interplay between the parts of systems is indispensable for analyzing, modeling, and predicting systems' behavior. Studying biological processes under this premise, systems biology combines experimental techniques and computational methods in order to construct predictive models. Both in building and utilizing models of biological systems, inverse problems arise at several occasions, for example, (i) when experimental time series and steady state data are used to construct biochemical reaction networks, (ii) when model parameters are identified that capture underlying mechanisms or (iii) when desired qualitative behavior such as bistability or limit cycle oscillations is engineered by proper choices of parameter combinations. In this paper we review principles of the modeling process in systems biology and illustrate the ill-posedness and regularization of parameter identification problems in that context. Furthermore, we discuss the methodology of qualitative inverse problems and demonstrate how sparsity enforcing regularization allows the determination of key reaction mechanisms underlying the qualitative behavior. (topical review)

Systems biology in critical-care nursing.

Science.gov (United States)

Schallom, Lynn; Thimmesch, Amanda R; Pierce, Janet D

2011-01-01

Systems biology applies advances in technology and new fields of study including genomics, transcriptomics, proteomics, and metabolomics to the development of new treatments and approaches of care for the critically ill and injured patient. An understanding of systems biology enhances a nurse's ability to implement evidence-based practice and to educate patients and families on novel testing and therapies. Systems biology is an integrated and holistic view of humans in relationship with the environment. Biomarkers are used to measure the presence and severity of disease and are rapidly expanding in systems biology endeavors. A systems biology approach using predictive, preventive, and participatory involvement is being utilized in a plethora of conditions of critical illness and injury including sepsis, cancer, pulmonary disease, and traumatic injuries.

Compartmental study of biological systems

International Nuclear Information System (INIS)

Moretti, J.L.

1975-01-01

The compartmental analysis of biological system is dealt with on several chapters devoted successively to: terminology; a mathematical and symbolic account of a system at equilibrium; different compartment systems; analysis of the experimental results. For this it is pointed out that the application of compartmental systems to biological phenomena is not always without danger. Sometimes the compartmental system established in a reference subject fails to conform in the patient. The compartments can divide into two or join together, completely changing the aspect of the system so that parameters calculated with the old model become entirely false. The conclusion is that the setting up of a compartmental system to represent a biological phenomenon is a tricky undertaking and the results must be constantly criticized and questioned [fr

Analysis of Synchronization for Coupled Hybrid Systems

DEFF Research Database (Denmark)

Li, Zheng; Wisniewski, Rafal

2006-01-01

In the control systems with coupled multi-subsystem, the subsystems might be synchronized (i.e. all the subsystems have the same operation states), which results in negative influence to the whole system. For example, in the supermarket refrigeration systems, the synchronized switch of each...... subsystem will cause low efficiency, inferior control performance and a high wear on the compressor. This paper takes the supermarket refrigeration systems as an example to analyze the synchronization and its coupling strengths of coupled hybrid systems, which may provide a base for further research...... of control strategies. This paper combines topology and section mapping theories together to show a new way of analyzing hybrid systems...

Philosophy of Systems and Synthetic Biology

DEFF Research Database (Denmark)

Green, Sara

2017-01-01

This entry aims to clarify how systems and synthetic biology contribute to and extend discussions within philosophy of science. Unlike fields such as developmental biology or molecular biology, systems and synthetic biology are not easily demarcated by a focus on a specific subject area or level...... of organization. Rather, they are characterized by the development and application of mathematical, computational, and synthetic modeling strategies in response to complex problems and challenges within the life sciences. Proponents of systems and synthetic biology often stress the necessity of a perspective...... that goes beyond the scope of molecular biology and genetic engineering, respectively. With the emphasis on systems and interaction networks, the approaches explicitly engage in one of the oldest philosophical discussions on the relationship between parts and wholes, or between reductionism and holism...

Defect-related internal dissipation in mechanical resonators and the study of coupled mechanical systems.

Energy Technology Data Exchange (ETDEWEB)

Friedmann, Thomas Aquinas; Czaplewski, David A.; Sullivan, John Patrick; Modine, Normand Arthur; Wendt, Joel Robert; Aslam, Dean (Michigan State University, Lansing, MI); Sepulveda-Alancastro, Nelson (University of Puerto Rico, Mayaguez, PR)

2007-01-01

Understanding internal dissipation in resonant mechanical systems at the micro- and nanoscale is of great technological and fundamental interest. Resonant mechanical systems are central to many sensor technologies, and microscale resonators form the basis of a variety of scanning probe microscopies. Furthermore, coupled resonant mechanical systems are of great utility for the study of complex dynamics in systems ranging from biology to electronics to photonics. In this work, we report the detailed experimental study of internal dissipation in micro- and nanomechanical oscillators fabricated from amorphous and crystalline diamond materials, atomistic modeling of dissipation in amorphous, defect-free, and defect-containing crystalline silicon, and experimental work on the properties of one-dimensional and two-dimensional coupled mechanical oscillator arrays. We have identified that internal dissipation in most micro- and nanoscale oscillators is limited by defect relaxation processes, with large differences in the nature of the defects as the local order of the material ranges from amorphous to crystalline. Atomistic simulations also showed a dominant role of defect relaxation processes in controlling internal dissipation. Our studies of one-dimensional and two-dimensional coupled oscillator arrays revealed that it is possible to create mechanical systems that should be ideal for the study of non-linear dynamics and localization.

Systems Biology

Indian Academy of Sciences (India)

IAS Admin

study and understand the function of biological systems, particu- larly, the response of such .... understand the organisation and behaviour of prokaryotic sys- tems. ... relationship of the structure of a target molecule to its ability to bind a certain ...

Integrating systems biology models and biomedical ontologies.

Science.gov (United States)

Hoehndorf, Robert; Dumontier, Michel; Gennari, John H; Wimalaratne, Sarala; de Bono, Bernard; Cook, Daniel L; Gkoutos, Georgios V

2011-08-11

Systems biology is an approach to biology that emphasizes the structure and dynamic behavior of biological systems and the interactions that occur within them. To succeed, systems biology crucially depends on the accessibility and integration of data across domains and levels of granularity. Biomedical ontologies were developed to facilitate such an integration of data and are often used to annotate biosimulation models in systems biology. We provide a framework to integrate representations of in silico systems biology with those of in vivo biology as described by biomedical ontologies and demonstrate this framework using the Systems Biology Markup Language. We developed the SBML Harvester software that automatically converts annotated SBML models into OWL and we apply our software to those biosimulation models that are contained in the BioModels Database. We utilize the resulting knowledge base for complex biological queries that can bridge levels of granularity, verify models based on the biological phenomenon they represent and provide a means to establish a basic qualitative layer on which to express the semantics of biosimulation models. We establish an information flow between biomedical ontologies and biosimulation models and we demonstrate that the integration of annotated biosimulation models and biomedical ontologies enables the verification of models as well as expressive queries. Establishing a bi-directional information flow between systems biology and biomedical ontologies has the potential to enable large-scale analyses of biological systems that span levels of granularity from molecules to organisms.

Calculating life? Duelling discourses in interdisciplinary systems biology.

Science.gov (United States)

Calvert, Jane; Fujimura, Joan H

2011-06-01

A high profile context in which physics and biology meet today is in the new field of systems biology. Systems biology is a fascinating subject for sociological investigation because the demands of interdisciplinary collaboration have brought epistemological issues and debates front and centre in discussions amongst systems biologists in conference settings, in publications, and in laboratory coffee rooms. One could argue that systems biologists are conducting their own philosophy of science. This paper explores the epistemic aspirations of the field by drawing on interviews with scientists working in systems biology, attendance at systems biology conferences and workshops, and visits to systems biology laboratories. It examines the discourses of systems biologists, looking at how they position their work in relation to previous types of biological inquiry, particularly molecular biology. For example, they raise the issue of reductionism to distinguish systems biology from molecular biology. This comparison with molecular biology leads to discussions about the goals and aspirations of systems biology, including epistemic commitments to quantification, rigor and predictability. Some systems biologists aspire to make biology more similar to physics and engineering by making living systems calculable, modelable and ultimately predictable-a research programme that is perhaps taken to its most extreme form in systems biology's sister discipline: synthetic biology. Other systems biologists, however, do not think that the standards of the physical sciences are the standards by which we should measure the achievements of systems biology, and doubt whether such standards will ever be applicable to 'dirty, unruly living systems'. This paper explores these epistemic tensions and reflects on their sociological dimensions and their consequences for future work in the life sciences. Copyright © 2010 Elsevier Ltd. All rights reserved.

Heuristic Strategies in Systems Biology

Directory of Open Access Journals (Sweden)

Fridolin Gross

2016-06-01

Full Text Available Systems biology is sometimes presented as providing a superior approach to the problem of biological complexity. Its use of ‘unbiased’ methods and formal quantitative tools might lead to the impression that the human factor is effectively eliminated. However, a closer look reveals that this impression is misguided. Systems biologists cannot simply assemble molecular information and compute biological behavior. Instead, systems biology’s main contribution is to accelerate the discovery of mechanisms by applying models as heuristic tools. These models rely on a variety of idealizing and simplifying assumptions in order to be efficient for this purpose. The strategies of systems biologists are similar to those of experimentalists in that they attempt to reduce the complexity of the discovery process. Analyzing and comparing these strategies, or ‘heuristics’, reveals the importance of the human factor in computational approaches and helps to situate systems biology within the epistemic landscape of the life sciences.

Partial coupling and differential regulation of biologically and photochemically labile dissolved organic carbon across boreal aquatic networks

Science.gov (United States)

Lapierre, J.-F.; del Giorgio, P. A.

2014-10-01

Despite the rapidly increasing volume of research on the biological and photochemical degradation of DOC (dissolved organic carbon) in aquatic environments, little is known of the large-scale patterns in biologically and photochemically degradable DOC (BDOC and PDOC, respectively) in continental watersheds, and on the links that exist between these two key properties that greatly influence the flow of carbon from continents to oceans. Here we explored the patterns in the concentrations and proportions of BDOC and PDOC across hundreds of boreal lakes, rivers and wetlands spanning a large range of system trophic status and terrestrial influence, and compared the drivers of these two reactive pools of DOC at the landscape level. Using standardized incubations of natural waters, we found that the concentrations of BDOC and PDOC covaried across all systems studied but were nevertheless related to different pools of dissolved organic matter (DOM; identified by fluorescence analyses) in ambient waters. Concentrations of nutrients and protein-like fluorescent DOM (FDOM) explained nearly half of the variation in BDOC, whereas PDOC was exclusively predicted by DOM optical properties, consistent with the photochemical degradability of specific FDOM pools that we experimentally determined. The concentrations of colored DOM (CDOM), which we use here as a proxy of terrestrial influence, almost entirely accounted for the observed relationship between FDOM and the concentrations of both BDOC and PDOC. The concentrations of CDOM and of the putative biolabile fluorescence component shifted from complete decoupling in clear-water environments to strong coupling in darker streams and wetlands. This suggests a baseline autochthonous BDOC pool fueled by internal production that is gradually overwhelmed by land-derived BDOC as terrestrial influence increases across landscape gradients. The importance of land as a major source of both biologically and photochemically degradable DOC for

Coupling component systems towards systems of systems

OpenAIRE

Autran , Frédéric; Auzelle , Jean-Philippe; Cattan , Denise; Garnier , Jean-Luc; Luzeaux , Dominique; Mayer , Frédérique; Peyrichon , Marc; Ruault , Jean-René

2008-01-01

International audience; Systems of systems (SoS) are a hot topic in our "fully connected global world". Our aim is not to provide another definition of what SoS are, but rather to focus on the adequacy of reusing standard system architecting techniques within this approach in order to improve performance, fault detection and safety issues in large-scale coupled systems that definitely qualify as SoS, whatever the definition is. A key issue will be to secure the availability of the services pr...

Ultra-Sensitive Elemental Analysis Using Plasmas 5.Speciation of Arsenic Compounds in Biological Samples by High Performance Liquid Chromatography-Inductively Coupled Plasma Mass Spectrometry System

Science.gov (United States)

Kaise, Toshikazu

Arsenic originating from the lithosphere is widely distributed in the environment. Many arsenicals in the environment are in organic and methylated species. These arsenic compounds in drinking water or food products of marine origin are absorbed in human digestive tracts, metabolized in the human body, and excreted viatheurine. Because arsenic shows varying biological a spects depending on its chemical species, the biological characteristics of arsenic must be determined. It is thought that some metabolic pathways for arsenic and some arsenic circulation exist in aqueous ecosystems. In this paper, the current status of the speciation analysis of arsenic by HPLC/ICP-MS (High Performance Liquid Chromatography-Inductively Coupled Plasma Mass spectrometry) in environmental and biological samples is summarized using recent data.

Comparing Brain Behavioral Systems in Couples Engaged in Infidelity and Normal Couples in Tabriz, Tehran and Karaj

Directory of Open Access Journals (Sweden)

Alireza Karimpour Vazifehkhorani

2017-10-01

Full Text Available Background and Objectives: This study aimed to compare Gary Behavioral Systems (behavioral activation system and behavioral inhibition system in normal couples and those engaged in marital infidelity. Material and Methods: The research was descriptive and causal-comparative. Study population consisted of normal couples and couples who were betrayed in the cities of Tehran, Karaj and Tabriz that were referred to counseling clinics. Study sample consisted of 100 clients; 50 normal couples and 50 couples who were involved in marital infidelity. Sampling was targeted. To collect data, Grey-Wilson's and wife infidelity questionnaires were used. Results: Inhibition of behavior in normal couples was higher than couples involved in marital infidelity which was significant at P Conclusion: Couples who have activation system of high sensitivity are more involved in the phenomenon of marital infidelity compared to the couples who are at high behavioral inhibition system.

Multi-disciplinary coupling for integrated design of propulsion systems

Science.gov (United States)

Chamis, C. C.; Singhal, S. N.

1993-01-01

Effective computational simulation procedures are described for modeling the inherent multi-disciplinary interactions for determining the true response of propulsion systems. Results are presented for propulsion system responses including multi-discipline coupling effects via (1) coupled multi-discipline tailoring, (2) an integrated system of multidisciplinary simulators, (3) coupled material-behavior/fabrication-process tailoring, (4) sensitivities using a probabilistic simulator, and (5) coupled materials/structures/fracture/probabilistic behavior simulator. The results show that the best designs can be determined if the analysis/tailoring methods account for the multi-disciplinary coupling effects. The coupling across disciplines can be used to develop an integrated interactive multi-discipline numerical propulsion system simulator.

Mammalian Synthetic Biology: Engineering Biological Systems.

Science.gov (United States)

Black, Joshua B; Perez-Pinera, Pablo; Gersbach, Charles A

2017-06-21

The programming of new functions into mammalian cells has tremendous application in research and medicine. Continued improvements in the capacity to sequence and synthesize DNA have rapidly increased our understanding of mechanisms of gene function and regulation on a genome-wide scale and have expanded the set of genetic components available for programming cell biology. The invention of new research tools, including targetable DNA-binding systems such as CRISPR/Cas9 and sensor-actuator devices that can recognize and respond to diverse chemical, mechanical, and optical inputs, has enabled precise control of complex cellular behaviors at unprecedented spatial and temporal resolution. These tools have been critical for the expansion of synthetic biology techniques from prokaryotic and lower eukaryotic hosts to mammalian systems. Recent progress in the development of genome and epigenome editing tools and in the engineering of designer cells with programmable genetic circuits is expanding approaches to prevent, diagnose, and treat disease and to establish personalized theranostic strategies for next-generation medicines. This review summarizes the development of these enabling technologies and their application to transforming mammalian synthetic biology into a distinct field in research and medicine.

Applicability of Computational Systems Biology in Toxicology

DEFF Research Database (Denmark)

Kongsbak, Kristine Grønning; Hadrup, Niels; Audouze, Karine Marie Laure

2014-01-01

be used to establish hypotheses on links between the chemical and human diseases. Such information can also be applied for designing more intelligent animal/cell experiments that can test the established hypotheses. Here, we describe how and why to apply an integrative systems biology method......Systems biology as a research field has emerged within the last few decades. Systems biology, often defined as the antithesis of the reductionist approach, integrates information about individual components of a biological system. In integrative systems biology, large data sets from various sources...... and databases are used to model and predict effects of chemicals on, for instance, human health. In toxicology, computational systems biology enables identification of important pathways and molecules from large data sets; tasks that can be extremely laborious when performed by a classical literature search...

Development of a coupled physical-biological ecosystem model ECOSMO - Part I: Model description and validation for the North Sea

DEFF Research Database (Denmark)

Schrum, Corinna; Alekseeva, I.; St. John, Michael

2006-01-01

A 3-D coupled biophysical model ECOSMO (ECOSystem MOdel) has been developed. The biological module of ECOSMO is based on lower trophic level interactions between two phyto- and two zooplankton components. The dynamics of the different phytoplankton components are governed by the availability...... of the macronutrients nitrogen, phosphate and silicate as well as light. Zooplankton production is simulated based on the consumption of the different phytoplankton groups and detritus. The biological module is coupled to a nonlinear 3-D baroclinic model. The physical and biological modules are driven by surface...... showed that the model, based on consideration of limiting processes, is able to reproduce the observed spatial and seasonal variability of the North Sea ecosystem e.g. the spring bloom, summer sub-surface production and the fall bloom. Distinct differences in regional characteristics of diatoms...

Ins and outs of systems biology vis-à-vis molecular biology: continuation or clear cut?

Science.gov (United States)

De Backer, Philippe; De Waele, Danny; Van Speybroeck, Linda

2010-03-01

The comprehension of living organisms in all their complexity poses a major challenge to the biological sciences. Recently, systems biology has been proposed as a new candidate in the development of such a comprehension. The main objective of this paper is to address what systems biology is and how it is practised. To this end, the basic tools of a systems biological approach are explored and illustrated. In addition, it is questioned whether systems biology 'revolutionizes' molecular biology and 'transcends' its assumed reductionism. The strength of this claim appears to depend on how molecular and systems biology are characterised and on how reductionism is interpreted. Doing credit to molecular biology and to methodological reductionism, it is argued that the distinction between molecular and systems biology is gradual rather than sharp. As such, the classical challenge in biology to manage, interpret and integrate biological data into functional wholes is further intensified by systems biology's use of modelling and bioinformatics, and by its scale enlargement.

Editorial overview : Systems biology for biotechnology

NARCIS (Netherlands)

Heinemann, Matthias; Pilpel, Yitzhak

About 15 years ago, systems biology was introduced as a novel approach to biological research. On the one side, its introduction was a result of the recognition that through solely the reductionist approach, we would ulti- mately not be able to understand how biological systems function as a whole.

Quantum Effects in Biological Systems

CERN Document Server

2016-01-01

Since the last decade the study of quantum mechanical phenomena in biological systems has become a vibrant field of research. Initially sparked by evidence of quantum effects in energy transport that is instrumental for photosynthesis, quantum biology asks the question of how methods and models from quantum theory can help us to understand fundamental mechanisms in living organisms. This approach entails a paradigm change challenging the related disciplines: The successful framework of quantum theory is taken out of its low-temperature, microscopic regimes and applied to hot and dense macroscopic environments, thereby extending the toolbox of biology and biochemistry at the same time. The Quantum Effects in Biological Systems conference is a platform for researchers from biology, chemistry and physics to present and discuss the latest developments in the field of quantum biology. After meetings in Lisbon (2009), Harvard (2010), Ulm (2011), Berkeley (2012), Vienna (2013), Singapore (2014) and Florence (2015),...

Static Analysis for Systems Biology

DEFF Research Database (Denmark)

Nielson, Flemming; Nielson, Hanne Riis; Rosa, D. Schuch da

2004-01-01

This paper shows how static analysis techniques can help understanding biological systems. Based on a simple example we illustrate the outcome of performing three different analyses extracting information of increasing precision. We conclude by reporting on the potential impact and exploitation o...... of these techniques in systems biology....

Self-similar solutions of certain coupled integrable systems

CERN Document Server

Chakravarty, S; Kent, S L

2003-01-01

Similarity reductions of the coupled nonlinear Schroedinger equation and an integrable version of the coupled Maxwell-Bloch system are obtained by applying non-translational symmetries. The reduced system of coupled ordinary differential equations are solved in terms of Painleve transcendents, leading to new exact self-similar solutions for these integrable equations.

Self-similar solutions of certain coupled integrable systems

International Nuclear Information System (INIS)

Chakravarty, S; Halburd, R G; Kent, S L

2003-01-01

Similarity reductions of the coupled nonlinear Schroedinger equation and an integrable version of the coupled Maxwell-Bloch system are obtained by applying non-translational symmetries. The reduced system of coupled ordinary differential equations are solved in terms of Painleve transcendents, leading to new exact self-similar solutions for these integrable equations

Omics/systems biology and cancer cachexia.

Science.gov (United States)

Gallagher, Iain J; Jacobi, Carsten; Tardif, Nicolas; Rooyackers, Olav; Fearon, Kenneth

2016-06-01

Cancer cachexia is a complex syndrome generated by interaction between the host and tumour cells with a background of treatment effects and toxicity. The complexity of the physiological pathways likely involved in cancer cachexia necessitates a holistic view of the relevant biology. Emergent properties are characteristic of complex systems with the result that the end result is more than the sum of its parts. Recognition of the importance of emergent properties in biology led to the concept of systems biology wherein a holistic approach is taken to the biology at hand. Systems biology approaches will therefore play an important role in work to uncover key mechanisms with therapeutic potential in cancer cachexia. The 'omics' technologies provide a global view of biological systems. Genomics, transcriptomics, proteomics, lipidomics and metabolomics approaches all have application in the study of cancer cachexia to generate systems level models of the behaviour of this syndrome. The current work reviews recent applications of these technologies to muscle atrophy in general and cancer cachexia in particular with a view to progress towards integration of these approaches to better understand the pathology and potential treatment pathways in cancer cachexia. Copyright © 2016. Published by Elsevier Ltd.

Emerging systems biology approaches in nanotoxicology: Towards a mechanism-based understanding of nanomaterial hazard and risk

Energy Technology Data Exchange (ETDEWEB)

Costa, Pedro M.; Fadeel, Bengt, E-mail: Bengt.Fadeel@ki.se

2016-05-15

Engineered nanomaterials are being developed for a variety of technological applications. However, the increasing use of nanomaterials in society has led to concerns about their potential adverse effects on human health and the environment. During the first decade of nanotoxicological research, the realization has emerged that effective risk assessment of the multitudes of new nanomaterials would benefit from a comprehensive understanding of their toxicological mechanisms, which is difficult to achieve with traditional, low-throughput, single end-point oriented approaches. Therefore, systems biology approaches are being progressively applied within the nano(eco)toxicological sciences. This novel paradigm implies that the study of biological systems should be integrative resulting in quantitative and predictive models of nanomaterial behaviour in a biological system. To this end, global ‘omics’ approaches with which to assess changes in genes, proteins, metabolites, etc. are deployed allowing for computational modelling of the biological effects of nanomaterials. Here, we highlight omics and systems biology studies in nanotoxicology, aiming towards the implementation of a systems nanotoxicology and mechanism-based risk assessment of nanomaterials. - Highlights: • Systems nanotoxicology is a multi-disciplinary approach to quantitative modelling. • Transcriptomics, proteomics and metabolomics remain the most common methods. • Global “omics” techniques should be coupled to computational modelling approaches. • The discovery of nano-specific toxicity pathways and biomarkers is a prioritized goal. • Overall, experimental nanosafety research must endeavour reproducibility and relevance.

Emerging systems biology approaches in nanotoxicology: Towards a mechanism-based understanding of nanomaterial hazard and risk

International Nuclear Information System (INIS)

Costa, Pedro M.; Fadeel, Bengt

2016-01-01

Engineered nanomaterials are being developed for a variety of technological applications. However, the increasing use of nanomaterials in society has led to concerns about their potential adverse effects on human health and the environment. During the first decade of nanotoxicological research, the realization has emerged that effective risk assessment of the multitudes of new nanomaterials would benefit from a comprehensive understanding of their toxicological mechanisms, which is difficult to achieve with traditional, low-throughput, single end-point oriented approaches. Therefore, systems biology approaches are being progressively applied within the nano(eco)toxicological sciences. This novel paradigm implies that the study of biological systems should be integrative resulting in quantitative and predictive models of nanomaterial behaviour in a biological system. To this end, global ‘omics’ approaches with which to assess changes in genes, proteins, metabolites, etc. are deployed allowing for computational modelling of the biological effects of nanomaterials. Here, we highlight omics and systems biology studies in nanotoxicology, aiming towards the implementation of a systems nanotoxicology and mechanism-based risk assessment of nanomaterials. - Highlights: • Systems nanotoxicology is a multi-disciplinary approach to quantitative modelling. • Transcriptomics, proteomics and metabolomics remain the most common methods. • Global “omics” techniques should be coupled to computational modelling approaches. • The discovery of nano-specific toxicity pathways and biomarkers is a prioritized goal. • Overall, experimental nanosafety research must endeavour reproducibility and relevance.

Analyzing the Biology on the System Level

OpenAIRE

Tong, Wei

2016-01-01

Although various genome projects have provided us enormous static sequence information, understanding of the sophisticated biology continues to require integrating the computational modeling, system analysis, technology development for experiments, and quantitative experiments all together to analyze the biology architecture on various levels, which is just the origin of systems biology subject. This review discusses the object, its characteristics, and research attentions in systems biology,...

Partial coupling and differential regulation of biologically and photo-chemically labile dissolved organic carbon across boreal aquatic networks

Science.gov (United States)

Lapierre, J.-F.; del Giorgio, P. A.

2014-05-01

Despite the rapidly increasing volume of research on the biological and photochemical degradation of DOC in aquatic environments, little is known on the large-scale patterns in biologically and photo-chemically degradable DOC (Bd-DOC and Pd-DOC, respectively) in continental watersheds, and on the links that exist between these two key properties that greatly influence the flow of carbon from continents to oceans. Here we explore the patterns of Bd- and Pd-DOC across hundreds of boreal lakes, rivers and wetlands spanning a large range of system trophy and terrestrial influence, and compared the drivers of these two reactive pools of DOC at the landscape level. Using standardized incubations of natural waters, we found that the concentrations of Bd- and Pd-DOC co-varied across all systems studied but were nevertheless related to different pools of dissolved organic matter (DOM, identified by fluorescence analyses) in ambient waters. A combination of nutrients and protein-like DOM explained nearly half of the variation in Bd-DOC, whereas Pd-DOC was exclusively predicted by DOM optical properties, consistent with the photochemical degradability of specific fluorescent DOM (FDOM) pools that we experimentally determined. The concentrations of colored DOM (CDOM), a proxy of terrestrial influence, almost entirely accounted for the observed relationship between FDOM and the concentrations of both Bd- and Pd-DOC. The concentrations of CDOM and of the putative bio-labile fluorescence component shifted from complete decoupling in clear-water environments to strong coupling in browner streams and wetlands. This suggests a baseline autochthonous Bd-DOC pool fuelled by internal production that is gradually overwhelmed by land-derived Bd-DOC as terrestrial influence increases across landscape gradients. The importance of land as a major source of both biologically and photo-chemically degradable DOC for continental watersheds resulted in a partial coupling of those carbon pools in

Development and applications of photosensitive device systems to studies of biological and organic materials. Progress report

International Nuclear Information System (INIS)

1984-01-01

The purpose was to develop and improve appropriate experimental techniques to the point where they could be applied to specific classes of biological problems. Progress is reported in the following areas: (1) area detectors; (2) x-ray diffraction studies of membranes; (3) electron transfer in loosely coupled systems; (4) bioluminescence and fluorescence; and (5) sonoluminescence

Vehicle systems: coupled and interactive dynamics analysis

Science.gov (United States)

Vantsevich, Vladimir V.

2014-11-01

This article formulates a new direction in vehicle dynamics, described as coupled and interactive vehicle system dynamics. Formalised procedures and analysis of case studies are presented. An analytical consideration, which explains the physics of coupled system dynamics and its consequences for dynamics of a vehicle, is given for several sets of systems including: (i) driveline and suspension of a 6×6 truck, (ii) a brake mechanism and a limited slip differential of a drive axle and (iii) a 4×4 vehicle steering system and driveline system. The article introduces a formal procedure to turn coupled system dynamics into interactive dynamics of systems. A new research direction in interactive dynamics of an active steering and a hybrid-electric power transmitting unit is presented and analysed to control power distribution between the drive axles of a 4×4 vehicle. A control strategy integrates energy efficiency and lateral dynamics by decoupling dynamics of the two systems thus forming their interactive dynamics.

Linear dynamic coupling in geared rotor systems

Science.gov (United States)

David, J. W.; Mitchell, L. D.

1986-01-01

The effects of high frequency oscillations caused by the gear mesh, on components of a geared system that can be modeled as rigid discs are analyzed using linear dynamic coupling terms. The coupled, nonlinear equations of motion for a disc attached to a rotating shaft are presented. The results of a trial problem analysis show that the inclusion of the linear dynamic coupling terms can produce significant changes in the predicted response of geared rotor systems, and that the produced sideband responses are greater than the unbalanced response. The method is useful in designing gear drives for heavy-lift helicopters, industrial speed reducers, naval propulsion systems, and heavy off-road equipment.

Adapting to Biology: Maintaining Container-Closure System Compatibility with the Therapeutic Biologic Revolution.

Science.gov (United States)

Degrazio, Dominick

Many pharmaceutical companies are transitioning their research and development drug product pipeline from traditional small-molecule injectables to the dimension of evolving therapeutic biologics. Important concerns associated with this changeover are becoming forefront, as challenges develop of varying complexity uncommon with the synthesis and production of traditional drugs. Therefore, alternative measures must be established that aim to preserve the efficacy and functionality of a biologic that might not be implemented for small molecules. Conserving protein stability is relative to perpetuating a net equilibrium of both intrinsic and extrinsic factors. Key to sustaining this balance is the ability of container-closure systems to maintain their compatibility with the ever-changing dynamics of therapeutic biologics. Failure to recognize and adjust the material properties of packaging components to support compatibility with therapeutic biologics can compromise patient safety, drug productivity, and biological stability. This review will examine the differences between small-molecule drugs and therapeutic biologics, lay a basic foundation for understanding the stability of therapeutic biologics, and demonstrate potential sources of container-closure systems' incompatibilities with therapeutic biologics at a mechanistic level. Many pharmaceutical companies are transitioning their research and development drug product pipeline from traditional small-molecule injectables to recombinantly derived therapeutic biologics. Concerns associated with this transformation are becoming prominent, as therapeutic biologics are uncharacteristic to small-molecule drugs. Maintaining the stability of a therapeutic biologic is a combination of balancing intrinsic factors and external elements within the biologic's microenvironment. An important aspect of this balance is relegated to the overall compatibility of primary, parenteral container-closure systems with therapeutic biologics

Evaluation of the simultaneous removal of recalcitrant drugs (bezafibrate, gemfibrozil, indomethacin and sulfamethoxazole) and biodegradable organic matter from synthetic wastewater by electro-oxidation coupled with a biological system.

Science.gov (United States)

Rodríguez-Nava, Odín; Ramírez-Saad, Hugo; Loera, Octavio; González, Ignacio

2016-12-01

Pharmaceutical degradation in conventional wastewater treatment plants (WWTP) represents a challenge since municipal wastewater and hospital effluents contain pharmaceuticals in low concentrations (recalcitrant and persistent in WWTP) and biodegradable organic matter (BOM) is the main pollutant. This work shows the feasibility of coupling electro-oxidation with a biological system for the simultaneous removal of recalcitrant drugs (bezafibrate, gemfibrozil, indomethacin and sulfamethoxazole (BGIS)) and BOM from wastewater. High removal efficiencies were attained without affecting the performance of activated sludge. BGIS degradation was performed by advanced electrochemical oxidation and the activated sludge process for BOM degradation in a continuous reactor. The selected electrochemical parameters from microelectrolysis tests (1.2 L s(-1) and 1.56 mA cm(-2)) were maintained to operate a filter press laboratory reactor FM01-LC using boron-doped diamond as the anode. The low current density was chosen in order to remove drugs without decreasing BOM and chlorine concentration control, so as to avoid bulking formation in the biological process. The wastewater previously treated by FM01-LC was fed directly (without chemical modification) to the activated sludge reactor to remove 100% of BGIS and 83% of BOM; conversely, the BGIS contained in wastewater without electrochemical pre-treatment were persistent in the biological process and promoted bulking formation.

The UKC2 regional coupled environmental prediction system

Science.gov (United States)

Lewis, Huw W.; Castillo Sanchez, Juan Manuel; Graham, Jennifer; Saulter, Andrew; Bornemann, Jorge; Arnold, Alex; Fallmann, Joachim; Harris, Chris; Pearson, David; Ramsdale, Steven; Martínez-de la Torre, Alberto; Bricheno, Lucy; Blyth, Eleanor; Bell, Victoria A.; Davies, Helen; Marthews, Toby R.; O'Neill, Clare; Rumbold, Heather; O'Dea, Enda; Brereton, Ashley; Guihou, Karen; Hines, Adrian; Butenschon, Momme; Dadson, Simon J.; Palmer, Tamzin; Holt, Jason; Reynard, Nick; Best, Martin; Edwards, John; Siddorn, John

2018-01-01

It is hypothesized that more accurate prediction and warning of natural hazards, such as of the impacts of severe weather mediated through various components of the environment, require a more integrated Earth System approach to forecasting. This hypothesis can be explored using regional coupled prediction systems, in which the known interactions and feedbacks between different physical and biogeochemical components of the environment across sky, sea and land can be simulated. Such systems are becoming increasingly common research tools. This paper describes the development of the UKC2 regional coupled research system, which has been delivered under the UK Environmental Prediction Prototype project. This provides the first implementation of an atmosphere-land-ocean-wave modelling system focussed on the United Kingdom and surrounding seas at km-scale resolution. The UKC2 coupled system incorporates models of the atmosphere (Met Office Unified Model), land surface with river routing (JULES), shelf-sea ocean (NEMO) and ocean waves (WAVEWATCH III). These components are coupled, via OASIS3-MCT libraries, at unprecedentedly high resolution across the UK within a north-western European regional domain. A research framework has been established to explore the representation of feedback processes in coupled and uncoupled modes, providing a new research tool for UK environmental science. This paper documents the technical design and implementation of UKC2, along with the associated evaluation framework. An analysis of new results comparing the output of the coupled UKC2 system with relevant forced control simulations for six contrasting case studies of 5-day duration is presented. Results demonstrate that performance can be achieved with the UKC2 system that is at least comparable to its component control simulations. For some cases, improvements in air temperature, sea surface temperature, wind speed, significant wave height and mean wave period highlight the potential

The UKC2 regional coupled environmental prediction system

Directory of Open Access Journals (Sweden)

H. W. Lewis

2018-01-01

Full Text Available It is hypothesized that more accurate prediction and warning of natural hazards, such as of the impacts of severe weather mediated through various components of the environment, require a more integrated Earth System approach to forecasting. This hypothesis can be explored using regional coupled prediction systems, in which the known interactions and feedbacks between different physical and biogeochemical components of the environment across sky, sea and land can be simulated. Such systems are becoming increasingly common research tools. This paper describes the development of the UKC2 regional coupled research system, which has been delivered under the UK Environmental Prediction Prototype project. This provides the first implementation of an atmosphere–land–ocean–wave modelling system focussed on the United Kingdom and surrounding seas at km-scale resolution. The UKC2 coupled system incorporates models of the atmosphere (Met Office Unified Model, land surface with river routing (JULES, shelf-sea ocean (NEMO and ocean waves (WAVEWATCH III. These components are coupled, via OASIS3-MCT libraries, at unprecedentedly high resolution across the UK within a north-western European regional domain. A research framework has been established to explore the representation of feedback processes in coupled and uncoupled modes, providing a new research tool for UK environmental science. This paper documents the technical design and implementation of UKC2, along with the associated evaluation framework. An analysis of new results comparing the output of the coupled UKC2 system with relevant forced control simulations for six contrasting case studies of 5-day duration is presented. Results demonstrate that performance can be achieved with the UKC2 system that is at least comparable to its component control simulations. For some cases, improvements in air temperature, sea surface temperature, wind speed, significant wave height and mean wave period

Multi-disciplinary coupling effects for integrated design of propulsion systems

Science.gov (United States)

Chamis, C. C.; Singhal, S. N.

1993-01-01

Effective computational simulation procedures are described for modeling the inherent multi-disciplinary interactions which govern the accurate response of propulsion systems. Results are presented for propulsion system responses including multi-disciplinary coupling effects using coupled multi-discipline thermal, structural, and acoustic tailoring; an integrated system of multi-disciplinary simulators; coupled material behavior/fabrication process tailoring; sensitivities using a probabilistic simulator; and coupled materials, structures, fracture, and probabilistic behavior simulator. The results demonstrate that superior designs can be achieved if the analysis/tailoring methods account for the multi-disciplinary coupling effects. The coupling across disciplines can be used to develop an integrated coupled multi-discipline numerical propulsion system simulator.

Identical synchronization of coupled Rossler systems

DEFF Research Database (Denmark)

Yanchuk, S.; Maistrenko, Y.; Mosekilde, Erik

1999-01-01

Analyzing the transverse stability of low periodic orbits embedded in the synchronized chaotic state for a system of two coupled Rössler oscillators, we obtain the conditions for synchronization and determine the coupling parameters for which riddled basins of attraction may arise. It is shown how...

A Converter from the Systems Biology Markup Language to the Synthetic Biology Open Language.

Science.gov (United States)

Nguyen, Tramy; Roehner, Nicholas; Zundel, Zach; Myers, Chris J

2016-06-17

Standards are important to synthetic biology because they enable exchange and reproducibility of genetic designs. This paper describes a procedure for converting between two standards: the Systems Biology Markup Language (SBML) and the Synthetic Biology Open Language (SBOL). SBML is a standard for behavioral models of biological systems at the molecular level. SBOL describes structural and basic qualitative behavioral aspects of a biological design. Converting SBML to SBOL enables a consistent connection between behavioral and structural information for a biological design. The conversion process described in this paper leverages Systems Biology Ontology (SBO) annotations to enable inference of a designs qualitative function.

The synchronization of asymmetric-structured electric coupling neuronal system

Science.gov (United States)

Wang, Guanping; Jin, Wuyin; Liu, Hao; Sun, Wei

2018-02-01

Based on the Hindmarsh-Rose (HR) model, the synchronization dynamics of asymmetric-structured electric coupling two neuronal system is investigated in this paper. It is discovered that when the time-delay scope and coupling strength for the synchronization are correlated positively under unequal time delay, the time-delay difference does not make a clear distinction between the two individual inter-spike intervals (ISI) bifurcation diagrams of the two coupled neurons. Therefore, the superficial difference of the system synchronization dynamics is not obvious for the unequal time-delay feedback. In the asymmetrical current incentives under asymmetric electric coupled system, the two neurons can only be almost completely synchronized in specific area of the interval which end-pointed with two discharge modes for a single neuron under different stimuli currents before coupling, but the intervention of time-delay feedback, together with the change of the coupling strength, can make the coupled system not only almost completely synchronized within anywhere in the front area, but also outside of it.

Ten questions about systems biology

DEFF Research Database (Denmark)

Joyner, Michael J; Pedersen, Bente K

2011-01-01

to understand how whole animals adapt to the real world. We argue that a lack of fluency in these concepts is a major stumbling block for what has been narrowly defined as 'systems biology' by some of its leading advocates. We also point out that it is a failure of regulation at multiple levels that causes many......In this paper we raise 'ten questions' broadly related to 'omics', the term systems biology, and why the new biology has failed to deliver major therapeutic advances for many common diseases, especially diabetes and cardiovascular disease. We argue that a fundamentally narrow and reductionist...

Ten questions about systems biology

DEFF Research Database (Denmark)

Joyner, Michael J; Pedersen, Bente K

2011-01-01

In this paper we raise 'ten questions' broadly related to 'omics', the term systems biology, and why the new biology has failed to deliver major therapeutic advances for many common diseases, especially diabetes and cardiovascular disease. We argue that a fundamentally narrow and reductionist...... to understand how whole animals adapt to the real world. We argue that a lack of fluency in these concepts is a major stumbling block for what has been narrowly defined as 'systems biology' by some of its leading advocates. We also point out that it is a failure of regulation at multiple levels that causes many...

Genomes, Phylogeny, and Evolutionary Systems Biology

Energy Technology Data Exchange (ETDEWEB)

Medina, Monica

2005-03-25

With the completion of the human genome and the growing number of diverse genomes being sequenced, a new age of evolutionary research is currently taking shape. The myriad of technological breakthroughs in biology that are leading to the unification of broad scientific fields such as molecular biology, biochemistry, physics, mathematics and computer science are now known as systems biology. Here I present an overview, with an emphasis on eukaryotes, of how the postgenomics era is adopting comparative approaches that go beyond comparisons among model organisms to shape the nascent field of evolutionary systems biology.

Measuring Relative Coupling Strength in Circadian Systems.

Science.gov (United States)

Schmal, Christoph; Herzog, Erik D; Herzel, Hanspeter

2018-02-01

Modern imaging techniques allow the monitoring of circadian rhythms of single cells. Coupling between these single cellular circadian oscillators can generate coherent periodic signals on the tissue level that subsequently orchestrate physiological outputs. The strength of coupling in such systems of oscillators is often unclear. In particular, effects on coupling strength by varying cell densities, by knockouts, and by inhibitor applications are debated. In this study, we suggest to quantify the relative coupling strength via analyzing period, phase, and amplitude distributions in ensembles of individual circadian oscillators. Simulations of different oscillator networks show that period and phase distributions become narrower with increasing coupling strength. Moreover, amplitudes can increase due to resonance effects. Variances of periods and phases decay monotonically with coupling strength, and can serve therefore as measures of relative coupling strength. Our theoretical predictions are confirmed by studying recently published experimental data from PERIOD2 expression in slices of the suprachiasmatic nucleus during and after the application of tetrodotoxin (TTX). On analyzing the corresponding period, phase, and amplitude distributions, we can show that treatment with TTX can be associated with a reduced coupling strength in the system of coupled oscillators. Analysis of an oscillator network derived directly from the data confirms our conclusions. We suggest that our approach is also applicable to quantify coupling in fibroblast cultures and hepatocyte networks, and for social synchronization of circadian rhythmicity in rodents, flies, and bees.

Symmetric coupling of four spin-1/2 systems

Science.gov (United States)

Suzuki, Jun; Englert, Berthold-Georg

2012-06-01

We address the non-binary coupling of identical angular momenta based upon the representation theory for the symmetric group. A correspondence is pointed out between the complete set of commuting operators and the reference-frame-free subsystems. We provide a detailed analysis of the coupling of three and four spin-1/2 systems and discuss a symmetric coupling of four spin-1/2 systems.

Coupled dynamic systems and Le Chatelier's principle in noise control

Science.gov (United States)

Maidanik, G.; Becker, K. J.

2004-05-01

Investigation of coupling an externally driven dynamic system-a master dynamic system-to a passive one-an adjunct dynamic system-reveals that the response of the adjunct dynamic system affects the precoupled response of the master dynamic system. The responses, in the two dynamic systems when coupled, are estimated by the stored energies (Es) and (E0), respectively. Since the adjunct dynamic system, prior to coupling, was with zero (0) stored energy, E0s=0, the precoupled stored energy (E00) in the master dynamic system is expected to be reduced to (E0) when coupling is instituted; i.e., one expects E0system would result from the coupling. It is argued that the change in the disposition of the stored energies as just described may not be the only change. The coupling may influence the external input power into the master dynamic system which may interfere with the expected noise control. Indeed, the coupling may influence the external input power such that the expected beneficial noise control may not materialize. Examples of these kinds of noise control reversals are cited.

Non-statistical behavior of coupled optical systems

International Nuclear Information System (INIS)

Perez, G.; Pando Lambruschini, C.; Sinha, S.; Cerdeira, H.A.

1991-10-01

We study globally coupled chaotic maps modeling an optical system, and find clear evidence of non-statistical behavior: the mean square deviation (MSD) of the mean field saturates with respect to increase in the number of elements coupled, after a critical value, and its distribution is clearly non-Gaussian. We also find that the power spectrum of the mean field displays well defined peaks, indicating a subtle coherence among different elements, even in the ''turbulent'' phase. This system is a physically realistic model that may be experimentally realizable. It is also a higher dimensional example (as each individual element is given by a complex map). Its study confirms that the phenomena observed in a wide class of coupled one-dimensional maps are present here as well. This gives more evidence to believe that such non-statistical behavior is probably generic in globally coupled systems. We also investigate the influence of parametric fluctuations on the MSD. (author). 10 refs, 7 figs, 1 tab

Coupled CFD - system-code simulation of a gas cooled reactor

International Nuclear Information System (INIS)

Yan, Yizhou; Rizwan-uddin

2011-01-01

A generic coupled CFD - system-code thermal hydraulic simulation approach was developed based on FLUENT and RELAP-3D, and applied to LWRs. The flexibility of the coupling methodology enables its application to advanced nuclear energy systems. Gas Turbine - Modular Helium Reactor (GT-MHR) is a Gen IV reactor design which can benefit from this innovative coupled simulation approach. Mixing in the lower plenum of the GT-MHR is investigated here using the CFD - system-code coupled simulation tool. Results of coupled simulations are presented and discussed. The potential of the coupled CFD - system-code approach for next generation of nuclear power plants is demonstrated. (author)

Aspergilli: Systems biology and industrial applications

DEFF Research Database (Denmark)

Knuf, Christoph; Nielsen, Jens

2012-01-01

possible to implement systems biology tools to advance metabolic engineering. These tools include genome-wide transcription analysis and genome-scale metabolic models. Herein, we review achievements in the field and highlight the impact of Aspergillus systems biology on industrial biotechnology....

Synchronization coupled systems to complex networks

CERN Document Server

Boccaletti, Stefano; del Genio, Charo I; Amann, Andreas

2018-01-01

A modern introduction to synchronization phenomena, this text presents recent discoveries and the current state of research in the field, from low-dimensional systems to complex networks. The book describes some of the main mechanisms of collective behaviour in dynamical systems, including simple coupled systems, chaotic systems, and systems of infinite-dimension. After introducing the reader to the basic concepts of nonlinear dynamics, the book explores the main synchronized states of coupled systems and describes the influence of noise and the occurrence of synchronous motion in multistable and spatially-extended systems. Finally, the authors discuss the underlying principles of collective dynamics on complex networks, providing an understanding of how networked systems are able to function as a whole in order to process information, perform coordinated tasks, and respond collectively to external perturbations. The demonstrations, numerous illustrations and application examples will help advanced graduate s...

Model checking biological systems described using ambient calculus

DEFF Research Database (Denmark)

Mardare, Radu Iulian; Priami, Corrado; Qualia, Paola

2005-01-01

Model checking biological systems described using ambient calculus. In Proc. of the second International Workshop on Computational Methods in Systems Biology (CMSB04), Lecture Notes in Bioinformatics 3082:85-103, Springer, 2005.......Model checking biological systems described using ambient calculus. In Proc. of the second International Workshop on Computational Methods in Systems Biology (CMSB04), Lecture Notes in Bioinformatics 3082:85-103, Springer, 2005....

Systems Biology, Systems Medicine, Systems Pharmacology: The What and The Why.

Science.gov (United States)

Stéphanou, Angélique; Fanchon, Eric; Innominato, Pasquale F; Ballesta, Annabelle

2018-05-09

Systems biology is today such a widespread discipline that it becomes difficult to propose a clear definition of what it really is. For some, it remains restricted to the genomic field. For many, it designates the integrated approach or the corpus of computational methods employed to handle the vast amount of biological or medical data and investigate the complexity of the living. Although defining systems biology might be difficult, on the other hand its purpose is clear: systems biology, with its emerging subfields systems medicine and systems pharmacology, clearly aims at making sense of complex observations/experimental and clinical datasets to improve our understanding of diseases and their treatments without putting aside the context in which they appear and develop. In this short review, we aim to specifically focus on these new subfields with the new theoretical tools and approaches that were developed in the context of cancer. Systems pharmacology and medicine now give hope for major improvements in cancer therapy, making personalized medicine closer to reality. As we will see, the current challenge is to be able to improve the clinical practice according to the paradigm shift of systems sciences.

Complexity, Analysis and Control of Singular Biological Systems

CERN Document Server

Zhang, Qingling; Zhang, Xue

2012-01-01

Complexity, Analysis and Control of Singular Biological Systems follows the control of real-world biological systems at both ecological and phyisological levels concentrating on the application of now-extensively-investigated singular system theory. Much effort has recently been dedicated to the modelling and analysis of developing bioeconomic systems and the text establishes singular examples of these, showing how proper control can help to maintain sustainable economic development of biological resources. The book begins from the essentials of singular systems theory and bifurcations before tackling  the use of various forms of control in singular biological systems using examples including predator-prey relationships and viral vaccination and quarantine control. Researchers and graduate students studying the control of complex biological systems are shown how a variety of methods can be brought to bear and practitioners working with the economics of biological systems and their control will also find the ...

Graphics processing units in bioinformatics, computational biology and systems biology.

Science.gov (United States)

Nobile, Marco S; Cazzaniga, Paolo; Tangherloni, Andrea; Besozzi, Daniela

2017-09-01

Several studies in Bioinformatics, Computational Biology and Systems Biology rely on the definition of physico-chemical or mathematical models of biological systems at different scales and levels of complexity, ranging from the interaction of atoms in single molecules up to genome-wide interaction networks. Traditional computational methods and software tools developed in these research fields share a common trait: they can be computationally demanding on Central Processing Units (CPUs), therefore limiting their applicability in many circumstances. To overcome this issue, general-purpose Graphics Processing Units (GPUs) are gaining an increasing attention by the scientific community, as they can considerably reduce the running time required by standard CPU-based software, and allow more intensive investigations of biological systems. In this review, we present a collection of GPU tools recently developed to perform computational analyses in life science disciplines, emphasizing the advantages and the drawbacks in the use of these parallel architectures. The complete list of GPU-powered tools here reviewed is available at http://bit.ly/gputools. © The Author 2016. Published by Oxford University Press.

Biological Systems Thinking for Control Engineering Design

Directory of Open Access Journals (Sweden)

D. J. Murray-Smith

2004-01-01

Full Text Available Artificial neural networks and genetic algorithms are often quoted in discussions about the contribution of biological systems thinking to engineering design. This paper reviews work on the neuromuscular system, a field in which biological systems thinking could make specific contributions to the development and design of automatic control systems for mechatronics and robotics applications. The paper suggests some specific areas in which a better understanding of this biological control system could be expected to contribute to control engineering design methods in the future. Particular emphasis is given to the nonlinear nature of elements within the neuromuscular system and to processes of neural signal processing, sensing and system adaptivity. Aspects of the biological system that are of particular significance for engineering control systems include sensor fusion, sensor redundancy and parallelism, together with advanced forms of signal processing for adaptive and learning control. 

Network Analyses in Systems Biology: New Strategies for Dealing with Biological Complexity

DEFF Research Database (Denmark)

Green, Sara; Serban, Maria; Scholl, Raphael

2018-01-01

of biological networks using tools from graph theory to the application of dynamical systems theory to understand the behavior of complex biological systems. We show how network approaches support and extend traditional mechanistic strategies but also offer novel strategies for dealing with biological...... strategies? When and how can network and mechanistic approaches interact in productive ways? In this paper we address these questions by focusing on how biological networks are represented and analyzed in a diverse class of case studies. Our examples span from the investigation of organizational properties...

Summer nitrogenous nutrient transport and its fate in the Taiwan Strait: A coupled physical-biological modeling approach

Science.gov (United States)

Wang, Jia; Hong, Huasheng; Jiang, Yuwu; Chai, Fei; Yan, Xiao-Hai

2013-09-01

In order to understand the fate of nutrients in the Taiwan Strait during summer, we built a coupled physical-biological numerical ocean model, which can capture the basic hydrographic and biological features within the strait. The nutrient that we chose to model is dissolved inorganic nitrogen (DIN). The model includes individual reservoirs for nitrate (NO3) and ammonium (NH4). Both the observational evidence and model results show that NO3 in the strait originates primarily from the upwelling subsurface water in the northern South China Sea (SCS) that enters the strait via the eastern and western routes separated by the Taiwan Bank. The coupled physical and biological effects on the NO3 transport at these two routes are highlighted in the study. For the western route, the shallow topography and the coastal upwelling intensify the biological uptake of NO3 in the whole water column. Consequently, the nitrogenous contribution by this route is mainly in form of the particulate organic nitrogen (PON). In contrast, NO3 is transported conservatively below the nitricline at the deep eastern route, contributing the whole NO3 supply in the TWS. The model estimates the fluxes of DIN and PON into the TWS, from the northern SCS, are 1.8 and 4 kmol s-1, respectively. Over half (˜1 kmol s-1) of the DIN is synthesized into PON by the phytoplankton in the strait. Overall, this study estimates the physical and biological effects on the nutrient transport in the TWS during summer.

Coherence protection in coupled quantum systems

Science.gov (United States)

Cammack, H. M.; Kirton, P.; Stace, T. M.; Eastham, P. R.; Keeling, J.; Lovett, B. W.

2018-02-01

The interaction of a quantum system with its environment causes decoherence, setting a fundamental limit on its suitability for quantum information processing. However, we show that if the system consists of coupled parts with different internal energy scales then the interaction of one part with a thermal bath need not lead to loss of coherence from the other. Remarkably, we find that the protected part can remain coherent for longer when the coupling to the bath becomes stronger or the temperature is raised. Our theory will enable the design of decoherence-resistant hybrid quantum computers.

A system for success: BMC Systems Biology, a new open access journal.

Science.gov (United States)

Hodgkinson, Matt J; Webb, Penelope A

2007-09-04

BMC Systems Biology is the first open access journal spanning the growing field of systems biology from molecules up to ecosystems. The journal has launched as more and more institutes are founded that are similarly dedicated to this new approach. BMC Systems Biology builds on the ongoing success of the BMC series, providing a venue for all sound research in the systems-level analysis of biology.

Hierarchical structure of biological systems: a bioengineering approach.

Science.gov (United States)

Alcocer-Cuarón, Carlos; Rivera, Ana L; Castaño, Victor M

2014-01-01

A general theory of biological systems, based on few fundamental propositions, allows a generalization of both Wierner and Berthalanffy approaches to theoretical biology. Here, a biological system is defined as a set of self-organized, differentiated elements that interact pair-wise through various networks and media, isolated from other sets by boundaries. Their relation to other systems can be described as a closed loop in a steady-state, which leads to a hierarchical structure and functioning of the biological system. Our thermodynamical approach of hierarchical character can be applied to biological systems of varying sizes through some general principles, based on the exchange of energy information and/or mass from and within the systems.

Synthetic Biology: Putting Synthesis into Biology

Science.gov (United States)

Liang, Jing; Luo, Yunzi; Zhao, Huimin

2010-01-01

The ability to manipulate living organisms is at the heart of a range of emerging technologies that serve to address important and current problems in environment, energy, and health. However, with all its complexity and interconnectivity, biology has for many years been recalcitrant to engineering manipulations. The recent advances in synthesis, analysis, and modeling methods have finally provided the tools necessary to manipulate living systems in meaningful ways, and have led to the coining of a field named synthetic biology. The scope of synthetic biology is as complicated as life itself – encompassing many branches of science, and across many scales of application. New DNA synthesis and assembly techniques have made routine the customization of very large DNA molecules. This in turn has allowed the incorporation of multiple genes and pathways. By coupling these with techniques that allow for the modeling and design of protein functions, scientists have now gained the tools to create completely novel biological machineries. Even the ultimate biological machinery – a self-replicating organism – is being pursued at this moment. It is the purpose of this review to dissect and organize these various components of synthetic biology into a coherent picture. PMID:21064036

An engineering design approach to systems biology.

Science.gov (United States)

Janes, Kevin A; Chandran, Preethi L; Ford, Roseanne M; Lazzara, Matthew J; Papin, Jason A; Peirce, Shayn M; Saucerman, Jeffrey J; Lauffenburger, Douglas A

2017-07-17

Measuring and modeling the integrated behavior of biomolecular-cellular networks is central to systems biology. Over several decades, systems biology has been shaped by quantitative biologists, physicists, mathematicians, and engineers in different ways. However, the basic and applied versions of systems biology are not typically distinguished, which blurs the separate aspirations of the field and its potential for real-world impact. Here, we articulate an engineering approach to systems biology, which applies educational philosophy, engineering design, and predictive models to solve contemporary problems in an age of biomedical Big Data. A concerted effort to train systems bioengineers will provide a versatile workforce capable of tackling the diverse challenges faced by the biotechnological and pharmaceutical sectors in a modern, information-dense economy.

Scaffolded biology.

Science.gov (United States)

Minelli, Alessandro

2016-09-01

Descriptions and interpretations of the natural world are dominated by dichotomies such as organism vs. environment, nature vs. nurture, genetic vs. epigenetic, but in the last couple of decades strong dissatisfaction with those partitions has been repeatedly voiced and a number of alternative perspectives have been suggested, from perspectives such as Dawkins' extended phenotype, Turner's extended organism, Oyama's Developmental Systems Theory and Odling-Smee's niche construction theory. Last in time is the description of biological phenomena in terms of hybrids between an organism (scaffolded system) and a living or non-living scaffold, forming unit systems to study processes such as reproduction and development. As scaffold, eventually, we can define any resource used by the biological system, especially in development and reproduction, without incorporating it as happens in the case of resources fueling metabolism. Addressing biological systems as functionally scaffolded systems may help pointing to functional relationships that can impart temporal marking to the developmental process and thus explain its irreversibility; revisiting the boundary between development and metabolism and also regeneration phenomena, by suggesting a conceptual framework within which to investigate phenomena of regular hypermorphic regeneration such as characteristic of deer antlers; fixing a periodization of development in terms of the times at which a scaffolding relationship begins or is terminated; and promoting plant galls to legitimate study objects of developmental biology.

The Feasibility of Systems Thinking in Biology Education

Science.gov (United States)

Boersma, Kerst; Waarlo, Arend Jan; Klaassen, Kees

2011-01-01

Systems thinking in biology education is an up and coming research topic, as yet with contrasting feasibility claims. In biology education systems thinking can be understood as thinking backward and forward between concrete biological objects and processes and systems models representing systems theoretical characteristics. Some studies claim that…

A micro-coupling for micro mechanical systems

Science.gov (United States)

Li, Wei; Zhou, Zhixiong; Zhang, Bi; Xiao, Yunya

2016-05-01

The error motions of micro mechanical systems, such as micro-spindles, increase with the increasing of the rotational speed, which not only decreases the rotational accuracy, but also promotes instability and limits the maximum operational speed. One effective way to deal with it is to use micro-flexible couplings between the drive and driven shafts so as to reduce error motions of the driven shaft. But the conventional couplings, such as diaphragm couplings, elastomeric couplings, bellows couplings, and grooved couplings, etc, cannot be directly used because of their large and complicated structures. This study presents a novel micro-coupling that consists of a flexible coupling and a shape memory alloy (SMA)-based clamp for micro mechanical systems. It is monolithic and can be directly machined from a shaft. The study performs design optimization and provides manufacturing considerations, including thermo-mechanical training of the SMA ring for the desired Two-Way-Shape-Memory effect (TWSMe). A prototype micro-coupling and a prototype micro-spindle using the proposed coupling are fabricated and tested. The testing results show that the prototype micro-coupling can bear a torque of above 5 N • mm and an axial force of 8.5 N and be fitted with an SMA ring for clamping action at room temperature (15 °C) and unclamping action below-5 °C. At the same time, the prototype micro-coupling can work at a rotational speed of above 200 kr/min with the application to a high-speed precision micro-spindle. Moreover, the radial runout error of the artifact, as a substitute for the micro-tool, is less than 3 μm while that of turbine shaft is above 7 μm. It can be concluded that the micro-coupling successfully accommodates misalignment errors of the prototype micro-spindle. This research proposes a micro-coupling which is featured with an SMA ring, and it is designed to clamp two shafts, and has smooth transmission, simple assembly, compact structure, zero-maintenance and

Ultrafast quantum computation in ultrastrongly coupled circuit QED systems

Science.gov (United States)

Wang, Yimin; Guo, Chu; Zhang, Guo-Qiang; Wang, Gangcheng; Wu, Chunfeng

2017-01-01

The latest technological progress of achieving the ultrastrong-coupling regime in circuit quantum electrodynamics (QED) systems has greatly promoted the developments of quantum physics, where novel quantum optics phenomena and potential computational benefits have been predicted. Here, we propose a scheme to accelerate the nontrivial two-qubit phase gate in a circuit QED system, where superconducting flux qubits are ultrastrongly coupled to a transmission line resonator (TLR), and two more TLRs are coupled to the ultrastrongly-coupled system for assistant. The nontrivial unconventional geometric phase gate between the two flux qubits is achieved based on close-loop displacements of the three-mode intracavity fields. Moreover, as there are three resonators contributing to the phase accumulation, the requirement of the coupling strength to realize the two-qubit gate can be reduced. Further reduction in the coupling strength to achieve a specific controlled-phase gate can be realized by adding more auxiliary resonators to the ultrastrongly-coupled system through superconducting quantum interference devices. We also present a study of our scheme with realistic parameters considering imperfect controls and noisy environment. Our scheme possesses the merits of ultrafastness and noise-tolerance due to the advantages of geometric phases. PMID:28281654

Answering biological questions: Querying a systems biology database for nutrigenomics

NARCIS (Netherlands)

Evelo, C.T.; Bochove, K. van; Saito, J.T.

2011-01-01

The requirement of systems biology for connecting different levels of biological research leads directly to a need for integrating vast amounts of diverse information in general and of omics data in particular. The nutritional phenotype database addresses this challenge for nutrigenomics. A

A Non-Homogeneous Dynamic Bayesian Network with Sequentially Coupled Interaction Parameters for Applications in Systems and Synthetic Biology

NARCIS (Netherlands)

Grzegorczyk, Marco; Husmeier, Dirk

2012-01-01

An important and challenging problem in systems biology is the inference of gene regulatory networks from short non-stationary time series of transcriptional profiles. A popular approach that has been widely applied to this end is based on dynamic Bayesian networks (DBNs), although traditional

Biochemical Frequency Control by Synchronisation of Coupled Repressilators: An In Silico Study of Modules for Circadian Clock Systems

Science.gov (United States)

Hinze, Thomas; Schumann, Mathias; Bodenstein, Christian; Heiland, Ines; Schuster, Stefan

2011-01-01

Exploration of chronobiological systems emerges as a growing research field within bioinformatics focusing on various applications in medicine, agriculture, and material sciences. From a systems biological perspective, the question arises whether biological control systems for regulation of oscillatory signals and their technical counterparts utilise similar mechanisms. If so, modelling approaches and parameterisation adopted from building blocks can help to identify general components for frequency control in circadian clocks along with gaining insight into mechanisms of clock synchronisation to external stimuli like the daily rhythm of sunlight and darkness. Phase-locked loops could be an interesting candidate in this context. Both, biology and engineering, can benefit from a unified view resulting from systems modularisation. In a first experimental study, we analyse a model of coupled repressilators. We demonstrate its ability to synchronise clock signals in a monofrequential manner. Several oscillators initially deviate in phase difference and frequency with respect to explicit reaction and diffusion rates. Accordingly, the duration of the synchronisation process depends on dedicated reaction and diffusion parameters whose settings still lack to be sufficiently captured analytically. PMID:22046179

Interactomes, manufacturomes and relational biology: analogies between systems biology and manufacturing systems

Science.gov (United States)

2011-01-01

Background We review and extend the work of Rosen and Casti who discuss category theory with regards to systems biology and manufacturing systems, respectively. Results We describe anticipatory systems, or long-range feed-forward chemical reaction chains, and compare them to open-loop manufacturing processes. We then close the loop by discussing metabolism-repair systems and describe the rationality of the self-referential equation f = f (f). This relationship is derived from some boundary conditions that, in molecular systems biology, can be stated as the cardinality of the following molecular sets must be about equal: metabolome, genome, proteome. We show that this conjecture is not likely correct so the problem of self-referential mappings for describing the boundary between living and nonliving systems remains an open question. We calculate a lower and upper bound for the number of edges in the molecular interaction network (the interactome) for two cellular organisms and for two manufacturomes for CMOS integrated circuit manufacturing. Conclusions We show that the relevant mapping relations may not be Abelian, and that these problems cannot yet be resolved because the interactomes and manufacturomes are incomplete. PMID:21689427

Lax pair and exact solutions of a discrete coupled system related to coupled KdV and coupled mKdV equations

International Nuclear Information System (INIS)

Liu Ping; Jia Man; Lou Senyue

2007-01-01

A modified Korteweg-de Vries (mKdV) lattice is also found to be a discrete Korteweg-de Vries (KdV) equation in this paper. The Lax pair for the discrete equation is found with the help of the Lax pair for a similar discrete equation. A Lax-integrable coupled extension of the lattice is posed, which is a common discrete version of both the coupled KdV and coupled mKdV systems. Some rational expansions of the Jacobian elliptic, trigonometric and hyperbolic functions are used to construct cnoidal waves, negaton and positon solutions of the discrete coupled system

Network biology: Describing biological systems by complex networks. Comment on "Network science of biological systems at different scales: A review" by M. Gosak et al.

Science.gov (United States)

Jalili, Mahdi

2018-03-01

I enjoyed reading Gosak et al. review on analysing biological systems from network science perspective [1]. Network science, first started within Physics community, is now a mature multidisciplinary field of science with many applications ranging from Ecology to biology, medicine, social sciences, engineering and computer science. Gosak et al. discussed how biological systems can be modelled and described by complex network theory which is an important application of network science. Although there has been considerable progress in network biology over the past two decades, this is just the beginning and network science has a great deal to offer to biology and medical sciences.

Predictive modeling of coupled multi-physics systems: I. Theory

International Nuclear Information System (INIS)

Cacuci, Dan Gabriel

2014-01-01

Highlights: • We developed “predictive modeling of coupled multi-physics systems (PMCMPS)”. • PMCMPS reduces predicted uncertainties in predicted model responses and parameters. • PMCMPS treats efficiently very large coupled systems. - Abstract: This work presents an innovative mathematical methodology for “predictive modeling of coupled multi-physics systems (PMCMPS).” This methodology takes into account fully the coupling terms between the systems but requires only the computational resources that would be needed to perform predictive modeling on each system separately. The PMCMPS methodology uses the maximum entropy principle to construct an optimal approximation of the unknown a priori distribution based on a priori known mean values and uncertainties characterizing the parameters and responses for both multi-physics models. This “maximum entropy”-approximate a priori distribution is combined, using Bayes’ theorem, with the “likelihood” provided by the multi-physics simulation models. Subsequently, the posterior distribution thus obtained is evaluated using the saddle-point method to obtain analytical expressions for the optimally predicted values for the multi-physics models parameters and responses along with corresponding reduced uncertainties. Noteworthy, the predictive modeling methodology for the coupled systems is constructed such that the systems can be considered sequentially rather than simultaneously, while preserving exactly the same results as if the systems were treated simultaneously. Consequently, very large coupled systems, which could perhaps exceed available computational resources if treated simultaneously, can be treated with the PMCMPS methodology presented in this work sequentially and without any loss of generality or information, requiring just the resources that would be needed if the systems were treated sequentially

Cluster Synchronization of Diffusively Coupled Nonlinear Systems: A Contraction-Based Approach

Science.gov (United States)

Aminzare, Zahra; Dey, Biswadip; Davison, Elizabeth N.; Leonard, Naomi Ehrich

2018-04-01

Finding the conditions that foster synchronization in networked nonlinear systems is critical to understanding a wide range of biological and mechanical systems. However, the conditions proved in the literature for synchronization in nonlinear systems with linear coupling, such as has been used to model neuronal networks, are in general not strict enough to accurately determine the system behavior. We leverage contraction theory to derive new sufficient conditions for cluster synchronization in terms of the network structure, for a network where the intrinsic nonlinear dynamics of each node may differ. Our result requires that network connections satisfy a cluster-input-equivalence condition, and we explore the influence of this requirement on network dynamics. For application to networks of nodes with FitzHugh-Nagumo dynamics, we show that our new sufficient condition is tighter than those found in previous analyses that used smooth or nonsmooth Lyapunov functions. Improving the analytical conditions for when cluster synchronization will occur based on network configuration is a significant step toward facilitating understanding and control of complex networked systems.

Sustainability Indicators for Coupled Human-Earth Systems

Science.gov (United States)

Motesharrei, S.; Rivas, J. R.; Kalnay, E.

2014-12-01

Over the last two centuries, the Human System went from having a small impact on the Earth System (including the Climate System) to becoming dominant, because both population and per capita consumption have grown extremely fast, especially since about 1950. We therefore argue that Human System Models must be included into Earth System Models through bidirectional couplings with feedbacks. In particular, population should be modeled endogenously, rather than exogenously as done currently in most Integrated Assessment Models. The growth of the Human System threatens to overwhelm the Carrying Capacity of the Earth System, and may be leading to catastrophic climate change and collapse. We propose a set of Ecological and Economic "Sustainability Indicators" that can employ large data-sets for developing and assessing effective mitigation and adaptation policies. Using the Human and Nature Dynamical Model (HANDY) and Coupled Human-Climate-Water Model (COWA), we carry out experiments with this set of Sustainability Indicators and show that they are applicable to various coupled systems including Population, Climate, Water, Energy, Agriculture, and Economy. Impact of nonrenewable resources and fossil fuels could also be understood using these indicators. We demonstrate interconnections of Ecological and Economic Indicators. Coupled systems often include feedbacks and can thus display counterintuitive dynamics. This makes it difficult for even experts to see coming catastrophes from just the raw data for different variables. Sustainability Indicators boil down the raw data into a set of simple numbers that cross their sustainability thresholds with a large time-lag before variables enter their catastrophic regimes. Therefore, we argue that Sustainability Indicators constitute a powerful but simple set of tools that could be directly used for making policies for sustainability.

Coupling-induced oscillations in nonhomogeneous, overdamped, bistable systems

International Nuclear Information System (INIS)

Hernandez, Mayra; In, Visarath; Longhini, Patrick; Palacios, Antonio; Bulsara, Adi; Kho, Andy

2008-01-01

Coupling-induced oscillations in a homogeneous network of overdamped bistable systems have been previously studied both theoretically and experimentally for a system of N (odd) elements, unidirectionally coupled in a ring topology. In this work, we extend the analysis of this system to include a network of nonhomogeneous elements with respect to the parameter that controls the topology of the potential function and the bistability of each element. In particular, we quantify the effects of the nonhomogeneity on the onset of oscillations and the response of the network to external (assumed to be constant and very small) perturbations, using our (recently developed) coupled core fluxgate magnetometer as a representative system. The potential applications of this work include signal detection and characterization for a large class of sensor systems

Coupling-induced oscillations in nonhomogeneous, overdamped, bistable systems

Energy Technology Data Exchange (ETDEWEB)

Hernandez, Mayra [Nonlinear Dynamical Systems Group, Department of Mathematics and Statistics, San Diego State University, San Diego, CA 92182 (United States)], E-mail: mayra.alina@yahoo.com; In, Visarath [Space and Naval Warfare Systems Center, Code 71730, 53560 Hull Street, San Diego, CA 92152-5001 (United States)], E-mail: visarath.in@navy.mil; Longhini, Patrick [Space and Naval Warfare Systems Center, Code 71730, 53560 Hull Street, San Diego, CA 92152-5001 (United States)], E-mail: longhini@navy.mil; Palacios, Antonio [Nonlinear Dynamical Systems Group, Department of Mathematics and Statistics, San Diego State University, San Diego, CA 92182 (United States)], E-mail: palacios@euler.sdsu.edu; Bulsara, Adi [Space and Naval Warfare Systems Center, Code 71730, 53560 Hull Street, San Diego, CA 92152-5001 (United States)], E-mail: bulsara@spawar.navy.mil; Kho, Andy [Space and Naval Warfare Systems Center, Code 71730, 53560 Hull Street, San Diego, CA 92152-5001 (United States)], E-mail: kho@spawar.navy.mil

2008-06-09

Coupling-induced oscillations in a homogeneous network of overdamped bistable systems have been previously studied both theoretically and experimentally for a system of N (odd) elements, unidirectionally coupled in a ring topology. In this work, we extend the analysis of this system to include a network of nonhomogeneous elements with respect to the parameter that controls the topology of the potential function and the bistability of each element. In particular, we quantify the effects of the nonhomogeneity on the onset of oscillations and the response of the network to external (assumed to be constant and very small) perturbations, using our (recently developed) coupled core fluxgate magnetometer as a representative system. The potential applications of this work include signal detection and characterization for a large class of sensor systems.

Photo-Responsive Graphene and Carbon Nanotubes to Control and Tackle Biological Systems

Science.gov (United States)

Cardano, Francesca; Frasconi, Marco; Giordani, Silvia

2018-01-01

Photo-responsive multifunctional nanomaterials are receiving considerable attention for biological applications because of their unique properties. The functionalization of the surface of carbon nanotubes (CNTs) and graphene, among other carbon based nanomaterials, with molecular switches that exhibit reversible transformations between two or more isomers in response to different kind of external stimuli, such as electromagnetic radiation, temperature and pH, has allowed the control of the optical and electrical properties of the nanomaterial. Light-controlled molecular switches, such as azobenzene and spiropyran, have attracted a lot of attention for nanomaterial's functionalization because of the remote modulation of their physicochemical properties using light stimulus. The enhanced properties of the hybrid materials obtained from the coupling of carbon based nanomaterials with light-responsive switches has enabled the fabrication of smart devices for various biological applications, including drug delivery, bioimaging and nanobiosensors. In this review, we highlight the properties of photo-responsive carbon nanomaterials obtained by the conjugation of CNTs and graphene with azobenzenes and spiropyrans molecules to investigate biological systems, devising possible future directions in the field. PMID:29707534

Photo-Responsive Graphene and Carbon Nanotubes to Control and Tackle Biological Systems

Science.gov (United States)

Cardano, Francesca; Frasconi, Marco; Giordani, Silvia

2018-04-01

Photo-responsive multifunctional nanomaterials are receiving considerable attention for biological applications because of their unique properties. The functionalization of the surface of carbon nanotubes (CNTs) and graphene, among other carbon based nanomaterials, with molecular switches that exhibit reversible transformations between two or more isomers in response to different kind of external stimuli, such as electromagnetic radiation, temperature and pH, has allowed the control of the optical and electrical properties of the nanomaterial. Light-controlled molecular switches, such as azobenzene and spiropyran, have attracted a lot of attention for nanomaterial’s functionalization because of the remote modulation of their physicochemical properties using light stimulus. The enhanced properties of the hybrid materials obtained from the coupling of carbon based nanomaterials with light-responsive switches has enabled the fabrication of smart devices for various biological applications, including drug delivery, bioimaging and nanobiosensors. In this review, we highlight the properties of photo-responsive carbon nanomaterials obtained by the conjugation of CNTs and graphene with azobenzenes and spiropyrans molecules to investigate biological systems, devising possible future directions in the field.

Biology and Mechanics of Blood Flows Part I: Biology

CERN Document Server

Thiriet, Marc

2008-01-01

Biology and Mechanics of Blood Flows presents the basic knowledge and state-of-the-art techniques necessary to carry out investigations of the cardiovascular system using modeling and simulation. Part I of this two-volume sequence, Biology, addresses the nanoscopic and microscopic scales. The nanoscale corresponds to the scale of biochemical reaction cascades involved in cell adaptation to mechanical stresses among other stimuli. The microscale is the scale of stress-induced tissue remodeling associated with acute or chronic loadings. The cardiovascular system, like any physiological system, has a complicated three-dimensional structure and composition. Its time dependent behavior is regulated, and this complex system has many components. In this authoritative work, the author provides a survey of relevant cell components and processes, with detailed coverage of the electrical and mechanical behaviors of vascular cells, tissues, and organs. Because the behaviors of vascular cells and tissues are tightly coupl...

Topics in mathematical biology

CERN Document Server

Hadeler, Karl Peter

2017-01-01

This book analyzes the impact of quiescent phases on biological models. Quiescence arises, for example, when moving individuals stop moving, hunting predators take a rest, infected individuals are isolated, or cells enter the quiescent compartment of the cell cycle. In the first chapter of Topics in Mathematical Biology general principles about coupled and quiescent systems are derived, including results on shrinking periodic orbits and stabilization of oscillations via quiescence. In subsequent chapters classical biological models are presented in detail and challenged by the introduction of quiescence. These models include delay equations, demographic models, age structured models, Lotka-Volterra systems, replicator systems, genetic models, game theory, Nash equilibria, evolutionary stable strategies, ecological models, epidemiological models, random walks and reaction-diffusion models. In each case we find new and interesting results such as stability of fixed points and/or periodic orbits, excitability...

Coupled vibrations in horizontal and vertical rotor-bearing systems

OpenAIRE

Luneno, Jean-Claude

2011-01-01

For dynamical systems having several degrees of freedom, motion in one direction can induce motion in the other. This means that there is a certain coupling between these two motions. Coupling can in some cases be a source of instability that causes self-excited vibrations in rotating machinery. In classical modeling of rotor systems, couplings other than those that are the result of gyroscopic effect are normally not considered. This is due to thecomplexity of the reasons for coupling which ...

Integrative radiation systems biology

International Nuclear Information System (INIS)

Unger, Kristian

2014-01-01

Maximisation of the ratio of normal tissue preservation and tumour cell reduction is the main concept of radiotherapy alone or combined with chemo-, immuno- or biologically targeted therapy. The foremost parameter influencing this ratio is radiation sensitivity and its modulation towards a more efficient killing of tumour cells and a better preservation of normal tissue at the same time is the overall aim of modern therapy schemas. Nevertheless, this requires a deep understanding of the molecular mechanisms of radiation sensitivity in order to identify its key players as potential therapeutic targets. Moreover, the success of conventional approaches that tried to statistically associate altered radiation sensitivity with any molecular phenotype such as gene expression proofed to be somewhat limited since the number of clinically used targets is rather sparse. However, currently a paradigm shift is taking place from pure frequentistic association analysis to the rather holistic systems biology approach that seeks to mathematically model the system to be investigated and to allow the prediction of an altered phenotype as the function of one single or a signature of biomarkers. Integrative systems biology also considers the data from different molecular levels such as the genome, transcriptome or proteome in order to partially or fully comprehend the causal chain of molecular mechanisms. An example for the application of this concept currently carried out at the Clinical Cooperation Group “Personalized Radiotherapy in Head and Neck Cancer” of the Helmholtz-Zentrum München and the LMU Munich is described. This review article strives for providing a compact overview on the state of the art of systems biology, its actual challenges, potential applications, chances and limitations in radiation oncology research working towards improved personalised therapy concepts using this relatively new methodology

A data integration approach for cell cycle analysis oriented to model simulation in systems biology

Directory of Open Access Journals (Sweden)

Mosca Ettore

2007-08-01

it aims to become a useful resource for collecting all the information related to actual and future models of this network. The flexibility of the database allows the addition of mathematical data which are used for simulating the behavior of the cell cycle components in the different models. The resource deals with two relevant problems in systems biology: data integration and mathematical simulation of a crucial biological process related to cancer, such as the cell cycle. In this way the resource is useful both to retrieve information about cell cycle model components and to analyze their dynamical properties. The Cell Cycle Database can be used to find system-level properties, such as stable steady states and oscillations, by coupling structure and dynamical information about models.

The markup is the model: reasoning about systems biology models in the Semantic Web era.

Science.gov (United States)

Kell, Douglas B; Mendes, Pedro

2008-06-07

Metabolic control analysis, co-invented by Reinhart Heinrich, is a formalism for the analysis of biochemical networks, and is a highly important intellectual forerunner of modern systems biology. Exchanging ideas and exchanging models are part of the international activities of science and scientists, and the Systems Biology Markup Language (SBML) allows one to perform the latter with great facility. Encoding such models in SBML allows their distributed analysis using loosely coupled workflows, and with the advent of the Internet the various software modules that one might use to analyze biochemical models can reside on entirely different computers and even on different continents. Optimization is at the core of many scientific and biotechnological activities, and Reinhart made many major contributions in this area, stimulating our own activities in the use of the methods of evolutionary computing for optimization.

Lie Point Symmetries and Exact Solutions of the Coupled Volterra System

International Nuclear Information System (INIS)

Ping, Liu; Sen-Yue, Lou

2010-01-01

The coupled Volterra system, an integrable discrete form of a coupled Korteweg–de Vries (KdV) system applied widely in fluids, Bose–Einstein condensation and atmospheric dynamics, is studied with the help of the Lie point symmetries. Two types of delayed differential reduction systems are derived from the coupled Volterra system by means of the symmetry reduction approach and symbolic computation. Cnoidal wave and solitary wave solutions for a delayed differential reduction system and the coupled Volterra system are proposed, respectively. (general)

Systemic couple therapy for dysthymia.

Science.gov (United States)

Montesano, Adrián; Feixas, Guillem; Muñoz, Dámaris; Compañ, Victoria

2014-03-01

We examined the effect of Systemic Couple Therapy on a patient diagnosed with dysthymic disorder and her partner. Marge and Peter, a middle-aged married couple, showed significant and meaningful changes in their pattern of interaction over the course of the therapy and, by the end of it, Marge no longer met the diagnostic criteria for dysthymic disorder. Her scores on the Structured Clinical Interview for DSM-IV Axis I Disorders (SCID-I) and Beck Depression Inventory, Second Edition (BDI-II) were in the clinical range before treatment and in the nonclinical one at the end of therapy. Although scores on Dyadic Adjustment Scale showed different patterns, both members reported significant improvement. The analysis of change in the alliance-related behaviors throughout the process concurred with change in couple's pattern of interaction. Treatment effects were maintained at 12-month follow-up. Highlights in the therapy process showed the importance of relational mechanisms of change, such as broadening the therapeutic focus into the couple's pattern of interaction, reducing expressed emotion and resentment, as well as increasing positive exchanges. The results of this evidence-based case study should prompt further investigation of couple therapy for dysthymia disorder. Randomized clinical trial design is needed to reach an evidence-based treatment status. (c) 2014 APA, all rights reserved.

Industrial systems biology and its impact on synthetic biology of yeast cell factories

DEFF Research Database (Denmark)

Fletcher, Eugene; Krivoruchko, Anastasia; Nielsen, Jens

2016-01-01

Engineering industrial cell factories to effectively yield a desired product while dealing with industrially relevant stresses is usually the most challenging step in the development of industrial production of chemicals using microbial fermentation processes. Using synthetic biology tools......, microbial cell factories such as Saccharomyces cerevisiae can be engineered to express synthetic pathways for the production of fuels, biopharmaceuticals, fragrances, and food flavors. However, directing fluxes through these synthetic pathways towards the desired product can be demanding due to complex...... regulation or poor gene expression. Systems biology, which applies computational tools and mathematical modeling to understand complex biological networks, can be used to guide synthetic biology design. Here, we present our perspective on how systems biology can impact synthetic biology towards the goal...

Metabolomics: Definitions and Significance in Systems Biology.

Science.gov (United States)

Klassen, Aline; Faccio, Andréa Tedesco; Canuto, Gisele André Baptista; da Cruz, Pedro Luis Rocha; Ribeiro, Henrique Caracho; Tavares, Marina Franco Maggi; Sussulini, Alessandra

2017-01-01

Nowadays, there is a growing interest in deeply understanding biological mechanisms not only at the molecular level (biological components) but also the effects of an ongoing biological process in the organism as a whole (biological functionality), as established by the concept of systems biology. Within this context, metabolomics is one of the most powerful bioanalytical strategies that allow obtaining a picture of the metabolites of an organism in the course of a biological process, being considered as a phenotyping tool. Briefly, metabolomics approach consists in identifying and determining the set of metabolites (or specific metabolites) in biological samples (tissues, cells, fluids, or organisms) under normal conditions in comparison with altered states promoted by disease, drug treatment, dietary intervention, or environmental modulation. The aim of this chapter is to review the fundamentals and definitions used in the metabolomics field, as well as to emphasize its importance in systems biology and clinical studies.

Physics of Coupled CME and Flare Systems

Science.gov (United States)

2016-12-21

AFRL-RV-PS- AFRL-RV-PS- TR-2016-0162 TR-2016-0162 PHYSICS OF COUPLED CME AND FLARE SYSTEMS K. S. Balasubramaniam, et al. 21 December 2016 Final...30 Sep 2016 4. TITLE AND SUBTITLE Physics of Coupled CME and Flare Systems 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 61102F...objectives for this task were: (i) derive measureable physical properties and discernible structural circumstances in solar active regions that

Improving emotion recognition systems by embedding cardiorespiratory coupling

International Nuclear Information System (INIS)

Valenza, Gaetano; Lanatá, Antonio; Scilingo, Enzo Pasquale

2013-01-01

This work aims at showing improved performances of an emotion recognition system embedding information gathered from cardiorespiratory (CR) coupling. Here, we propose a novel methodology able to robustly identify up to 25 regions of a two-dimensional space model, namely the well-known circumplex model of affect (CMA). The novelty of embedding CR coupling information in an autonomic nervous system-based feature space better reveals the sympathetic activations upon emotional stimuli. A CR synchrogram analysis was used to quantify such a coupling in terms of number of heartbeats per respiratory period. Physiological data were gathered from 35 healthy subjects emotionally elicited by means of affective pictures of the international affective picture system database. In this study, we finely detected five levels of arousal and five levels of valence as well as the neutral state, whose combinations were used for identifying 25 different affective states in the CMA plane. We show that the inclusion of the bivariate CR measures in a previously developed system based only on monovariate measures of heart rate variability, respiration dynamics and electrodermal response dramatically increases the recognition accuracy of a quadratic discriminant classifier, obtaining more than 90% of correct classification per class. Finally, we propose a comprehensive description of the CR coupling during sympathetic elicitation adapting an existing theoretical nonlinear model with external driving. The theoretical idea behind this model is that the CR system is comprised of weakly coupled self-sustained oscillators that, when exposed to an external perturbation (i.e. sympathetic activity), becomes synchronized and less sensible to input variations. Given the demonstrated role of the CR coupling, this model can constitute a general tool which is easily embedded in other model-based emotion recognition systems. (paper)

The coupled nonlinear dynamics of a lift system

Energy Technology Data Exchange (ETDEWEB)

Crespo, Rafael Sánchez, E-mail: rafael.sanchezcrespo@northampton.ac.uk, E-mail: stefan.kaczmarczyk@northampton.ac.uk, E-mail: phil.picton@northampton.ac.uk, E-mail: huijuan.su@northampton.ac.uk; Kaczmarczyk, Stefan, E-mail: rafael.sanchezcrespo@northampton.ac.uk, E-mail: stefan.kaczmarczyk@northampton.ac.uk, E-mail: phil.picton@northampton.ac.uk, E-mail: huijuan.su@northampton.ac.uk; Picton, Phil, E-mail: rafael.sanchezcrespo@northampton.ac.uk, E-mail: stefan.kaczmarczyk@northampton.ac.uk, E-mail: phil.picton@northampton.ac.uk, E-mail: huijuan.su@northampton.ac.uk; Su, Huijuan, E-mail: rafael.sanchezcrespo@northampton.ac.uk, E-mail: stefan.kaczmarczyk@northampton.ac.uk, E-mail: phil.picton@northampton.ac.uk, E-mail: huijuan.su@northampton.ac.uk [The University of Northampton, School of Science and Technology, Avenue Campus, St George' s Avenue, Northampton (United Kingdom)

2014-12-10

Coupled lateral and longitudinal vibrations of suspension and compensating ropes in a high-rise lift system are often induced by the building motions due to wind or seismic excitations. When the frequencies of the building become near the natural frequencies of the ropes, large resonance motions of the system may result. This leads to adverse coupled dynamic phenomena involving nonplanar motions of the ropes, impact loads between the ropes and the shaft walls, as well as vertical vibrations of the car, counterweight and compensating sheave. Such an adverse dynamic behaviour of the system endangers the safety of the installation. This paper presents two mathematical models describing the nonlinear responses of a suspension/ compensating rope system coupled with the elevator car / compensating sheave motions. The models accommodate the nonlinear couplings between the lateral and longitudinal modes, with and without longitudinal inertia of the ropes. The partial differential nonlinear equations of motion are derived using Hamilton Principle. Then, the Galerkin method is used to discretise the equations of motion and to develop a nonlinear ordinary differential equation model. Approximate numerical solutions are determined and the behaviour of the system is analysed.

Tinamit: Making coupled system dynamics models accessible to stakeholders

Science.gov (United States)

Malard, Julien; Inam Baig, Azhar; Rojas Díaz, Marcela; Hassanzadeh, Elmira; Adamowski, Jan; Tuy, Héctor; Melgar-Quiñonez, Hugo

2017-04-01

Model coupling is increasingly used as a method of combining the best of two models when representing socio-environmental systems, though barriers to successful model adoption by stakeholders are particularly present with the use of coupled models, due to their high complexity and typically low implementation flexibility. Coupled system dynamics - physically-based modelling is a promising method to improve stakeholder participation in environmental modelling while retaining a high level of complexity for physical process representation, as the system dynamics components are readily understandable and can be built by stakeholders themselves. However, this method is not without limitations in practice, including 1) inflexible and complicated coupling methods, 2) difficult model maintenance after the end of the project, and 3) a wide variety of end-user cultures and languages. We have developed the open-source Python-language software tool Tinamit to overcome some of these limitations to the adoption of stakeholder-based coupled system dynamics - physically-based modelling. The software is unique in 1) its inclusion of both a graphical user interface (GUI) and a library of available commands (API) that allow users with little or no coding abilities to rapidly, effectively, and flexibly couple models, 2) its multilingual support for the GUI, allowing users to couple models in their preferred language (and to add new languages as necessary for their community work), and 3) its modular structure allowing for very easy model coupling and modification without the direct use of code, and to which programming-savvy users can easily add support for new types of physically-based models. We discuss how the use of Tinamit for model coupling can greatly increase the accessibility of coupled models to stakeholders, using an example of a stakeholder-built system dynamics model of soil salinity issues in Pakistan coupled with the physically-based soil salinity and water flow model

Systems Biology of Industrial Microorganisms

Science.gov (United States)

Papini, Marta; Salazar, Margarita; Nielsen, Jens

The field of industrial biotechnology is expanding rapidly as the chemical industry is looking towards more sustainable production of chemicals that can be used as fuels or building blocks for production of solvents and materials. In connection with the development of sustainable bioprocesses, it is a major challenge to design and develop efficient cell factories that can ensure cost efficient conversion of the raw material into the chemical of interest. This is achieved through metabolic engineering, where the metabolism of the cell factory is engineered such that there is an efficient conversion of sugars, the typical raw materials in the fermentation industry, into the desired product. However, engineering of cellular metabolism is often challenging due to the complex regulation that has evolved in connection with adaptation of the different microorganisms to their ecological niches. In order to map these regulatory structures and further de-regulate them, as well as identify ingenious metabolic engineering strategies that full-fill mass balance constraints, tools from systems biology can be applied. This involves both high-throughput analysis tools like transcriptome, proteome and metabolome analysis, as well as the use of mathematical modeling to simulate the phenotypes resulting from the different metabolic engineering strategies. It is in fact expected that systems biology may substantially improve the process of cell factory development, and we therefore propose the term Industrial Systems Biology for how systems biology will enhance the development of industrial biotechnology for sustainable chemical production.

From immunology to MRI data anlysis: Problems in mathematical biology

Science.gov (United States)

Waters, Ryan Samuel

This thesis represents a collection of four distinct biological projects rising from immunology and metabolomics that required unique and creative mathematical approaches. One project focuses on understanding the role IL-2 plays in immune response regulation and exploring how these effects can be altered. We developed several dynamic models of the receptor signaling network which we analyze analytically and numerically. In a second project focused also on MS, we sought to create a system for grading magnetic resonance images (MRI) with good correlation with disability. The goal is for these MRI scores to provide a better standard for large-scale clinical drug trials, which limits the bias associated with differences in available MRI technology and general grader/participant variability. The third project involves the study of the CRISPR adaptive immune system in bacteria. Bacterial cells recognize and acquire snippets of exogenous genetic material, which they incorporate into their DNA. In this project we explore the optimal design for the CRISPR system given a viral distribution to maximize its probability of survival. The final project involves the study of the benefits for colocalization of coupled enzymes in metabolic pathways. The hypothesized kinetic advantage, known as `channeling', of putting coupled enzymes closer together has been used as justification for the colocalization of coupled enzymes in biological systems. We developed and analyzed a simple partial differential equation of the diffusion of the intermediate substrate between coupled enzymes to explore the phenomena of channeling. The four projects of my thesis represent very distinct biological problems that required a variety of techniques from diverse areas of mathematics ranging from dynamical modeling to statistics, Fourier series and calculus of variations. In each case, quantitative techniques were used to address biological questions from a mathematical perspective ultimately providing

Bifurcation of transition paths induced by coupled bistable systems.

Science.gov (United States)

Tian, Chengzhe; Mitarai, Namiko

2016-06-07

We discuss the transition paths in a coupled bistable system consisting of interacting multiple identical bistable motifs. We propose a simple model of coupled bistable gene circuits as an example and show that its transition paths are bifurcating. We then derive a criterion to predict the bifurcation of transition paths in a generalized coupled bistable system. We confirm the validity of the theory for the example system by numerical simulation. We also demonstrate in the example system that, if the steady states of individual gene circuits are not changed by the coupling, the bifurcation pattern is not dependent on the number of gene circuits. We further show that the transition rate exponentially decreases with the number of gene circuits when the transition path does not bifurcate, while a bifurcation facilitates the transition by lowering the quasi-potential energy barrier.

Sensitivity analysis approaches applied to systems biology models.

Science.gov (United States)

Zi, Z

2011-11-01

With the rising application of systems biology, sensitivity analysis methods have been widely applied to study the biological systems, including metabolic networks, signalling pathways and genetic circuits. Sensitivity analysis can provide valuable insights about how robust the biological responses are with respect to the changes of biological parameters and which model inputs are the key factors that affect the model outputs. In addition, sensitivity analysis is valuable for guiding experimental analysis, model reduction and parameter estimation. Local and global sensitivity analysis approaches are the two types of sensitivity analysis that are commonly applied in systems biology. Local sensitivity analysis is a classic method that studies the impact of small perturbations on the model outputs. On the other hand, global sensitivity analysis approaches have been applied to understand how the model outputs are affected by large variations of the model input parameters. In this review, the author introduces the basic concepts of sensitivity analysis approaches applied to systems biology models. Moreover, the author discusses the advantages and disadvantages of different sensitivity analysis methods, how to choose a proper sensitivity analysis approach, the available sensitivity analysis tools for systems biology models and the caveats in the interpretation of sensitivity analysis results.

Influence of regional hydrogeological systems at a local scale: Analyzing the coupled effects of hydrochemistry and biological activity in a Fe and CO_2 rich spring

International Nuclear Information System (INIS)

Menció, A.; Guasch, H.; Soler, D.; Canelles, A.; Zamorano, M.; Brusi, D.

2016-01-01

A multidisciplinary approach was used in this study to determine the origin of a Fe and CO_2 rich spring, an extreme freshwater system and to evaluate the coupled effects of hydrochemistry and biological activity at a local scale. An electrical resistivity tomography survey was conducted to delineate the geological context in which water emerges from a Plio-Quaternary supracrustal fault zone, and a bulk resistivity decrease was detected when CO_2 rich groundwater occurred. Nine water samples, together with eight biofilm samples, and three sediment samples were taken along the spring canal for their analysis. Major ions, nutrients, and metals were analysed in water samples. Sediment analyses determined the main solid phases precipitated (mainly as CaCO_3 and Fe(OH)_3(a)). Biofilm analyses permitted to obtain biovolume per cell measures, total biovolume values, diatom density, chlorophyll a concentrations, and the Margalef Index values. Inverse modeling and batch reaction models were used to determine the physicochemical processes affecting the spring water, obtaining the total amount of CaCO_3/L formed; the Fe and Mn compounds, which mainly precipitated as Fe(OH)_3(a) and Mn(OH)_2; as well as the total CO_2 released to the atmosphere. Analyzing these results together with the patterns of variation of hydrochemical and biological parameters, different interactions were observed: a) the effects of Fe inhibition in travertine formation, even though when the highest CO_2 release was occurring; b) the fate and effects of chemicals limiting and/or inhibiting algal growth (mainly Fe, As and phosphate); c) the lack of coincidence between algal growth and tufa limestone precipitation; d) the relationship between some divalent metals (Mn and Co) and biotic activity. - Highlights: • Electrical resistivity tomography detected CO_2 rich groundwater. • High Fe concentrations inhibits both algal growth and CaCO_3 precipitation. • Tufa precipitation doesn't coincide with the

Dynamical hysteresis and spatial synchronization in coupled non

Indian Academy of Sciences (India)

... of complex biological systems, e.g. seizures in the epileptic brain can be viewed as transitions between different dynamical phases caused by time dependence in the brain's internal coupling. ... Pramana – Journal of Physics | News.

Biospheric feedback effects in a synchronously coupled model of human and Earth systems

Energy Technology Data Exchange (ETDEWEB)

Thornton, Peter E.; Calvin, Katherine V.; Jones, Andrew D.; Di Vittorio, Alan; Bond-Lamberty, Benjamin; Chini, Louise M.; Shi, Xiaoying; Mao, Jiafu; Collins, William D.; Edmonds, James A.; Thomson, Allison M.; Truesdale, John E.; Craig, Anthony P.; Branstetter, M.; Hurtt, George C.

2017-06-12

Fossil fuel combustion and land-use change are the first and second largest contributors to industrial-era increases in atmospheric carbon dioxide concentration, which is itself the largest driver of present-day climate change1. Projections of fossil fuel consumption and land-use change are thus fundamental inputs for coupled Earth system models (ESM) used to estimate the physical and biological consequences of future climate system forcing2,3. While empirical datasets are available to inform historical analyses4,5, assessments of future climate change have relied on projections of energy and land use based on energy economic models, constrained using historical and present-day data and forced with assumptions about future policy, land-use patterns, and socio-economic development trajectories6. Here we show that the influence of biospheric change – the integrated effect of climatic, ecological, and geochemical processes – on land ecosystems has a significant impact on energy, agriculture, and land-use projections for the 21st century. Such feedbacks have been ignored in previous ESM studies of future climate. We find that synchronous exposure of land ecosystem productivity in the economic system to biospheric change as it develops in an ESM results in a 10% reduction of land area used for crop cultivation; increased managed forest area and land carbon; a 15-20% decrease in global crop price; and a 17% reduction in fossil fuel emissions for a low-mid range forcing scenario7. These simulation results demonstrate that biospheric change can significantly alter primary human system forcings to the climate system. This synchronous two-way coupling approach removes inconsistencies in description of climate change between human and biosphere components of the coupled model, mitigating a major source of uncertainty identified in assessments of future climate projections8-10.

Systems Biology for Organotypic Cell Cultures

Energy Technology Data Exchange (ETDEWEB)

Grego, Sonia [RTI International, Research Triangle Park, NC (United States); Dougherty, Edward R. [Texas A & M Univ., College Station, TX (United States); Alexander, Francis J. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Auerbach, Scott S. [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Berridge, Brian R. [GlaxoSmithKline, Research Triangle Park, NC (United States); Bittner, Michael L. [Translational Genomics Research Inst., Phoenix, AZ (United States); Casey, Warren [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Cooley, Philip C. [RTI International, Research Triangle Park, NC (United States); Dash, Ajit [HemoShear Therapeutics, Charlottesville, VA (United States); Ferguson, Stephen S. [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Fennell, Timothy R. [RTI International, Research Triangle Park, NC (United States); Hawkins, Brian T. [RTI International, Research Triangle Park, NC (United States); Hickey, Anthony J. [RTI International, Research Triangle Park, NC (United States); Kleensang, Andre [Johns Hopkins Univ., Baltimore, MD (United States). Center for Alternatives to Animal Testing; Liebman, Michael N. [IPQ Analytics, Kennett Square, PA (United States); Martin, Florian [Phillip Morris International, Neuchatel (Switzerland); Maull, Elizabeth A. [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Paragas, Jason [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Qiao, Guilin [Defense Threat Reduction Agency, Ft. Belvoir, VA (United States); Ramaiahgari, Sreenivasa [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Sumner, Susan J. [RTI International, Research Triangle Park, NC (United States); Yoon, Miyoung [The Hamner Inst. for Health Sciences, Research Triangle Park, NC (United States); ScitoVation, Research Triangle Park, NC (United States)

2016-08-04

Translating in vitro biological data into actionable information related to human health holds the potential to improve disease treatment and risk assessment of chemical exposures. While genomics has identified regulatory pathways at the cellular level, translation to the organism level requires a multiscale approach accounting for intra-cellular regulation, inter-cellular interaction, and tissue/organ-level effects. Tissue-level effects can now be probed in vitro thanks to recently developed systems of three-dimensional (3D), multicellular, “organotypic” cell cultures, which mimic functional responses of living tissue. However, there remains a knowledge gap regarding interactions across different biological scales, complicating accurate prediction of health outcomes from molecular/genomic data and tissue responses. Systems biology aims at mathematical modeling of complex, non-linear biological systems. We propose to apply a systems biology approach to achieve a computational representation of tissue-level physiological responses by integrating empirical data derived from organotypic culture systems with computational models of intracellular pathways to better predict human responses. Successful implementation of this integrated approach will provide a powerful tool for faster, more accurate and cost-effective screening of potential toxicants and therapeutics. On September 11, 2015, an interdisciplinary group of scientists, engineers, and clinicians gathered for a workshop in Research Triangle Park, North Carolina, to discuss this ambitious goal. Participants represented laboratory-based and computational modeling approaches to pharmacology and toxicology, as well as the pharmaceutical industry, government, non-profits, and academia. Discussions focused on identifying critical system perturbations to model, the computational tools required, and the experimental approaches best suited to generating key data. This consensus report summarizes the discussions held.

Biospheric feedback effects in a synchronously coupled model of human and Earth systems

Science.gov (United States)

Thornton, P. E.; Calvin, K. V.; Jones, A. D.; Di Vittorio, A. V.; Bond-Lamberty, B. P.; Chini, L. P.; Shi, X.; Mao, J.; Collins, W. D.; Edmonds, J.; Hurtt, G. C.

2017-12-01

Fossil fuel combustion and land-use change are the two largest contributors to industrial-era increases in atmospheric CO2 concentration. Projections of these are thus fundamental inputs for coupled Earth system models (ESMs) used to estimate the physical and biological consequences of future climate system forcing. While historical datasets are available to inform past and current climate analyses, assessments of future climate change have relied on projections of energy and land use from energy economic models, constrained by assumptions about future policy, land-use patterns, and socio-economic development trajectories. In this work we show that the climatic impacts on land ecosystems drives significant feedbacks in energy, agriculture, land-use, and carbon cycle projections for the 21st century. We find that exposure of human appropriated land ecosystem productivity to biospheric change results in reductions of land area used for crops; increases in managed forest area and carbon stocks; decreases in global crop prices; and reduction in fossil fuel emissions for a low-mid range forcing scenario. Land ecosystem response to increased carbon dioxide concentration, increased anthropogenic nitrogen deposition, and changes in temperature and precipitation all play a role. The feedbacks between climate-induced biospheric change and human system forcings to the climate system demonstrated in this work are handled inconsistently, or excluded altogether, in the one-way asynchronous coupling of energy economic models to ESMs used to date.

Fuzzy Control of Cold Storage Refrigeration System with Dynamic Coupling Compensation

Directory of Open Access Journals (Sweden)

Xiliang Ma

2018-01-01

Full Text Available Cold storage refrigeration systems possess the characteristics of multiple input and output and strong coupling, which brings challenges to the optimize control. To reduce the adverse effects of the coupling and improve the overall control performance of cold storage refrigeration systems, a control strategy with dynamic coupling compensation was studied. First, dynamic model of a cold storage refrigeration system was established based on the requirements of the control system. At the same time, the coupling between the components was studied. Second, to reduce the adverse effects of the coupling, a fuzzy controller with dynamic coupling compensation was designed. As for the fuzzy controller, a self-tuning fuzzy controller was served as the primary controller, and an adaptive neural network was adopted to compensate the dynamic coupling. Finally, the proposed control strategy was employed to the cold storage refrigeration system, and simulations were carried out in the condition of start-up, variable load, and variable degree of superheat, respectively. The simulation results verify the effectiveness of the fuzzy control method with dynamic coupling compensation.

Impact of Thermodynamic Principles in Systems Biology

NARCIS (Netherlands)

Heijnen, J.J.

2010-01-01

It is shown that properties of biological systems which are relevant for systems biology motivated mathematical modelling are strongly shaped by general thermodynamic principles such as osmotic limit, Gibbs energy dissipation, near equilibria and thermodynamic driving force. Each of these aspects

Biological Soft Robotics.

Science.gov (United States)

Feinberg, Adam W

2015-01-01

In nature, nanometer-scale molecular motors are used to generate force within cells for diverse processes from transcription and transport to muscle contraction. This adaptability and scalability across wide temporal, spatial, and force regimes have spurred the development of biological soft robotic systems that seek to mimic and extend these capabilities. This review describes how molecular motors are hierarchically organized into larger-scale structures in order to provide a basic understanding of how these systems work in nature and the complexity and functionality we hope to replicate in biological soft robotics. These span the subcellular scale to macroscale, and this article focuses on the integration of biological components with synthetic materials, coupled with bioinspired robotic design. Key examples include nanoscale molecular motor-powered actuators, microscale bacteria-controlled devices, and macroscale muscle-powered robots that grasp, walk, and swim. Finally, the current challenges and future opportunities in the field are addressed.

Systems Biology of Metabolism: Annual Review of Biochemistry

DEFF Research Database (Denmark)

Nielsen, Jens

2017-01-01

Metabolism is highly complex and involves thousands of different connected reactions; it is therefore necessary to use mathematical models for holistic studies. The use of mathematical models in biology is referred to as systems biology. In this review, the principles of systems biology are descr...

On non-linear dynamics of a coupled electro-mechanical system

DEFF Research Database (Denmark)

Darula, Radoslav; Sorokin, Sergey

2012-01-01

Electro-mechanical devices are an example of coupled multi-disciplinary weakly non-linear systems. Dynamics of such systems is described in this paper by means of two mutually coupled differential equations. The first one, describing an electrical system, is of the first order and the second one...... excitation. The results are verified using a numerical model created in MATLAB Simulink environment. Effect of non-linear terms on dynamical response of the coupled system is investigated; the backbone and envelope curves are analyzed. The two phenomena, which exist in the electro-mechanical system: (a......, for mechanical system, is of the second order. The governing equations are coupled via linear and weakly non-linear terms. A classical perturbation method, a method of multiple scales, is used to find a steadystate response of the electro-mechanical system exposed to a harmonic close-resonance mechanical...

Toxicity of silver nanoparticles in biological systems: Does the complexity of biological systems matter?

Science.gov (United States)

Vazquez-Muñoz, Roberto; Borrego, Belen; Juárez-Moreno, Karla; García-García, Maritza; Mota Morales, Josué D; Bogdanchikova, Nina; Huerta-Saquero, Alejandro

2017-07-05

Currently, nanomaterials are more frequently in our daily life, specifically in biomedicine, electronics, food, textiles and catalysis just to name a few. Although nanomaterials provide many benefits, recently their toxicity profiles have begun to be explored. In this work, the toxic effects of silver nanoparticles (35nm-average diameter and Polyvinyl-Pyrrolidone-coated) on biological systems of different levels of complexity was assessed in a comprehensive and comparatively way, through a variety of viability and toxicological assays. The studied organisms included viruses, bacteria, microalgae, fungi, animal and human cells (including cancer cell lines). It was found that biological systems of different taxonomical groups are inhibited at concentrations of silver nanoparticles within the same order of magnitude. Thus, the toxicity of nanomaterials on biological/living systems, constrained by their complexity, e.g. taxonomic groups, resulted contrary to the expected. The fact that cells and virus are inhibited with a concentration of silver nanoparticles within the same order of magnitude could be explained considering that silver nanoparticles affects very primitive cellular mechanisms by interacting with fundamental structures for cells and virus alike. Copyright © 2017 Elsevier B.V. All rights reserved.

Perturbation of coupling matrices and its effect on the synchronizability in arrays of coupled chaotic systems

International Nuclear Information System (INIS)

Wu, C.W.

2003-01-01

In a recent paper, wavelet analysis is used to perturb the coupling matrix in an array of identical chaotic systems in order to improve its synchronization. When the coupling matrix is symmetric, the synchronization criterion is determined by the second smallest eigenvalue λ 2 of the coupling matrix and the problem is reduced to studying how λ 2 of the coupling matrix changes with perturbation. In the aforementioned paper, a small percentage of the wavelet coefficients are modified. However, this results in a perturbed matrix where every element is modified and nonzero. The purpose of this Letter is to present some results on the change of λ 2 due to perturbation. In particular, we show that as the number of systems n→∞, perturbations which only add local coupling will not change λ 2 . On the other hand, we show that there exists perturbations which modify an arbitrarily small percentage of matrix elements, each of which is changed by an arbitrarily small amount and yet can make λ 2 arbitrarily large. These results give conditions on what the perturbation should be in order to improve the synchronizability in an array of coupled chaotic systems. This analysis allows us to justify and explain some of the synchronization phenomena observed in a recently studied network where random coupling is added to a locally connected array. We propose to classify various classes of coupling matrices such as small world networks and scale free networks according to their synchronizability in the limit. Finally, we briefly discuss the case of time-varying coupling

The Systems Biology Research Tool: evolvable open-source software

Directory of Open Access Journals (Sweden)

Wright Jeremiah

2008-06-01

Full Text Available Abstract Background Research in the field of systems biology requires software for a variety of purposes. Software must be used to store, retrieve, analyze, and sometimes even to collect the data obtained from system-level (often high-throughput experiments. Software must also be used to implement mathematical models and algorithms required for simulation and theoretical predictions on the system-level. Results We introduce a free, easy-to-use, open-source, integrated software platform called the Systems Biology Research Tool (SBRT to facilitate the computational aspects of systems biology. The SBRT currently performs 35 methods for analyzing stoichiometric networks and 16 methods from fields such as graph theory, geometry, algebra, and combinatorics. New computational techniques can be added to the SBRT via process plug-ins, providing a high degree of evolvability and a unifying framework for software development in systems biology. Conclusion The Systems Biology Research Tool represents a technological advance for systems biology. This software can be used to make sophisticated computational techniques accessible to everyone (including those with no programming ability, to facilitate cooperation among researchers, and to expedite progress in the field of systems biology.

Dynamical System Approach for Edge Detection Using Coupled FitzHugh-Nagumo Neurons.

Science.gov (United States)

Li, Shaobai; Dasmahapatra, Srinandan; Maharatna, Koushik

2015-12-01

The prospect of emulating the impressive computational capabilities of biological systems has led to considerable interest in the design of analog circuits that are potentially implementable in very large scale integration CMOS technology and are guided by biologically motivated models. For example, simple image processing tasks, such as the detection of edges in binary and grayscale images, have been performed by networks of FitzHugh-Nagumo-type neurons using the reaction-diffusion models. However, in these studies, the one-to-one mapping of image pixels to component neurons makes the size of the network a critical factor in any such implementation. In this paper, we develop a simplified version of the employed reaction-diffusion model in three steps. In the first step, we perform a detailed study to locate this threshold using continuous Lyapunov exponents from dynamical system theory. Furthermore, we render the diffusion in the system to be anisotropic, with the degree of anisotropy being set by the gradients of grayscale values in each image. The final step involves a simplification of the model that is achieved by eliminating the terms that couple the membrane potentials of adjacent neurons. We apply our technique to detect edges in data sets of artificially generated and real images, and we demonstrate that the performance is as good if not better than that of the previous methods without increasing the size of the network.

MCD 80: A modular coupling system for power line carrier transmission

Energy Technology Data Exchange (ETDEWEB)

Fischer, B; Mayer, M

1983-05-01

Power line carrier (PLC) links are of great importance to power supply utilities. The communications equipment is linked to the H.V. system by a coupling device. Brown Boveri have developed a new modular coupling system MCD 80 which is compact, programmable and economical. The benefit of years of experience in the field went into its development. With the new system, optimum PLC couplings, R.F. through-connections and junction networks are possible for all H.V. transmission systems. A general look at the subject of PLC couplings is followed by a closer look at the main components, such as the programmable high pass coupling unit, band pass coupling unit, hybrid, separating filter, R.F. junction network and attenuator. Some typical examples are described.

Persistent Memory in Single Node Delay-Coupled Reservoir Computing.

Science.gov (United States)

Kovac, André David; Koall, Maximilian; Pipa, Gordon; Toutounji, Hazem

2016-01-01

Delays are ubiquitous in biological systems, ranging from genetic regulatory networks and synaptic conductances, to predator/pray population interactions. The evidence is mounting, not only to the presence of delays as physical constraints in signal propagation speed, but also to their functional role in providing dynamical diversity to the systems that comprise them. The latter observation in biological systems inspired the recent development of a computational architecture that harnesses this dynamical diversity, by delay-coupling a single nonlinear element to itself. This architecture is a particular realization of Reservoir Computing, where stimuli are injected into the system in time rather than in space as is the case with classical recurrent neural network realizations. This architecture also exhibits an internal memory which fades in time, an important prerequisite to the functioning of any reservoir computing device. However, fading memory is also a limitation to any computation that requires persistent storage. In order to overcome this limitation, the current work introduces an extended version to the single node Delay-Coupled Reservoir, that is based on trained linear feedback. We show by numerical simulations that adding task-specific linear feedback to the single node Delay-Coupled Reservoir extends the class of solvable tasks to those that require nonfading memory. We demonstrate, through several case studies, the ability of the extended system to carry out complex nonlinear computations that depend on past information, whereas the computational power of the system with fading memory alone quickly deteriorates. Our findings provide the theoretical basis for future physical realizations of a biologically-inspired ultrafast computing device with extended functionality.

Performance of a directly-coupled PV water pumping system

International Nuclear Information System (INIS)

Mokeddem, Abdelmalek; Midoun, Abdelhamid; Kadri, D.; Hiadsi, Said; Raja, Iftikhar A.

2011-01-01

Highlights: → Directly coupled PV water pumping system installed and performance studied. → Configured for two static heads, operate without electronic control and auxiliary power. → The system attains steady state soon after any abrupt change. → Cost effective and useful for low head communicating wells system. - Abstract: This paper describes the experimental study carried out to investigate the performance of a simple, directly coupled dc photovoltaic (PV) powered water pumping system. The system comprises of a 1.5 kWp PV array, dc motor and a centrifugal pump. The experiment was conducted over a period of 4 months and the system performance was monitored under different climatic conditions and varying solar irradiance with two static head configurations. Although the motor-pump efficiency did not exceed 30%, which is typical for directly-coupled photovoltaic pumping systems, such a system is clearly suitable for low head irrigation in the remote areas, not connected to the national grid and where access to water comes as first priority issue than access to technology. The system operates without battery and complex electronic control, therefore not only the initial cost is low but also maintenance, repairing and replacement cost can be saved. The study showed that directly coupled system attains steady state soon after any abrupt change.

Progress in Computational Physics (PiCP) Vol 2 Coupled Fluid Flow in Energy, Biology and Environmental Research

CERN Document Server

Ehrhardt, Matthias

2012-01-01

This second volume contains both, the mathematical analysis of the coupling between fluid flow and porous media flow and state-of-the art numerical techniques, like tailor-made finite element and finite volume methods. Readers will come across articles devoted to concrete applications of these models in the field of energy, biology and environmental research.

Complex systems of biological interest stability under ionising radiations

International Nuclear Information System (INIS)

Maclot, Sylvain

2014-01-01

This PhD work presents the study of stability of molecular systems of biological interest in the gas phase after interaction with ionising radiations. The use of ionising radiation can probe the physical chemistry of complex systems at the molecular scale and thus consider their intrinsic properties. Beyond the fundamental aspect, this work is part of the overall understanding of radiation effects on living organisms and in particular the use of ionizing radiation in radiotherapy. Specifically, this study focused on the use of low-energy multiply charged ions (tens of keV) provided by the GANIL (Caen), which includes most of the experiments presented. In addition, experiments using VUV photons were also conducted at synchrotron ELETTRA (Trieste, Italy). The bio-molecular systems studied are amino acids and nucleic acid constituents. Using an experimental crossed beams device allows interaction between biomolecules and ionising radiation leads mainly to the ionization and fragmentation of the system. The study of its relaxation dynamics is by time-of-flight mass spectrometry coupled to a coincidences measurements method. It is shown that an approach combining experiment and theory allows a detailed study of the fragmentation dynamics of complex systems. The results indicate that fragmentation is generally governed by the Coulomb repulsion but the intramolecular rearrangements involve specific relaxation mechanisms. (author) [fr

On the interplay between mathematics and biology: hallmarks toward a new systems biology.

Science.gov (United States)

Bellomo, Nicola; Elaiw, Ahmed; Althiabi, Abdullah M; Alghamdi, Mohammed Ali

2015-03-01

This paper proposes a critical analysis of the existing literature on mathematical tools developed toward systems biology approaches and, out of this overview, develops a new approach whose main features can be briefly summarized as follows: derivation of mathematical structures suitable to capture the complexity of biological, hence living, systems, modeling, by appropriate mathematical tools, Darwinian type dynamics, namely mutations followed by selection and evolution. Moreover, multiscale methods to move from genes to cells, and from cells to tissue are analyzed in view of a new systems biology approach. Copyright © 2014 Elsevier B.V. All rights reserved.

Computational Modeling of Biological Systems From Molecules to Pathways

CERN Document Server

2012-01-01

Computational modeling is emerging as a powerful new approach for studying and manipulating biological systems. Many diverse methods have been developed to model, visualize, and rationally alter these systems at various length scales, from atomic resolution to the level of cellular pathways. Processes taking place at larger time and length scales, such as molecular evolution, have also greatly benefited from new breeds of computational approaches. Computational Modeling of Biological Systems: From Molecules to Pathways provides an overview of established computational methods for the modeling of biologically and medically relevant systems. It is suitable for researchers and professionals working in the fields of biophysics, computational biology, systems biology, and molecular medicine.

Spin Pumping in Electrodynamically Coupled Magnon-Photon Systems.

Science.gov (United States)

Bai, Lihui; Harder, M; Chen, Y P; Fan, X; Xiao, J Q; Hu, C-M

2015-06-05

We use electrical detection, in combination with microwave transmission, to investigate both resonant and nonresonant magnon-photon coupling at room temperature. Spin pumping in a dynamically coupled magnon-photon system is found to be distinctly different from previous experiments. Characteristic coupling features such as modes anticrossing, linewidth evolution, peculiar line shape, and resonance broadening are systematically measured and consistently analyzed by a theoretical model set on the foundation of classical electrodynamic coupling. Our experimental and theoretical approach paves the way for pursuing microwave coherent manipulation of pure spin current via the combination of spin pumping and magnon-photon coupling.

Systems Biology — the Broader Perspective

Directory of Open Access Journals (Sweden)

Jonathan Bard

2013-06-01

Full Text Available Systems biology has two general aims: a narrow one, which is to discover how complex networks of proteins work, and a broader one, which is to integrate the molecular and network data with the generation and function of organism phenotypes. Doing all this involves complex methodologies, but underpinning the subject are more general conceptual problems about upwards and downwards causality, complexity and information storage, and their solutions provide the constraints within which these methodologies can be used. This essay considers these general aspects and the particular role of protein networks; their functional outputs are often the processes driving phenotypic change and physiological function—networks are, in a sense, the units of systems biology much as proteins are for molecular biology. It goes on to argue that the natural language for systems-biological descriptions of biological phenomena is the mathematical graph (a set of connected facts of the general form [process] (e.g., [activates] . Such graphs not only integrate events at different levels but emphasize the distributed nature of control as well as displaying a great deal of data. The implications and successes of these ideas for physiology, pharmacology, development and evolution are briefly considered. The paper concludes with some challenges for the future.

Coupling functions: Universal insights into dynamical interaction mechanisms

Science.gov (United States)

Stankovski, Tomislav; Pereira, Tiago; McClintock, Peter V. E.; Stefanovska, Aneta

2017-10-01

The dynamical systems found in nature are rarely isolated. Instead they interact and influence each other. The coupling functions that connect them contain detailed information about the functional mechanisms underlying the interactions and prescribe the physical rule specifying how an interaction occurs. A coherent and comprehensive review is presented encompassing the rapid progress made recently in the analysis, understanding, and applications of coupling functions. The basic concepts and characteristics of coupling functions are presented through demonstrative examples of different domains, revealing the mechanisms and emphasizing their multivariate nature. The theory of coupling functions is discussed through gradually increasing complexity from strong and weak interactions to globally coupled systems and networks. A variety of methods that have been developed for the detection and reconstruction of coupling functions from measured data is described. These methods are based on different statistical techniques for dynamical inference. Stemming from physics, such methods are being applied in diverse areas of science and technology, including chemistry, biology, physiology, neuroscience, social sciences, mechanics, and secure communications. This breadth of application illustrates the universality of coupling functions for studying the interaction mechanisms of coupled dynamical systems.

Synchronization of hypernetworks of coupled dynamical systems

International Nuclear Information System (INIS)

Sorrentino, Francesco

2012-01-01

We consider the synchronization of coupled dynamical systems when different types of interactions are simultaneously present. We assume that a set of dynamical systems is coupled through the connections of two or more distinct networks (each of which corresponds to a distinct type of interaction), and we refer to such a system as a dynamical hypernetwork. Applications include neural networks made up of both electrical gap junctions and chemical synapses, the coordinated motion of shoals of fish communicating through both vision and flow sensing, and hypernetworks of coupled chaotic oscillators. We first analyze the case of a hypernetwork made up of m = 2 networks. We look for the necessary and sufficient conditions for synchronization. We attempt to reduce the linear stability problem to a master stability function (MSF) form, i.e. decoupling the effects of the coupling functions from the structure of the networks. Unfortunately, we are unable to obtain a reduction in an MSF form for the general case. However, we show that such a reduction is possible in three cases of interest: (i) the Laplacian matrices associated with the two networks commute; (ii) one of the two networks is unweighted and fully connected; and (iii) one of the two networks is such that the coupling strength from node i to node j is a function of j but not of i. Furthermore, we define a class of networks such that if either one of the two coupling networks belongs to this class, the reduction can be obtained independently of the other network. As an example of interest, we study synchronization of a neural hypernetwork for which the connections can be either chemical synapses or electrical gap junctions. We propose a generalization of our stability results to the case of hypernetworks formed of m ⩾ 2 networks. (paper)

GMD Coupling to Power Systems and Disturbance Mitigation

Energy Technology Data Exchange (ETDEWEB)

Rivera, Michael Kelly [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Bent, Russell Whitford [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

2018-01-24

Presentation includes slides on Geomagnetic Disturbance: Ground Fields; Geomagnetic Disturbance: Coupling to Bulk Electric System; Geomagnetic Disturbance: Transformers; GMD Assessment Workflow (TPL-007-1); FERC order 830; Goals; SuperMag (1 min data) Nov. 20-21, 2003 Storm (DST = -422); Spherical Harmonics; Spherical Harmonics Nov. 20-21, 2003 Storm (DST = -422); DST vs HN0,0; Fluctuations vs. DST; Fluctuations; Conclusions and Next Steps; GMD Assessment Workflow (TPL-007-1); EMP E3 Coupling to Texas 2000 Bus Model; E3 Coupling Comparison (total GIC) Varying Ground Zero; E3 Coupling Comparison (total MVAR) Varying Ground Zero; E3 Coupling Comparison (GIC) at Peak Ground Zero; E3 Coupling Comparison (GIC) at Peak Ground Zero; and Conclusion.

Boundary control of nonlinear coupled heat systems using backstepping

KAUST Repository

Bendevis, Paul

2016-10-20

A state feedback boundary controller is designed for a 2D coupled PDE system modelling heat transfer in a membrane distillation system for water desalination. Fluid is separated into two compartments with nonlinear coupling at a membrane boundary. The controller sets the temperature on one boundary in order to track a temperature difference across the membrane boundary. The control objective is achieved by an extension of backstepping methods to these coupled equations. Stability of the target system via Lyapunov like methods, and the invertibility of the integral transformation are used to show the stability of the tracking error.

Systems Biology and Stem Cell Pluripotency

DEFF Research Database (Denmark)

Mashayekhi, Kaveh; Hall, Vanessa Jane; Freude, Kristine

2016-01-01

Recent breakthroughs in stem cell biology have accelerated research in the area of regenerative medicine. Over the past years, it has become possible to derive patient-specific stem cells which can be used to generate different cell populations for potential cell therapy. Systems biological...... modeling of stem cell pluripotency and differentiation have largely been based on prior knowledge of signaling pathways, gene regulatory networks, and epigenetic factors. However, there is a great need to extend the complexity of the modeling and to integrate different types of data, which would further...... improve systems biology and its uses in the field. In this chapter, we first give a general background on stem cell biology and regenerative medicine. Stem cell potency is introduced together with the hierarchy of stem cells ranging from pluripotent embryonic stem cells (ESCs) and induced pluripotent stem...

A program code generator for multiphysics biological simulation using markup languages.

Science.gov (United States)

Amano, Akira; Kawabata, Masanari; Yamashita, Yoshiharu; Rusty Punzalan, Florencio; Shimayoshi, Takao; Kuwabara, Hiroaki; Kunieda, Yoshitoshi

2012-01-01

To cope with the complexity of the biological function simulation models, model representation with description language is becoming popular. However, simulation software itself becomes complex in these environment, thus, it is difficult to modify the simulation conditions, target computation resources or calculation methods. In the complex biological function simulation software, there are 1) model equations, 2) boundary conditions and 3) calculation schemes. Use of description model file is useful for first point and partly second point, however, third point is difficult to handle for various calculation schemes which is required for simulation models constructed from two or more elementary models. We introduce a simulation software generation system which use description language based description of coupling calculation scheme together with cell model description file. By using this software, we can easily generate biological simulation code with variety of coupling calculation schemes. To show the efficiency of our system, example of coupling calculation scheme with three elementary models are shown.

Industrial systems biology and its impact on synthetic biology of yeast cell factories.

Science.gov (United States)

Fletcher, Eugene; Krivoruchko, Anastasia; Nielsen, Jens

2016-06-01

Engineering industrial cell factories to effectively yield a desired product while dealing with industrially relevant stresses is usually the most challenging step in the development of industrial production of chemicals using microbial fermentation processes. Using synthetic biology tools, microbial cell factories such as Saccharomyces cerevisiae can be engineered to express synthetic pathways for the production of fuels, biopharmaceuticals, fragrances, and food flavors. However, directing fluxes through these synthetic pathways towards the desired product can be demanding due to complex regulation or poor gene expression. Systems biology, which applies computational tools and mathematical modeling to understand complex biological networks, can be used to guide synthetic biology design. Here, we present our perspective on how systems biology can impact synthetic biology towards the goal of developing improved yeast cell factories. Biotechnol. Bioeng. 2016;113: 1164-1170. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Oscillation death in a coupled van der Pol–Mathieu system

Indian Academy of Sciences (India)

We have shown that the system arrives at an OD regime when coupling strength ..... system as β (left axis) is decreased from a large value, while the green .... the Centre Manifold Theorem to show that this coupled system possesses an ...

Optoelectronic system and apparatus for connection to biological systems

Science.gov (United States)

Okandan, Murat; Nielson, Gregory N.

2018-03-06

The present invention relates to a biological probe structure, as well as apparatuses, systems, and methods employing this structure. In particular embodiments, the structure includes a hermetically sealed unit configured to receive and transmit one or more optical signals. Furthermore, the structure can be implanted subcutaneously and interrogated externally. In this manner, a minimally invasive method can be employed to detect, treat, and/or assess the biological target. Additional methods and systems are also provided.

A review of imaging techniques for systems biology

Directory of Open Access Journals (Sweden)

Po Ming J

2008-08-01

Full Text Available Abstract This paper presents a review of imaging techniques and of their utility in system biology. During the last decade systems biology has matured into a distinct field and imaging has been increasingly used to enable the interplay of experimental and theoretical biology. In this review, we describe and compare the roles of microscopy, ultrasound, CT (Computed Tomography, MRI (Magnetic Resonance Imaging, PET (Positron Emission Tomography, and molecular probes such as quantum dots and nanoshells in systems biology. As a unified application area among these different imaging techniques, examples in cancer targeting are highlighted.

Exchange bias in nearly perpendicularly coupled ferromagnetic/ferromagnetic system

International Nuclear Information System (INIS)

Bu, K.M.; Kwon, H.Y.; Oh, S.W.; Won, C.

2012-01-01

Exchange bias phenomena appear not only in ferromagnetic/antiferromagnetic systems but also in ferromagnetic/ferromagnetic systems in which two layers are nearly perpendicularly coupled. We investigated the origin of the symmetry-breaking mechanism and the relationship between the exchange bias and the system's energy parameters. We compared the results of computational Monte Carlo simulations with those of theoretical model calculation. We found that the exchange bias exhibited nonlinear behaviors, including sign reversal and singularities. These complicated behaviors were caused by two distinct magnetization processes depending on the interlayer coupling strength. The exchange bias reached a maximum at the transition between the two magnetization processes. - Highlights: ► Exchange bias phenomena are found in perpendicularly coupled F/F systems. ► Exchange bias exhibits nonlinear behaviors, including sign reversal and singularities. ► These complicated behaviors were caused by two distinct magnetization processes. ► Exchange bias reached a maximum at the transition between the two magnetization processes. ► We established an equation to maximize the exchange bias in perpendicularly coupled F/F system.

Density matrix of strongly coupled quantum dot - microcavity system

International Nuclear Information System (INIS)

Nguyen Van Hop

2009-01-01

Any two-level quantum system can be used as a quantum bit (qubit) - the basic element of all devices and systems for quantum information and quantum computation. Recently it was proposed to study the strongly coupled system consisting of a two-level quantum dot and a monoenergetic photon gas in a microcavity-the strongly coupled quantum dot-microcavity (QD-MC) system for short, with the Jaynes-Cumming total Hamiltonian, for the application in the quantum information processing. Different approximations were applied in the theoretical study of this system. In this work, on the basis of the exact solution of the Schrodinger equation for this system without dissipation we derive the exact formulae for its density matrix. The realization of a qubit in this system is discussed. The solution of the system of rate equation for the strongly coupled QD-MC system in the presence of the interaction with the environment was also established in the first order approximation with respect to this interaction.

Rigid-flexible coupling dynamics of three-dimensional hub-beams system

International Nuclear Information System (INIS)

Liu Jinyang; Lu Hao

2007-01-01

In the previous research of the coupling dynamics of a hub-beam system, coupling between the rotational motion of hub and the torsion deformation of beam is not taken into account since the system undergoes planar motion. Due to the small longitudinal deformation, coupling between the rotational motion of hub and the longitudinal deformation of beam is also neglected. In this paper, rigid-flexible coupling dynamics is extended to a hub-beams system with three-dimensional large overall motion. Not only coupling between the large overall motion and the bending deformation, but also coupling between the large overall motion and the torsional deformation are taken into account. In case of temperature increase, the longitudinal deformation caused by the thermal expansion is significant, such that coupling between the large overall motion and the longitudinal deformation is also investigated. Combining the characteristics of the hybrid coordinate formulation and the absolute nodal coordinate formulation, the system generalized coordinates include the relative nodal displacement and the slope of each beam element with respect to the body-fixed frame of the hub, and the variables related to the spatial large overall motion of the hub and beams. Based on precise strain-displacement relation, the geometric stiffening effect is taken into account, and the rigid-flexible coupling dynamic equations are derived using velocity variational principle. Finite element method is employed for discretization. Simulation of a hub-beams system is used to show the coupling effect between the large overall motion and the torsional deformation as well as the longitudinal deformation. Furthermore, conservation of energy in case of free motion is shown to verify the formulation

Nuclear Hybrid Energy System Modeling: RELAP5 Dynamic Coupling Capabilities

Energy Technology Data Exchange (ETDEWEB)

Piyush Sabharwall; Nolan Anderson; Haihua Zhao; Shannon Bragg-Sitton; George Mesina

2012-09-01

The nuclear hybrid energy systems (NHES) research team is currently developing a dynamic simulation of an integrated hybrid energy system. A detailed simulation of proposed NHES architectures will allow initial computational demonstration of a tightly coupled NHES to identify key reactor subsystem requirements, identify candidate reactor technologies for a hybrid system, and identify key challenges to operation of the coupled system. This work will provide a baseline for later coupling of design-specific reactor models through industry collaboration. The modeling capability addressed in this report focuses on the reactor subsystem simulation.

Continuous limits for an integrable coupling system of Toda equation hierarchy

International Nuclear Information System (INIS)

Li Li; Yu Fajun

2009-01-01

In this Letter, we present an integrable coupling system of lattice hierarchy and its continuous limits by using of Lie algebra sl(4). By introducing a complex discrete spectral problem, the integrable coupling system of Toda lattice hierarchy is derived. It is shown that a new complex lattice spectral problem converges to the integrable couplings of discrete soliton equation hierarchy, which has the integrable coupling system of C-KdV hierarchy as a new kind of continuous limit.

Continuous limits for an integrable coupling system of Toda equation hierarchy

Energy Technology Data Exchange (ETDEWEB)

Li Li [College of Maths and Systematic Science, Shenyang Normal University, Shenyang 110034 (China); Yu Fajun, E-mail: yfajun@163.co [College of Maths and Systematic Science, Shenyang Normal University, Shenyang 110034 (China)

2009-09-21

In this Letter, we present an integrable coupling system of lattice hierarchy and its continuous limits by using of Lie algebra sl(4). By introducing a complex discrete spectral problem, the integrable coupling system of Toda lattice hierarchy is derived. It is shown that a new complex lattice spectral problem converges to the integrable couplings of discrete soliton equation hierarchy, which has the integrable coupling system of C-KdV hierarchy as a new kind of continuous limit.

Electrochemical reverse engineering: A systems-level tool to probe the redox-based molecular communication of biology.

Science.gov (United States)

Li, Jinyang; Liu, Yi; Kim, Eunkyoung; March, John C; Bentley, William E; Payne, Gregory F

2017-04-01

The intestine is the site of digestion and forms a critical interface between the host and the outside world. This interface is composed of host epithelium and a complex microbiota which is "connected" through an extensive web of chemical and biological interactions that determine the balance between health and disease for the host. This biology and the associated chemical dialogues occur within a context of a steep oxygen gradient that provides the driving force for a variety of reduction and oxidation (redox) reactions. While some redox couples (e.g., catecholics) can spontaneously exchange electrons, many others are kinetically "insulated" (e.g., biothiols) allowing the biology to set and control their redox states far from equilibrium. It is well known that within cells, such non-equilibrated redox couples are poised to transfer electrons to perform reactions essential to immune defense (e.g., transfer from NADH to O 2 for reactive oxygen species, ROS, generation) and protection from such oxidative stresses (e.g., glutathione-based reduction of ROS). More recently, it has been recognized that some of these redox-active species (e.g., H 2 O 2 ) cross membranes and diffuse into the extracellular environment including lumen to transmit redox information that is received by atomically-specific receptors (e.g., cysteine-based sulfur switches) that regulate biological functions. Thus, redox has emerged as an important modality in the chemical signaling that occurs in the intestine and there have been emerging efforts to develop the experimental tools needed to probe this modality. We suggest that electrochemistry provides a unique tool to experimentally probe redox interactions at a systems level. Importantly, electrochemistry offers the potential to enlist the extensive theories established in signal processing in an effort to "reverse engineer" the molecular communication occurring in this complex biological system. Here, we review our efforts to develop this

The Neumann Type Systems and Algebro-Geometric Solutions of a System of Coupled Integrable Equations

International Nuclear Information System (INIS)

Chen Jinbing; Qiao Zhijun

2011-01-01

A system of (1+1)-dimensional coupled integrable equations is decomposed into a pair of new Neumann type systems that separate the spatial and temporal variables for this system over a symplectic submanifold. Then, the Neumann type flows associated with the coupled integrable equations are integrated on the complex tour of a Riemann surface. Finally, the algebro-geometric solutions expressed by Riemann theta functions of the system of coupled integrable equations are obtained by means of the Jacobi inversion.

Meshing Force of Misaligned Spline Coupling and the Influence on Rotor System

Directory of Open Access Journals (Sweden)

Guang Zhao

2008-01-01

Full Text Available Meshing force of misaligned spline coupling is derived, dynamic equation of rotor-spline coupling system is established based on finite element analysis, the influence of meshing force on rotor-spline coupling system is simulated by numerical integral method. According to the theoretical analysis, meshing force of spline coupling is related to coupling parameters, misalignment, transmitting torque, static misalignment, dynamic vibration displacement, and so on. The meshing force increases nonlinearly with increasing the spline thickness and static misalignment or decreasing alignment meshing distance (AMD. Stiffness of coupling relates to dynamic vibration displacement, and static misalignment is not a constant. Dynamic behaviors of rotor-spline coupling system reveal the following: 1X-rotating speed is the main response frequency of system when there is no misalignment; while 2X-rotating speed appears when misalignment is present. Moreover, when misalignment increases, vibration of the system gets intricate; shaft orbit departs from origin, and magnitudes of all frequencies increase. Research results can provide important criterions on both optimization design of spline coupling and trouble shooting of rotor systems.

A system for success: BMC Systems Biology, a new open access journal

OpenAIRE

Webb Penelope A; Hodgkinson Matt J

2007-01-01

Abstract BMC Systems Biology is the first open access journal spanning the growing field of systems biology from molecules up to ecosystems. The journal has launched as more and more institutes are founded that are similarly dedicated to this new approach. BMC Systems Biology builds on the ongoing success of the BMC series, providing a venue for all sound research in the systems-level analysis of biology.

Systems biology of neutrophil differentiation and immune response

DEFF Research Database (Denmark)

Theilgaard-Mönch, Kim; Porse, Bo T; Borregaard, Niels

2005-01-01

Systems biology has emerged as a new scientific field, which aims at investigating biological processes at the genomic and proteomic levels. Recent studies have unravelled aspects of neutrophil differentiation and immune responses at the systems level using high-throughput technologies. These stu......Systems biology has emerged as a new scientific field, which aims at investigating biological processes at the genomic and proteomic levels. Recent studies have unravelled aspects of neutrophil differentiation and immune responses at the systems level using high-throughput technologies....... These studies have identified a plethora of novel effector proteins stored in the granules of neutrophils. In addition, these studies provide evidence that neutrophil differentiation and immune response are governed by a highly coordinated transcriptional programme that regulates cellular fate and function...

Biological Potential in Serpentinizing Systems

Science.gov (United States)

Hoehler, Tori M.

2016-01-01

Generation of the microbial substrate hydrogen during serpentinization, the aqueous alteration of ultramafic rocks, has focused interest on the potential of serpentinizing systems to support biological communities or even the origin of life. However the process also generates considerable alkalinity, a challenge to life, and both pH and hydrogen concentrations vary widely across natural systems as a result of different host rock and fluid composition and differing physical and hydrogeologic conditions. Biological potential is expected to vary in concert. We examined the impact of such variability on the bioenergetics of an example metabolism, methanogenesis, using a cell-scale reactive transport model to compare rates of metabolic energy generation as a function of physicochemical environment. Potential rates vary over more than 5 orders of magnitude, including bioenergetically non-viable conditions, across the range of naturally occurring conditions. In parallel, we assayed rates of hydrogen metabolism in wells associated with the actively serpentinizing Coast Range Ophiolite, which includes conditions more alkaline and considerably less reducing than is typical of serpentinizing systems. Hydrogen metabolism is observed at pH approaching 12 but, consistent with the model predictions, biological methanogenesis is not observed.

Influence of regional hydrogeological systems at a local scale: Analyzing the coupled effects of hydrochemistry and biological activity in a Fe and CO{sub 2} rich spring

Energy Technology Data Exchange (ETDEWEB)

Menció, A., E-mail: anna.mencio@udg.edu [Grup de Geologia Aplicada i Ambiental (GAiA), Department of Environmental Sciences, University of Girona, Faculty of Sciences, Campus de Montilivi, 17071 Girona (Spain); Guasch, H., E-mail: helena.guasch@udg.edu [Grup de Recerca en Ecosistemes Continentals (GRECO), Institute of Aquatic Ecology, University of Girona, Faculty of Sciences, Campus de Montilivi, 17071 Girona (Spain); Soler, D.; Canelles, A.; Zamorano, M.; Brusi, D. [Grup de Geologia Aplicada i Ambiental (GAiA), Department of Environmental Sciences, University of Girona, Faculty of Sciences, Campus de Montilivi, 17071 Girona (Spain)

2016-11-01

A multidisciplinary approach was used in this study to determine the origin of a Fe and CO{sub 2} rich spring, an extreme freshwater system and to evaluate the coupled effects of hydrochemistry and biological activity at a local scale. An electrical resistivity tomography survey was conducted to delineate the geological context in which water emerges from a Plio-Quaternary supracrustal fault zone, and a bulk resistivity decrease was detected when CO{sub 2} rich groundwater occurred. Nine water samples, together with eight biofilm samples, and three sediment samples were taken along the spring canal for their analysis. Major ions, nutrients, and metals were analysed in water samples. Sediment analyses determined the main solid phases precipitated (mainly as CaCO{sub 3} and Fe(OH){sub 3}(a)). Biofilm analyses permitted to obtain biovolume per cell measures, total biovolume values, diatom density, chlorophyll a concentrations, and the Margalef Index values. Inverse modeling and batch reaction models were used to determine the physicochemical processes affecting the spring water, obtaining the total amount of CaCO{sub 3}/L formed; the Fe and Mn compounds, which mainly precipitated as Fe(OH){sub 3}(a) and Mn(OH){sub 2}; as well as the total CO{sub 2} released to the atmosphere. Analyzing these results together with the patterns of variation of hydrochemical and biological parameters, different interactions were observed: a) the effects of Fe inhibition in travertine formation, even though when the highest CO{sub 2} release was occurring; b) the fate and effects of chemicals limiting and/or inhibiting algal growth (mainly Fe, As and phosphate); c) the lack of coincidence between algal growth and tufa limestone precipitation; d) the relationship between some divalent metals (Mn and Co) and biotic activity. - Highlights: • Electrical resistivity tomography detected CO{sub 2} rich groundwater. • High Fe concentrations inhibits both algal growth and CaCO{sub 3

Instabilities and nonstatistical behavior in globally coupled systems

International Nuclear Information System (INIS)

Perez, G.; Cerdeira, H.A.

1992-01-01

The mean field in a globally coupled system of chaotic logistic maps does not obey the standard rules of statistics, even for systems of very large sizes. This indicates the existence of intrinsic instabilities in its evolution. Here these instabilities are related to the very nonsmooth behavior of mean values in a single logistic map, as a function of its parameter. Problems of this kind do not affect a similar system of coupled tent maps, where good statistical behavior has been found. We also explore the transition between these two regimes

On the limitations of standard statistical modeling in biological systems: a full Bayesian approach for biology.

Science.gov (United States)

Gomez-Ramirez, Jaime; Sanz, Ricardo

2013-09-01

One of the most important scientific challenges today is the quantitative and predictive understanding of biological function. Classical mathematical and computational approaches have been enormously successful in modeling inert matter, but they may be inadequate to address inherent features of biological systems. We address the conceptual and methodological obstacles that lie in the inverse problem in biological systems modeling. We introduce a full Bayesian approach (FBA), a theoretical framework to study biological function, in which probability distributions are conditional on biophysical information that physically resides in the biological system that is studied by the scientist. Copyright © 2013 Elsevier Ltd. All rights reserved.

Modeling of Coupled Chaotic Oscillators

International Nuclear Information System (INIS)

Lai, Y.; Grebogi, C.

1999-01-01

Chaotic dynamics may impose severe limits to deterministic modeling by dynamical equations of natural systems. We give theoretical argument that severe modeling difficulties may occur for high-dimensional chaotic systems in the sense that no model is able to produce reasonably long solutions that are realized by nature. We make these ideas concrete by investigating systems of coupled chaotic oscillators. They arise in many situations of physical and biological interests, and they also arise from discretization of nonlinear partial differential equations. copyright 1999 The American Physical Society

Systems biology approach to bioremediation

Energy Technology Data Exchange (ETDEWEB)

Chakraborty, Romy; Wu, Cindy H.; Hazen, Terry C.

2012-06-01

Bioremediation has historically been approached as a ‘black box’ in terms of our fundamental understanding. Thus it succeeds and fails, seldom without a complete understanding of why. Systems biology is an integrated research approach to study complex biological systems, by investigating interactions and networks at the molecular, cellular, community, and ecosystem level. The knowledge of these interactions within individual components is fundamental to understanding the dynamics of the ecosystem under investigation. Finally, understanding and modeling functional microbial community structure and stress responses in environments at all levels have tremendous implications for our fundamental understanding of hydrobiogeochemical processes and the potential for making bioremediation breakthroughs and illuminating the ‘black box’.

Vibro-acoustic modeling and analysis of a coupled acoustic system comprising a partially opened cavity coupled with a flexible plate

Science.gov (United States)

Shi, Shuangxia; Su, Zhu; Jin, Guoyong; Liu, Zhigang

2018-01-01

This paper is concerned with the modeling and solution method of a three-dimensional (3D) coupled acoustic system comprising a partially opened cavity coupled with a flexible plate and an exterior field of semi-infinite size, which is ubiquitously encountered in architectural acoustics and is a reasonable representation of many engineering occasions. A general solution method is presented to predict the dynamic behaviors of the three-dimensional (3D) acoustic coupled system, in which the displacement of the plate and the sound pressure in the cavity are respectively constructed in the form of the two-dimensional and three-dimensional modified Fourier series with several auxiliary functions introduced to ensure the uniform convergence of the solution over the entire solution domain. The effect of the opening is taken into account via the work done by the sound pressure acting at the coupling aperture that is contributed from the vibration of particles on the acoustic coupling interface and on the structural-acoustic coupling interface. Both the acoustic coupling between finite cavity and exterior field and the structural-acoustic coupling between flexible plate and interior acoustic field are considered in the vibro-acoustic modeling of the three-dimensional acoustic coupled acoustic system. The dynamic responses of the coupled structural-acoustic system are obtained using the Rayleigh-Ritz procedure based on the energy expressions for the coupled system. The accuracy and effectiveness of the proposed method are validated through numerical examples and comparison with results obtained by the boundary element analysis. Furthermore, the influence of the opening and the cavity volume on the acoustic behaviors of opened cavity system is studied.

The quantum Zeno and anti-Zeno effects with strong system-environment coupling.

Science.gov (United States)

Chaudhry, Adam Zaman

2017-05-11

To date, studies of the quantum Zeno and anti-Zeno effects focus on quantum systems that are weakly interacting with their environment. In this paper, we investigate what happens to a quantum system under the action of repeated measurements if the quantum system is strongly interacting with its environment. We consider as the quantum system a single two-level system coupled strongly to a collection of harmonic oscillators. A so-called polaron transformation is then used to make the problem in the strong system-environment coupling regime tractable. We find that the strong coupling case exhibits quantitative and qualitative differences as compared with the weak coupling case. In particular, the effective decay rate does not depend linearly on the spectral density of the environment. This then means that, in the strong coupling regime that we investigate, increasing the system-environment coupling strength can actually decrease the effective decay rate. We also consider a collection of two-level atoms coupled strongly with a common environment. In this case, we find that there are further differences between the weak and strong coupling cases since the two-level atoms can now indirectly interact with one another due to the common environment.

BetaWB - A language for modular representation of biological systems

DEFF Research Database (Denmark)

Ihekwaba, Adoha; Larcher, Roberto; Mardare, Radu Iulian

2007-01-01

A. Ihekwaba, R. Larcher, R. Mardare, C. Priami. BetaWB - A language for modular representation of biological systems. In Proc. of International Conference on Systems Biology (ICSB), 2007......A. Ihekwaba, R. Larcher, R. Mardare, C. Priami. BetaWB - A language for modular representation of biological systems. In Proc. of International Conference on Systems Biology (ICSB), 2007...

From Grouping to Coupling: A New Perceptual Organization in Vision, Psychology, and Biology

Science.gov (United States)

Pinna, Baingio; Porcheddu, Daniele; Deiana, Katia

2016-01-01

In this work, perceptual organization has been studied with the same spirit and phenomenological methods used by Gestalt psychologists. This was accomplished through new conditions that cannot be explained in terms of the classical principles of grouping. Perceptual grouping represents the way through which our visual system builds integrated elements on the basis of the maximal homogeneity among the components of the stimulus pattern. Our results demonstrated the inconsistency of organization by grouping, and more importantly, the inconsistency of the principle of similarity. On the contrary, they suggested the unique role played by the principle of dissimilarity among elements that behaves like an accent or a visual emphasis within a whole. The principle of accentuation was here considered as imparting a directional structure to the elements and to the whole object thus creating new phenomena. The salience of the resulting phenomena reveals the supremacy of dissimilarity in relation to similarity and the fact that it belongs to a further organization dynamics that we called “coupling.” In biology, coupling and its principle of accentuation are very strongly related to disruptive camouflage. Moreover, they are source of sexual attraction. They advertise the presence and elicit species identification/communication. In human beings accentuation is needed to show ourselves to others, to understand the way we dress, choose, and create clothes or invent fashion, the way we change our body accentuating several parts and hiding some others, the way we use maquillage. The existence of maquillage itself is derived from the need to accentuate something with the purpose to increase sexual attraction, to exhibit physical strength and beauty, to show or hide social status (e.g., being the king, a warrior, a priest, etc.). Last but not least, accentuation plays a basic role also in making it easier or difficult to read and understand written words. PMID:27471483

Wave failure at strong coupling in intracellular C a2 + signaling system with clustered channels

Science.gov (United States)

Li, Xiang; Wu, Yuning; Gao, Xuejuan; Cai, Meichun; Shuai, Jianwei

2018-01-01

As an important intracellular signal, C a2 + ions control diverse cellular functions. In this paper, we discuss the C a2 + signaling with a two-dimensional model in which the inositol 1,4,5-trisphosphate (I P3 ) receptor channels are distributed in clusters on the endoplasmic reticulum membrane. The wave failure at large C a2 + diffusion coupling is discussed in detail in the model. We show that with varying model parameters the wave failure is a robust behavior with either deterministic or stochastic channel dynamics. We suggest that the wave failure should be a general behavior in inhomogeneous diffusing systems with clustered excitable regions and may occur in biological C a2 + signaling systems.

Surprises of the Transformer as a Coupled Oscillator System

Science.gov (United States)

Silva, J. P.; Silvestre, A. J.

2008-01-01

We study a system of two RLC oscillators coupled through a variable mutual inductance. The system is interesting because it exhibits some peculiar features of coupled oscillators: (i) there are two natural frequencies; (ii) in general, the resonant frequencies do not coincide with the natural frequencies; (iii) the resonant frequencies of both…

[Coupling coordinated development of ecological-economic system in Loess Plateau].

Science.gov (United States)

Zhang, Qing-Feng; Wu, Fa-Qi; Wang, Li; Wang, Jian

2011-06-01

Based on system theory, a coupling coordinated development model of ecological-economic system in Loess Plateau was established, and the evaluation criteria and basic types of the coordinated development of the ecological-economic system were proposed. The county-level coupling coordinated development of the ecological-economic system was also discussed, based on the local characteristics. The interactions between the ecological and economic systems in Loess Plateau could be divided into four stages, i.e., seriously disordered development stage, mild-disordered development stage, low-level coordinated development stage, and high level well-coordinated development stage. At each stage, there existed a cyclic process of profit and loss-antagonist-running-dominant-synchronous development. The coupling development degree of the ecological-economic system in Loess Plateau was overall at a lower level, being about 62.7% of the counties at serious disorder, 30.1% of the counties at mild disorder, and 7.1% of the counties at low but coordinated level. The coupling development degree based on the model established in this study could better reflect the current social-economic and ecological environment situations, especially the status of coordination. To fully understand the coupling of ecological-economic system and to adopt appropriate development mode would be of significance to promote the county-level coordinated development in Loess Plateau.

A graphical method for reducing and relating models in systems biology.

Science.gov (United States)

Gay, Steven; Soliman, Sylvain; Fages, François

2010-09-15

In Systems Biology, an increasing collection of models of various biological processes is currently developed and made available in publicly accessible repositories, such as biomodels.net for instance, through common exchange formats such as SBML. To date, however, there is no general method to relate different models to each other by abstraction or reduction relationships, and this task is left to the modeler for re-using and coupling models. In mathematical biology, model reduction techniques have been studied for a long time, mainly in the case where a model exhibits different time scales, or different spatial phases, which can be analyzed separately. These techniques are however far too restrictive to be applied on a large scale in systems biology, and do not take into account abstractions other than time or phase decompositions. Our purpose here is to propose a general computational method for relating models together, by considering primarily the structure of the interactions and abstracting from their dynamics in a first step. We present a graph-theoretic formalism with node merge and delete operations, in which model reductions can be studied as graph matching problems. From this setting, we derive an algorithm for deciding whether there exists a reduction from one model to another, and evaluate it on the computation of the reduction relations between all SBML models of the biomodels.net repository. In particular, in the case of the numerous models of MAPK signalling, and of the circadian clock, biologically meaningful mappings between models of each class are automatically inferred from the structure of the interactions. We conclude on the generality of our graphical method, on its limits with respect to the representation of the structure of the interactions in SBML, and on some perspectives for dealing with the dynamics. The algorithms described in this article are implemented in the open-source software modeling platform BIOCHAM available at http

Problems of autonomy in coupled double-circuit systems of modern power plant automatic control systems

International Nuclear Information System (INIS)

Bilenko, V.A.; Davydov, N.I.

1979-01-01

Studied is the problem of autonomy in multicircuit systems of modern power plant automatic control systems; each part of the system has been carried out using the double-circuit scheme. Presented are the problems of neutralization of coupling between separate channels of power plant automatic control system. The conditions of autonomy in coupled double-circuit systems are obtained. The transfer functions of compensation devices are obtained and the variants of their connecting schemes are presented. Analyzed are possible variants of simplification of the coupled system adjustment process by its reduction to the series of consequent steps without using iteration procedures

Chemical event chain model of coupled genetic oscillators.

Science.gov (United States)

Jörg, David J; Morelli, Luis G; Jülicher, Frank

2018-03-01

We introduce a stochastic model of coupled genetic oscillators in which chains of chemical events involved in gene regulation and expression are represented as sequences of Poisson processes. We characterize steady states by their frequency, their quality factor, and their synchrony by the oscillator cross correlation. The steady state is determined by coupling and exhibits stochastic transitions between different modes. The interplay of stochasticity and nonlinearity leads to isolated regions in parameter space in which the coupled system works best as a biological pacemaker. Key features of the stochastic oscillations can be captured by an effective model for phase oscillators that are coupled by signals with distributed delays.

Chemical event chain model of coupled genetic oscillators

Science.gov (United States)

Jörg, David J.; Morelli, Luis G.; Jülicher, Frank

2018-03-01

We introduce a stochastic model of coupled genetic oscillators in which chains of chemical events involved in gene regulation and expression are represented as sequences of Poisson processes. We characterize steady states by their frequency, their quality factor, and their synchrony by the oscillator cross correlation. The steady state is determined by coupling and exhibits stochastic transitions between different modes. The interplay of stochasticity and nonlinearity leads to isolated regions in parameter space in which the coupled system works best as a biological pacemaker. Key features of the stochastic oscillations can be captured by an effective model for phase oscillators that are coupled by signals with distributed delays.

Persistent Memory in Single Node Delay-Coupled Reservoir Computing.

Directory of Open Access Journals (Sweden)

André David Kovac

Full Text Available Delays are ubiquitous in biological systems, ranging from genetic regulatory networks and synaptic conductances, to predator/pray population interactions. The evidence is mounting, not only to the presence of delays as physical constraints in signal propagation speed, but also to their functional role in providing dynamical diversity to the systems that comprise them. The latter observation in biological systems inspired the recent development of a computational architecture that harnesses this dynamical diversity, by delay-coupling a single nonlinear element to itself. This architecture is a particular realization of Reservoir Computing, where stimuli are injected into the system in time rather than in space as is the case with classical recurrent neural network realizations. This architecture also exhibits an internal memory which fades in time, an important prerequisite to the functioning of any reservoir computing device. However, fading memory is also a limitation to any computation that requires persistent storage. In order to overcome this limitation, the current work introduces an extended version to the single node Delay-Coupled Reservoir, that is based on trained linear feedback. We show by numerical simulations that adding task-specific linear feedback to the single node Delay-Coupled Reservoir extends the class of solvable tasks to those that require nonfading memory. We demonstrate, through several case studies, the ability of the extended system to carry out complex nonlinear computations that depend on past information, whereas the computational power of the system with fading memory alone quickly deteriorates. Our findings provide the theoretical basis for future physical realizations of a biologically-inspired ultrafast computing device with extended functionality.

Yeast systems biology to unravel the network of life

DEFF Research Database (Denmark)

Mustacchi, Roberta; Hohmann, S; Nielsen, Jens

2006-01-01

Systems biology focuses on obtaining a quantitative description of complete biological systems, even complete cellular function. In this way, it will be possible to perform computer-guided design of novel drugs, advanced therapies for treatment of complex diseases, and to perform in silico design....... Furthermore, it serves as an industrial workhorse for production of a wide range of chemicals and pharmaceuticals. Systems biology involves the combination of novel experimental techniques from different disciplines as well as functional genomics, bioinformatics and mathematical modelling, and hence no single...... laboratory has access to all the necessary competences. For this reason the Yeast Systems Biology Network (YSBN) has been established. YSBN will coordinate research efforts, in yeast systems biology and, through the recently obtained EU funding for a Coordination Action, it will be possible to set...

3S - Systematic, systemic, and systems biology and toxicology.

Science.gov (United States)

Smirnova, Lena; Kleinstreuer, Nicole; Corvi, Raffaella; Levchenko, Andre; Fitzpatrick, Suzanne C; Hartung, Thomas

2018-01-01

A biological system is more than the sum of its parts - it accomplishes many functions via synergy. Deconstructing the system down to the molecular mechanism level necessitates the complement of reconstructing functions on all levels, i.e., in our conceptualization of biology and its perturbations, our experimental models and computer modelling. Toxicology contains the somewhat arbitrary subclass "systemic toxicities"; however, there is no relevant toxic insult or general disease that is not systemic. At least inflammation and repair are involved that require coordinated signaling mechanisms across the organism. However, the more body components involved, the greater the challenge to reca-pitulate such toxicities using non-animal models. Here, the shortcomings of current systemic testing and the development of alternative approaches are summarized. We argue that we need a systematic approach to integrating existing knowledge as exemplified by systematic reviews and other evidence-based approaches. Such knowledge can guide us in modelling these systems using bioengineering and virtual computer models, i.e., via systems biology or systems toxicology approaches. Experimental multi-organ-on-chip and microphysiological systems (MPS) provide a more physiological view of the organism, facilitating more comprehensive coverage of systemic toxicities, i.e., the perturbation on organism level, without using substitute organisms (animals). The next challenge is to establish disease models, i.e., micropathophysiological systems (MPPS), to expand their utility to encompass biomedicine. Combining computational and experimental systems approaches and the chal-lenges of validating them are discussed. The suggested 3S approach promises to leverage 21st century technology and systematic thinking to achieve a paradigm change in studying systemic effects.

Dynamics of vehicle-road coupled system

CERN Document Server

Yang, Shaopu; Li, Shaohua

2015-01-01

Vehicle dynamics and road dynamics are usually considered to be two largely independent subjects. In vehicle dynamics, road surface roughness is generally regarded as random excitation of the vehicle, while in road dynamics, the vehicle is generally regarded as a moving load acting on the pavement. This book suggests a new research concept to integrate the vehicle and the road system with the help of a tire model, and establishes a cross-subject research framework dubbed vehicle-pavement coupled system dynamics. In this context, the dynamics of the vehicle, road and the vehicle-road coupled system are investigated by means of theoretical analysis, numerical simulations and field tests. This book will be a valuable resource for university professors, graduate students and engineers majoring in automotive design, mechanical engineering, highway engineering and other related areas. Shaopu Yang is a professor and deputy president of Shijiazhuang Tiedao University, China; Liqun Chen is a professor at Shanghai Univ...

Normal-Mode Splitting in a Weakly Coupled Optomechanical System

Science.gov (United States)

Rossi, Massimiliano; Kralj, Nenad; Zippilli, Stefano; Natali, Riccardo; Borrielli, Antonio; Pandraud, Gregory; Serra, Enrico; Di Giuseppe, Giovanni; Vitali, David

2018-02-01

Normal-mode splitting is the most evident signature of strong coupling between two interacting subsystems. It occurs when two subsystems exchange energy between themselves faster than they dissipate it to the environment. Here we experimentally show that a weakly coupled optomechanical system at room temperature can manifest normal-mode splitting when the pump field fluctuations are antisquashed by a phase-sensitive feedback loop operating close to its instability threshold. Under these conditions the optical cavity exhibits an effectively reduced decay rate, so that the system is effectively promoted to the strong coupling regime.

Coupled response spectrum analysis of secondary systems using uncoupled modal properties

International Nuclear Information System (INIS)

Gupta, A.K.; Jaw Jingwen

1986-01-01

A method of performing coupled response spectrum analysis of secondary systems is presented. The response spectrum specified at the base of the primary system is used as the input. The complex coupled mode shapes along with frequencies and damping values are calculated using an efficient and accurate perturbation scheme. The new method is applied to a 2 DOF secondary system coupled with a 6 DOF secondary system. The masses and the stiffness of the secondary system are varied to get nine different cases. The coupled system is subjected to El Centro (S00E, 1940) ground motion. It is shown that the response values from the present method are in good agreement with those from the coupled time history analysis. The conventional floor response spectrum method gives response values which are consistently much higher than the corresponding values from the time history analysis. It is concluded that the present method is sufficiently straightforward and efficient, and that it yields accurate response values. (orig.)

A dedicated database system for handling multi-level data in systems biology.

Science.gov (United States)

Pornputtapong, Natapol; Wanichthanarak, Kwanjeera; Nilsson, Avlant; Nookaew, Intawat; Nielsen, Jens

2014-01-01

Advances in high-throughput technologies have enabled extensive generation of multi-level omics data. These data are crucial for systems biology research, though they are complex, heterogeneous, highly dynamic, incomplete and distributed among public databases. This leads to difficulties in data accessibility and often results in errors when data are merged and integrated from varied resources. Therefore, integration and management of systems biological data remain very challenging. To overcome this, we designed and developed a dedicated database system that can serve and solve the vital issues in data management and hereby facilitate data integration, modeling and analysis in systems biology within a sole database. In addition, a yeast data repository was implemented as an integrated database environment which is operated by the database system. Two applications were implemented to demonstrate extensibility and utilization of the system. Both illustrate how the user can access the database via the web query function and implemented scripts. These scripts are specific for two sample cases: 1) Detecting the pheromone pathway in protein interaction networks; and 2) Finding metabolic reactions regulated by Snf1 kinase. In this study we present the design of database system which offers an extensible environment to efficiently capture the majority of biological entities and relations encountered in systems biology. Critical functions and control processes were designed and implemented to ensure consistent, efficient, secure and reliable transactions. The two sample cases on the yeast integrated data clearly demonstrate the value of a sole database environment for systems biology research.

Strategies for structuring interdisciplinary education in Systems Biology

DEFF Research Database (Denmark)

Cvijovic, Marija; Höfer, Thomas; Aćimović, Jure

2016-01-01

function by employing experimental data, mathematical models and computational simulations. As Systems Biology is inherently multidisciplinary, education within this field meets numerous hurdles including departmental barriers, availability of all required expertise locally, appropriate teaching material...... and example curricula. As university education at the Bachelor’s level is traditionally built upon disciplinary degrees, we believe that the most effective way to implement education in Systems Biology would be at the Master’s level, as it offers a more flexible framework. Our team of experts and active...... performers of Systems Biology education suggest here (i) a definition of the skills that students should acquire within a Master’s programme in Systems Biology, (ii) a possible basic educational curriculum with flexibility to adjust to different application areas and local research strengths, (iii...

Chaos desynchronization in strongly coupled systems

International Nuclear Information System (INIS)

Wu Ye; Liu Weiqing; Xiao, Jinghua; Zhan Meng

2007-01-01

The dynamics of chaos desynchronization in strongly coupled oscillator systems is studied. We find a new bifurcation from synchronous chaotic state, chaotic short wave bifurcation, i.e. a chaotic desynchronization attractor is new born in the systems due to chaos desynchronization. In comparison with the usual periodic short wave bifurcation, very rich but distinct phenomena are observed

Modelling Nephron Autoregulation and Synchronization in Coupled Nephron Systems

DEFF Research Database (Denmark)

Laugesen, Jakob Lund

between oscillating period-doubling systems is the topic of the larger part of the study. Since synchronization is a fundamental phenomenon in all sciences, it is treated from a general viewpoint by analyzing one of the most simple dynamical systems, the R¨ossler system, both in an externally forced...... version and in the form of two mutually coupled oscillators. The bifurcational mechanism to resonant dynamics and chaotic phase synchronization is described in detail. The transition from synchronized to non-synchronized dynamics is known to take place at a dense set of saddlenode bifurcations that run...... to exist in an externally forced nephron model and in a model of two vascular coupled nephrons, underlining that the discussed phenomena are of a common nature to forced and coupled period-doubling systems....

On the use of Locally Dense Basis Sets in the Calculation of EPR Hyperfine Couplings

DEFF Research Database (Denmark)

Hedegård, Erik D.; Sauer, Stephan P. A.; Milhøj, Birgitte O.

2013-01-01

The usage of locally dense basis sets in the calculation of Electron Paramagnetic Resonance (EPR) hyperne coupling constants is investigated at the level of Density Functional Theory (DFT) for two model systems of biologically important transition metal complexes: One for the active site in the c......The usage of locally dense basis sets in the calculation of Electron Paramagnetic Resonance (EPR) hyperne coupling constants is investigated at the level of Density Functional Theory (DFT) for two model systems of biologically important transition metal complexes: One for the active site...

On the use of locally dense basis sets in the calculation of EPR hyperfine couplings

DEFF Research Database (Denmark)

Milhøj, Birgitte Olai; Hedegård, Erik D.; Sauer, Stephan P. A.

2013-01-01

The usage of locally dense basis sets in the calculation of Electron Paramagnetic Resonance (EPR) hyperne coupling constants is investigated at the level of Density Functional Theory (DFT) for two model systems of biologically important transition metal complexes: One for the active site in the c......The usage of locally dense basis sets in the calculation of Electron Paramagnetic Resonance (EPR) hyperne coupling constants is investigated at the level of Density Functional Theory (DFT) for two model systems of biologically important transition metal complexes: One for the active site...

bcl::Cluster : A method for clustering biological molecules coupled with visualization in the Pymol Molecular Graphics System.

Science.gov (United States)

Alexander, Nathan; Woetzel, Nils; Meiler, Jens

2011-02-01

Clustering algorithms are used as data analysis tools in a wide variety of applications in Biology. Clustering has become especially important in protein structure prediction and virtual high throughput screening methods. In protein structure prediction, clustering is used to structure the conformational space of thousands of protein models. In virtual high throughput screening, databases with millions of drug-like molecules are organized by structural similarity, e.g. common scaffolds. The tree-like dendrogram structure obtained from hierarchical clustering can provide a qualitative overview of the results, which is important for focusing detailed analysis. However, in practice it is difficult to relate specific components of the dendrogram directly back to the objects of which it is comprised and to display all desired information within the two dimensions of the dendrogram. The current work presents a hierarchical agglomerative clustering method termed bcl::Cluster. bcl::Cluster utilizes the Pymol Molecular Graphics System to graphically depict dendrograms in three dimensions. This allows simultaneous display of relevant biological molecules as well as additional information about the clusters and the members comprising them.

Instabilities and nonstatistical behavior in globally coupled systems

International Nuclear Information System (INIS)

Perez, G.; Cerdeira, H.A.

1992-08-01

The mean field in a globally coupled system of chaotic logistic maps does not obey the standard rules of statistics, even for systems of very large sizes. This indicates the existence of intrinsic instabilities in its evolution. Here these instabilities are related to the very non-smooth behavior of mean values in a single logistic map, as a function of its parameter. Problems of this kind do not affect a similar system of coupled tent maps, where good statistical behavior has been found. We also explore the transition between these two regimes. (author). 15 refs, 9 figs

Redefining plant systems biology: from cell to ecosystem

NARCIS (Netherlands)

Keurentjes, J.J.B.; Angenent, G.C.; Dicke, M.; Martins Dos Santos, V.A.P.; Molenaar, J.; Van der Putten, W.H.; de Ruiter, P.C.; Struik, P.C.; Thomma, B.P.H.J.

2011-01-01

Molecular biologists typically restrict systems biology to cellular levels. By contrast, ecologists define biological systems as communities of interacting individuals at different trophic levels that process energy, nutrient and information flows. Modern plant breeding needs to increase

Multi-level and hybrid modelling approaches for systems biology.

Science.gov (United States)

Bardini, R; Politano, G; Benso, A; Di Carlo, S

2017-01-01

During the last decades, high-throughput techniques allowed for the extraction of a huge amount of data from biological systems, unveiling more of their underling complexity. Biological systems encompass a wide range of space and time scales, functioning according to flexible hierarchies of mechanisms making an intertwined and dynamic interplay of regulations. This becomes particularly evident in processes such as ontogenesis, where regulative assets change according to process context and timing, making structural phenotype and architectural complexities emerge from a single cell, through local interactions. The information collected from biological systems are naturally organized according to the functional levels composing the system itself. In systems biology, biological information often comes from overlapping but different scientific domains, each one having its own way of representing phenomena under study. That is, the different parts of the system to be modelled may be described with different formalisms. For a model to have improved accuracy and capability for making a good knowledge base, it is good to comprise different system levels, suitably handling the relative formalisms. Models which are both multi-level and hybrid satisfy both these requirements, making a very useful tool in computational systems biology. This paper reviews some of the main contributions in this field.

Electromagnetic fields in biological systems

National Research Council Canada - National Science Library

Lin, James C

2012-01-01

"Focusing on exposure, induced fields, and absorbed energy, this volume covers the interaction of electromagnetic fields and waves with biological systems, spanning static fields to terahertz waves...

Tunable promoters in synthetic and systems biology

DEFF Research Database (Denmark)

Dehli, Tore; Solem, Christian; Jensen, Peter Ruhdal

2012-01-01

in synthetic biology. A number of tools exist to manipulate the steps in between gene sequence and functional protein in living cells, but out of these the most straight-forward approach is to alter the gene expression level by manipulating the promoter sequence. Some of the promoter tuning tools available......Synthetic and systems biologists need standardized, modular and orthogonal tools yielding predictable functions in vivo. In systems biology such tools are needed to quantitatively analyze the behavior of biological systems while the efficient engineering of artificial gene networks is central...... for accomplishing such altered gene expression levels are discussed here along with examples of their use, and ideas for new tools are described. The road ahead looks very promising for synthetic and systems biologists as tools to achieve just about anything in terms of tuning and timing multiple gene expression...

Composite systems of dilute and dense couplings

International Nuclear Information System (INIS)

Raymond, J R; Saad, D

2008-01-01

Composite systems, where couplings are of two types, a combination of strong dilute and weak dense couplings of Ising spins, are examined through the replica method. The dilute and dense parts are considered to have independent canonical disordered or uniform bond distributions; mixing the models by variation of a parameter γ alongside inverse temperature β we analyse the respective thermodynamic solutions. We describe the variation in high temperature transitions as mixing occurs; in the vicinity of these transitions we exactly analyse the competing effects of the dense and sparse models. By using the replica symmetric ansatz and population dynamics we described the low temperature behaviour of mixed systems

Systems biology solutions for biochemical production challenges

DEFF Research Database (Denmark)

Hansen, Anne Sofie Lærke; Lennen, Rebecca M; Sonnenschein, Nikolaus

2017-01-01

There is an urgent need to significantly accelerate the development of microbial cell factories to produce fuels and chemicals from renewable feedstocks in order to facilitate the transition to a biobased society. Methods commonly used within the field of systems biology including omics...... characterization, genome-scale metabolic modeling, and adaptive laboratory evolution can be readily deployed in metabolic engineering projects. However, high performance strains usually carry tens of genetic modifications and need to operate in challenging environmental conditions. This additional complexity...... compared to basic science research requires pushing systems biology strategies to their limits and often spurs innovative developments that benefit fields outside metabolic engineering. Here we survey recent advanced applications of systems biology methods in engineering microbial production strains...

Synthetic Biology: Engineering Living Systems from Biophysical Principles.

Science.gov (United States)

Bartley, Bryan A; Kim, Kyung; Medley, J Kyle; Sauro, Herbert M

2017-03-28

Synthetic biology was founded as a biophysical discipline that sought explanations for the origins of life from chemical and physical first principles. Modern synthetic biology has been reinvented as an engineering discipline to design new organisms as well as to better understand fundamental biological mechanisms. However, success is still largely limited to the laboratory and transformative applications of synthetic biology are still in their infancy. Here, we review six principles of living systems and how they compare and contrast with engineered systems. We cite specific examples from the synthetic biology literature that illustrate these principles and speculate on their implications for further study. To fully realize the promise of synthetic biology, we must be aware of life's unique properties. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Bunched soliton states in weakly coupled sine-Gordon systems

DEFF Research Database (Denmark)

Grønbech-Jensen, N.; Samuelsen, Mogens Rugholm; Lomdahl, P. S.

1990-01-01

The interaction between solitons of two weakly coupled sine-Gordon systems is considered. In particular, the stability of bunched states is investigated, and perturbation results are compared with numerical results.......The interaction between solitons of two weakly coupled sine-Gordon systems is considered. In particular, the stability of bunched states is investigated, and perturbation results are compared with numerical results....

Reconstruction of ensembles of coupled time-delay systems from time series.

Science.gov (United States)

Sysoev, I V; Prokhorov, M D; Ponomarenko, V I; Bezruchko, B P

2014-06-01

We propose a method to recover from time series the parameters of coupled time-delay systems and the architecture of couplings between them. The method is based on a reconstruction of model delay-differential equations and estimation of statistical significance of couplings. It can be applied to networks composed of nonidentical nodes with an arbitrary number of unidirectional and bidirectional couplings. We test our method on chaotic and periodic time series produced by model equations of ensembles of diffusively coupled time-delay systems in the presence of noise, and apply it to experimental time series obtained from electronic oscillators with delayed feedback coupled by resistors.

Chaos synchronization of coupled hyperchaotic system

International Nuclear Information System (INIS)

Yang Lixin; Chu Yandong; Zhang Jiangang; Li Xianfeng

2009-01-01

Chaos synchronization, as an important topic, has become an active research subject in nonlinear science. Over the past two decades, chaos synchronization between nonlinear systems has been extensively studied, and many types of synchronization have been announced. This paper introduces synchronization of coupled hyperchaotic system, based on the Lapunov stability theory, asymptotic stability of the system is guaranteed by means of Lapunov function. The numerical simulation was provided in order to show the effectiveness of this method for the synchronization of the chaotic hyperchaotic Chen system and Rossler system.

Improving the security of optoelectronic delayed feedback system by parameter modulation and system coupling

Science.gov (United States)

Liu, Lingfeng; Miao, Suoxia; Cheng, Mengfan; Gao, Xiaojing

2016-02-01

A coupled system with varying parameters is proposed to improve the security of optoelectronic delayed feedback system. This system is coupled by two parameter-varied optoelectronic delayed feedback systems with chaotic modulation. Dynamics performance results show that this system has a higher complexity compared to the original one. Furthermore, this system can conceal the time delay effectively against the autocorrelation function and delayed mutual information method and can increase the dimension space of secure parameters to resist brute-force attack by introducing the digital chaotic systems.

The aims of systems biology: between molecules and organisms.

Science.gov (United States)

Noble, D

2011-05-01

The systems approach to biology has a long history. Its recent rapid resurgence at the turn of the century reflects the problems encountered in interpreting the sequencing of the genome and the failure of that immense achievement to provide rapid and direct solutions to major multi-factorial diseases. This paper argues that systems biology is necessarily multilevel and that there is no privileged level of causality in biological systems. It is an approach rather than a separate discipline. Functionality arises from biological networks that interact with the genome, the environment and the phenotype. This view of biology is very different from the gene-centred views of neo-Darwinism and molecular biology. In neuroscience, the systems approach leads naturally to 2 important conclusions: first, that the idea of 'programs' in the brain is confusing, and second, that the self is better interpreted as a process than as an object. © Georg Thieme Verlag KG Stuttgart · New York.

Stochastic Resonance in a System of Coupled Chaotic Oscillators

International Nuclear Information System (INIS)

Krawiecki, A.

1999-01-01

Noise-free stochastic resonance is investigated numerically in a system of two coupled chaotic Roessler oscillators. Periodic signal is applied either additively or multiplicatively to the coupling term. When the coupling constant is varied the oscillators lose synchronization via attractor bubbling or on-off intermittency. Properly chosen signals are analyzed which reflect the sequence of synchronized (laminar) phases and non-synchronized bursts in the time evolution of the oscillators. Maximum of the signal-to-noise ratio as a function of the coupling constant is observed. Dependence of the signal-to-noise ratio on the frequency of the periodic signal and parameter mismatch between the oscillators is investigated. Possible applications of stochastic resonance in the recovery of signals in secure communication systems based on chaotic synchronization are briefly discussed. (author)

Integrable coupling system of fractional soliton equation hierarchy

Energy Technology Data Exchange (ETDEWEB)

Yu Fajun, E-mail: yfajun@163.co [College of Maths and Systematic Science, Shenyang Normal University, Shenyang 110034 (China)

2009-10-05

In this Letter, we consider the derivatives and integrals of fractional order and present a class of the integrable coupling system of the fractional order soliton equations. The fractional order coupled Boussinesq and KdV equations are the special cases of this class. Furthermore, the fractional AKNS soliton equation hierarchy is obtained.

Relaxation of coupled nuclear spin systems

International Nuclear Information System (INIS)

Koenigsberger, E.

1985-05-01

The subject of the present work is the relaxation behaviour of scalarly coupled spin-1/2 systems. In the theoretical part the semiclassical Redfield equations are used. Dipolar (D), Chemical Shift Anisotropy (CSA) and Random Field (RF) interactions are considered as relaxation mechanisms. Cross correlations of dipolar interactions of different nuclei pairs and those between the D and the CSA mechanisms are important. The model of anisotropic molecular rotational relaxation and the extreme narrowing approximation are used to obtain the spectral density functions. The longitudinal relaxation data are analyzed into normal modes following Werbelow and Grant. The time evolution of normal modes is derived for the AX system with D-CSA cross terms. In the experimental part the hypothesis of dimerization in the cinnamic acid and the methyl cinnamate - AMX systems with DD cross terms - is corroborated by T 1 -time measurements and a calculation of the diffusion constants. In pentachlorobenzene - an AX system - taking into account of D-CSA cross terms enables the complete determination of movements anosotropy and the determination of the sign of the indirect coupling constant 1 Jsub(CH). (G.Q.)

Modelling of complex heat transfer systems by the coupling method

Energy Technology Data Exchange (ETDEWEB)

Bacot, P.; Bonfils, R.; Neveu, A.; Ribuot, J. (Centre d' Energetique de l' Ecole des Mines de Paris, 75 (France))

1985-04-01

The coupling method proposed here is designed to reduce the size of matrices which appear in the modelling of heat transfer systems. It consists in isolating the elements that can be modelled separately, and among the input variables of a component, identifying those which will couple it to another component. By grouping these types of variable, one can thus identify a so-called coupling matrix of reduced size, and relate it to the overall system. This matrix allows the calculation of the coupling temperatures as a function of external stresses, and of the state of the overall system at the previous instant. The internal temperatures of the components are determined from for previous ones. Two examples of applications are presented, one concerning a dwelling unit, and the second a solar water heater.

A coupled systems code-CFD MHD solver for fusion blanket design

Energy Technology Data Exchange (ETDEWEB)

Wolfendale, Michael J., E-mail: m.wolfendale11@imperial.ac.uk; Bluck, Michael J.

2015-10-15

Highlights: • A coupled systems code-CFD MHD solver for fusion blanket applications is proposed. • Development of a thermal hydraulic systems code with MHD capabilities is detailed. • A code coupling methodology based on the use of TCP socket communications is detailed. • Validation cases are briefly discussed for the systems code and coupled solver. - Abstract: The network of flow channels in a fusion blanket can be modelled using a 1D thermal hydraulic systems code. For more complex components such as junctions and manifolds, the simplifications employed in such codes can become invalid, requiring more detailed analyses. For magnetic confinement reactor blanket designs using a conducting fluid as coolant/breeder, the difficulties in flow modelling are particularly severe due to MHD effects. Blanket analysis is an ideal candidate for the application of a code coupling methodology, with a thermal hydraulic systems code modelling portions of the blanket amenable to 1D analysis, and CFD providing detail where necessary. A systems code, MHD-SYS, has been developed and validated against existing analyses. The code shows good agreement in the prediction of MHD pressure loss and the temperature profile in the fluid and wall regions of the blanket breeding zone. MHD-SYS has been coupled to an MHD solver developed in OpenFOAM and the coupled solver validated for test geometries in preparation for modelling blanket systems.

Coupled vibrations in horizontal and vertical rotor-bearings systems

OpenAIRE

Luneno, Jean-Claude

2010-01-01

For dynamical systems having several degrees of freedom, motion in one direction can induce motion in the other and/or vice versa. This means that there is a certain coupling between these two motions. Coupling can in some cases be a source of instability that causes self-excited vibrations in rotating machinery. In modeling hydropower rotors, couplings other than those that are the result of gyroscopic effect are normally not considered. This is due to the complexity of the reasons for coupl...

Systems Biology: Impressions from a Newcomer Graduate Student in 2016

Science.gov (United States)

Simpson, Melanie Rae

2016-01-01

As a newcomer, the philosophical basis of systems biology seems intuitive and appealing, the underlying philosophy being that the whole of a living system cannot be completely understood by the study of its individual parts. Yet answers to the questions "What is systems biology?" and "What constitutes a systems biology approach in…

Development and verification of a coupled code system RETRAN-MASTER-TORC

International Nuclear Information System (INIS)

Cho, J.Y.; Song, J.S.; Joo, H.G.; Zee, S.Q.

2004-01-01

Recently, coupled thermal-hydraulics (T-H) and three-dimensional kinetics codes have been widely used for the best-estimate simulations such as the main steam line break (MSLB) and locked rotor problems. This work is to develop and verify one of such codes by coupling the system T-H code RETRAN, the 3-D kinetics code MASTER and sub-channel analysis code TORC. The MASTER code has already been applied to such simulations after coupling with the MARS or RETRAN-3D multi-dimensional system T-H codes. The MASTER code contains a sub-channel analysis code COBRA-III C/P, and the coupled systems MARSMASTER-COBRA and RETRAN-MASTER-COBRA had been already developed and verified. With these previous studies, a new coupled system of RETRAN-MASTER-TORC is to be developed and verified for the standard best-estimate simulation code package in Korea. The TORC code has already been applied to the thermal hydraulics design of the several ABB/CE type plants and Korean Standard Nuclear Power Plants (KSNP). This justifies the choice of TORC rather than COBRA. Because the coupling between RETRAN and MASTER codes are already established and verified, this work is simplified to couple the TORC sub-channel T-H code with the MASTER neutronics code. The TORC code is a standalone code that solves the T-H equations for a given core problem from reading the input file and finally printing the converged solutions. However, in the coupled system, because TORC receives the pin power distributions from the neutronics code MASTER and transfers the T-H results to MASTER iteratively, TORC needs to be controlled by the MASTER code and does not need to solve the given problem completely at each iteration step. By this reason, the coupling of the TORC code with the MASTER code requires several modifications in the I/O treatment, flow iteration and calculation logics. The next section of this paper describes the modifications in the TORC code. The TORC control logic of the MASTER code is then followed. The

Triple-effect absorption refrigeration system with double-condenser coupling

Science.gov (United States)

DeVault, Robert C.; Biermann, Wendell J.

1993-01-01

A triple effect absorption refrigeration system is provided with a double-condenser coupling and a parallel or series circuit for feeding the refrigerant-containing absorbent solution through the high, medium, and low temperature generators utilized in the triple-effect system. The high temperature condenser receiving vaporous refrigerant from the high temperature generator is double coupled to both the medium temperature generator and the low temperature generator to enhance the internal recovery of heat within the system and thereby increase the thermal efficiency thereof.

Mathematical methods in systems biology.

Science.gov (United States)

Kashdan, Eugene; Duncan, Dominique; Parnell, Andrew; Schattler, Heinz

2016-12-01

The editors of this Special Issue of Mathematical Biosciences and Engineering were the organizers for the Third International Workshop "Mathematical Methods in System Biology" that took place on June 15-18, 2015 at the University College Dublin in Ireland. As stated in the workshop goals, we managed to attract a good mix of mathematicians and statisticians working on biological and medical applications with biologists and clinicians interested in presenting their challenging problems and looking to find mathematical and statistical tools for their solutions.

Nanoscale technology in biological systems

CERN Document Server

Greco, Ralph S; Smith, R Lane

2004-01-01

Reviewing recent accomplishments in the field of nanobiology Nanoscale Technology in Biological Systems introduces the application of nanoscale matrices to human biology. It focuses on the applications of nanotechnology fabrication to biomedical devices and discusses new physical methods for cell isolation and manipulation and intracellular communication at the molecular level. It also explores the application of nanobiology to cardiovascular diseases, oncology, transplantation, and a range of related disciplines. This book build a strong background in nanotechnology and nanobiology ideal for

The Roessler system as a model for chronotherapy

International Nuclear Information System (INIS)

Betancourt-Mar, Juvencio Alberto; Alarcon-Montelongo, Ivan Salvador; Nieto-Villar, Jose Manuel

2005-01-01

The biological systems are opened and are kept far from thermodynamics equilibrium. For these reasons, biological systems are always exposed to external perturbations, which may produce alterations on these rhythms as a consequence of coupling synchronization of the autonomous oscillator with perturbation. Coupling of therapeutic perturbations, such as drugs and radiation, on biological systems delivery to biological rhythms is known as chronotherapy. We used the Roessler system as a theoretical model for chronotherapy, generalized this formalism for chaotic behaviour. We found that when the Roessler is more dissipative, such as c increase, the systems become more robust to the perturbations

Design And Construction Of Wireless Charging System Using Inductive Coupling

Directory of Open Access Journals (Sweden)

Do Lam Mung

2015-06-01

Full Text Available Abstract Wireless charging system described by using the method of inductive coupling. In this project oscillation circuit converts DC energy to AC energytransmitter coil to transmit magnetic field by passing frequency and then induce the receiver coil. The properties of Induction coupling are wavemagnetic field-wideband rangevery shortcm efficiencyhight and operation frequencyLF-bandseveral handred kHz.The project shows as a small charging for 5V battery of phone in this method. The system bases on coupling magnetic field then designed and constructed as two parts. There are transmitter part and receiver part. The transmitter coil transmitter part transmits coupling magnetic field to receiver coil receiver part by passing frequency at about 1.67MHz. The Amperes law Biot-Savart law and Faraday law are used to calculate the inductive coupling between the transmitter coil and the receiver coil. The calculation of this law shows how many power transfer in receiver part when how many distance between the transmitter coil and the receiver coil. The system is safe for users and neighbouring electronic devices. To get more accurate wireless charging system it needs to change the design of the following keywords.

Modeling of biological intelligence for SCM system optimization.

Science.gov (United States)

Chen, Shengyong; Zheng, Yujun; Cattani, Carlo; Wang, Wanliang

2012-01-01

This article summarizes some methods from biological intelligence for modeling and optimization of supply chain management (SCM) systems, including genetic algorithms, evolutionary programming, differential evolution, swarm intelligence, artificial immune, and other biological intelligence related methods. An SCM system is adaptive, dynamic, open self-organizing, which is maintained by flows of information, materials, goods, funds, and energy. Traditional methods for modeling and optimizing complex SCM systems require huge amounts of computing resources, and biological intelligence-based solutions can often provide valuable alternatives for efficiently solving problems. The paper summarizes the recent related methods for the design and optimization of SCM systems, which covers the most widely used genetic algorithms and other evolutionary algorithms.

Modeling of Biological Intelligence for SCM System Optimization

Directory of Open Access Journals (Sweden)

Shengyong Chen

2012-01-01

Full Text Available This article summarizes some methods from biological intelligence for modeling and optimization of supply chain management (SCM systems, including genetic algorithms, evolutionary programming, differential evolution, swarm intelligence, artificial immune, and other biological intelligence related methods. An SCM system is adaptive, dynamic, open self-organizing, which is maintained by flows of information, materials, goods, funds, and energy. Traditional methods for modeling and optimizing complex SCM systems require huge amounts of computing resources, and biological intelligence-based solutions can often provide valuable alternatives for efficiently solving problems. The paper summarizes the recent related methods for the design and optimization of SCM systems, which covers the most widely used genetic algorithms and other evolutionary algorithms.

Modeling of Biological Intelligence for SCM System Optimization

Science.gov (United States)

Chen, Shengyong; Zheng, Yujun; Cattani, Carlo; Wang, Wanliang

2012-01-01

This article summarizes some methods from biological intelligence for modeling and optimization of supply chain management (SCM) systems, including genetic algorithms, evolutionary programming, differential evolution, swarm intelligence, artificial immune, and other biological intelligence related methods. An SCM system is adaptive, dynamic, open self-organizing, which is maintained by flows of information, materials, goods, funds, and energy. Traditional methods for modeling and optimizing complex SCM systems require huge amounts of computing resources, and biological intelligence-based solutions can often provide valuable alternatives for efficiently solving problems. The paper summarizes the recent related methods for the design and optimization of SCM systems, which covers the most widely used genetic algorithms and other evolutionary algorithms. PMID:22162724

Systems biology at work

NARCIS (Netherlands)

Martins Dos Santos, V.A.P.; Damborsky, J.

2010-01-01

In his editorial overview for the 2008 Special Issue on this topic, the late Jaroslav Stark pointedly noted that systems biology is no longer a niche pursuit, but a recognized discipline in its own right “noisily” coming of age [1]. Whilst general underlying principles and basic techniques are now

Multi-wing hyperchaotic attractors from coupled Lorenz systems

International Nuclear Information System (INIS)

Grassi, Giuseppe; Severance, Frank L.; Miller, Damon A.

2009-01-01

This paper illustrates an approach to generate multi-wing attractors in coupled Lorenz systems. In particular, novel four-wing (eight-wing) hyperchaotic attractors are generated by coupling two (three) identical Lorenz systems. The paper shows that the equilibria of the proposed systems have certain symmetries with respect to specific coordinate planes and the eigenvalues of the associated Jacobian matrices exhibit the property of similarity. In analogy with the original Lorenz system, where the two-wings of the butterfly attractor are located around the two equilibria with the unstable pair of complex-conjugate eigenvalues, this paper shows that the four-wings (eight-wings) of these attractors are located around the four (eight) equilibria with two (three) pairs of unstable complex-conjugate eigenvalues.

Coupling vibration research on Vehicle-bridge system

Science.gov (United States)

Zhou, Jiguo; Wang, Guihua

2018-01-01

The vehicle-bridge coupling system forms when vehicle running on a bridge. It will generate a relatively large influence on the driving comfort and driving safe when the vibration of the vehicle is bigger. A three-dimensional vehicle-bridge system with biaxial seven degrees of freedom has been establish in this paper based on finite numerical simulation. Adopting the finite element transient numerical simulation to realize the numerical simulation of vehicle-bridge system coupling vibration. Then, analyze the dynamic response of vehicle and bridge while different numbers of vehicles running on the bridge. Got the variation rule of vertical vibration of car body and bridge, and that of the contact force between the wheel and bridge deck. The research results have a reference value for the analysis about the vehicle running on a large-span cabled bridge.

8th Workshop on Coupled Descriptor Systems

CERN Document Server

Bartel, Andreas; Günther, Michael; Maten, E; Müller, Peter

2014-01-01

This book contains the proceedings of the 8th Workshop on Coupled Descriptor Systems held March 2013 in the Castle of Eringerfeld, Geseke in the neighborhood of Paderborn, Germany. It examines the wide range of current research topics in descriptor systems, including mathematical modeling, index analysis, wellposedness of problems, stiffness and different time-scales, cosimulation and splitting methods and convergence analysis. In addition, the book also presents applications from the automotive and circuit industries that show that descriptor systems provide challenging problems from the point of view of both theory and practice.   The book contains nine papers and is organized into three parts: control, simulation, and model order reduction. It will serve as an ideal resource for applied mathematicians and engineers, in particular those from mechanics and electromagnetics, who work with coupled differential equations.

Advances in Structural Biology and the Application to Biological Filament Systems.

Science.gov (United States)

Popp, David; Koh, Fujiet; Scipion, Clement P M; Ghoshdastider, Umesh; Narita, Akihiro; Holmes, Kenneth C; Robinson, Robert C

2018-04-01

Structural biology has experienced several transformative technological advances in recent years. These include: development of extremely bright X-ray sources (microfocus synchrotron beamlines and free electron lasers) and the use of electrons to extend protein crystallography to ever decreasing crystal sizes; and an increase in the resolution attainable by cryo-electron microscopy. Here we discuss the use of these techniques in general terms and highlight their application for biological filament systems, an area that is severely underrepresented in atomic resolution structures. We assemble a model of a capped tropomyosin-actin minifilament to demonstrate the utility of combining structures determined by different techniques. Finally, we survey the methods that attempt to transform high resolution structural biology into more physiological environments, such as the cell. Together these techniques promise a compelling decade for structural biology and, more importantly, they will provide exciting discoveries in understanding the designs and purposes of biological machines. © 2018 The Authors. BioEssays Published by WILEY Periodicals, Inc.

Systems biology for molecular life sciences and its impact in biomedicine.

Science.gov (United States)

Medina, Miguel Ángel

2013-03-01

Modern systems biology is already contributing to a radical transformation of molecular life sciences and biomedicine, and it is expected to have a real impact in the clinical setting in the next years. In this review, the emergence of systems biology is contextualized with a historic overview, and its present state is depicted. The present and expected future contribution of systems biology to the development of molecular medicine is underscored. Concerning the present situation, this review includes a reflection on the "inflation" of biological data and the urgent need for tools and procedures to make hidden information emerge. Descriptions of the impact of networks and models and the available resources and tools for applying them in systems biology approaches to molecular medicine are provided as well. The actual current impact of systems biology in molecular medicine is illustrated, reviewing two cases, namely, those of systems pharmacology and cancer systems biology. Finally, some of the expected contributions of systems biology to the immediate future of molecular medicine are commented.

Coupling of 3D neutronics models with the system code ATHLET

International Nuclear Information System (INIS)

Langenbuch, S.; Velkov, K.

1999-01-01

The system code ATHLET for plant transient and accident analysis has been coupled with 3D neutronics models, like QUABOX/CUBBOX, for the realistic evaluation of some specific safety problems under discussion. The considerations for the coupling approach and its realization are discussed. The specific features of the coupled code system established are explained and experience from first applications is presented. (author)

Chemical and biological activity in open flows: A dynamical system approach

International Nuclear Information System (INIS)

Tel, Tamas; Moura, Alessandro de; Grebogi, Celso; Karolyi, Gyoergy

2005-01-01

Chemical and biological processes often take place in fluid flows. Many of them, like environmental or microfluidical ones, generate filamentary patterns which have a fractal structure, due to the presence of chaos in the underlying advection dynamics. In such cases, hydrodynamical stirring strongly couples to the reactivity of the advected species: the outcome of the reaction is then typically different from that of the same reaction taking place in a well-mixed environment. Here we review recent progress in this field, which became possible due to the application of methods taken from dynamical system theory. We place special emphasis on the derivation of effective rate equations which contain singular terms expressing the fact that the reaction takes place on a moving fractal catalyst, on the unstable foliation of the reaction free advection dynamics

The effect of finite response–time in coupled dynamical systems

Indian Academy of Sciences (India)

The paper investigates synchronization in unidirectionally coupled dynamical systems wherein the influence of drive on response is cumulative: coupling signals are integrated over a time interval . A major consequence of integrative coupling is that the onset of the generalized and phase synchronization occurs at higher ...

The effect of finite response–time in coupled dynamical systems

Indian Academy of Sciences (India)

Abstract. The paper investigates synchronization in unidirectionally coupled dynamical systems wherein the influence of drive on response is cumulative: coupling signals are integrated over a time interval τ. A major consequence of integrative coupling is that the onset of the generalized and phase synchronization occurs ...

Surprises of the transformer as a coupled oscillator system

International Nuclear Information System (INIS)

Silva, J P; Silvestre, A J

2008-01-01

We study a system of two RLC oscillators coupled through a variable mutual inductance. The system is interesting because it exhibits some peculiar features of coupled oscillators: (i) there are two natural frequencies; (ii) in general, the resonant frequencies do not coincide with the natural frequencies; (iii) the resonant frequencies of both oscillators differ; (iv) for certain choices of parameters, there is only one resonant frequency, instead of the two expected

Surprises of the transformer as a coupled oscillator system

Energy Technology Data Exchange (ETDEWEB)

Silva, J P; Silvestre, A J [Instituto Superior de Engenharia de Lisboa, Rua Conselheiro EmIdio Navarro, 1950-062 Lisboa (Portugal)], E-mail: jpsilva@deea.isel.ipl.pt, E-mail: asilvestre@deq.isel.ipl.pt

2008-05-15

We study a system of two RLC oscillators coupled through a variable mutual inductance. The system is interesting because it exhibits some peculiar features of coupled oscillators: (i) there are two natural frequencies; (ii) in general, the resonant frequencies do not coincide with the natural frequencies; (iii) the resonant frequencies of both oscillators differ; (iv) for certain choices of parameters, there is only one resonant frequency, instead of the two expected.

Thermal coupling system analysis of a nuclear desalination plant

International Nuclear Information System (INIS)

Adak, A.K.; Srivastava, V.K.; Tewari, P.K.

2010-01-01

When a nuclear reactor is used to supply steam for desalination plant, the method of coupling has a significant technical and economic impact. The exact method of coupling depends upon the type of reactor and type of desalination plant. As a part of Nuclear Desalination Demonstration Project (NDDP), BARC has successfully commissioned a 4500 m 3 /day MSF desalination plant coupled to Madras Atomic Power Station (MAPS) at Kalpakkam. Desalination plant coupled to nuclear power plant of Pressurized Heavy Water Reactor (PHWR) type is a good example of dual-purpose nuclear desalination plant. This paper presents the thermal coupling system analysis of this plant along with technical and safety aspects. (author)

Plant Systems Biology (editorial)

Science.gov (United States)

In June 2003, Plant Physiology published an Arabidopsis special issue devoted to plant systems biology. The intention of Natasha Raikhel and Gloria Coruzzi, the two editors of this first-of-its-kind issue, was ‘‘to help nucleate this new effort within the plant community’’ as they considered that ‘‘...

Multilayer network modeling of integrated biological systems. Comment on "Network science of biological systems at different scales: A review" by Gosak et al.

Science.gov (United States)

De Domenico, Manlio

2018-03-01

Biological systems, from a cell to the human brain, are inherently complex. A powerful representation of such systems, described by an intricate web of relationships across multiple scales, is provided by complex networks. Recently, several studies are highlighting how simple networks - obtained by aggregating or neglecting temporal or categorical description of biological data - are not able to account for the richness of information characterizing biological systems. More complex models, namely multilayer networks, are needed to account for interdependencies, often varying across time, of biological interacting units within a cell, a tissue or parts of an organism.

Modular System for Shelves and Coasts (MOSSCO v1.0) - a flexible and multi-component framework for coupled coastal ocean ecosystem modelling

Science.gov (United States)

Lemmen, Carsten; Hofmeister, Richard; Klingbeil, Knut; Hassan Nasermoaddeli, M.; Kerimoglu, Onur; Burchard, Hans; Kösters, Frank; Wirtz, Kai W.

2018-03-01

Shelf and coastal sea processes extend from the atmosphere through the water column and into the seabed. These processes reflect intimate interactions between physical, chemical, and biological states on multiple scales. As a consequence, coastal system modelling requires a high and flexible degree of process and domain integration; this has so far hardly been achieved by current model systems. The lack of modularity and flexibility in integrated models hinders the exchange of data and model components and has historically imposed the supremacy of specific physical driver models. We present the Modular System for Shelves and Coasts (MOSSCO; http://www.mossco.de), a novel domain and process coupling system tailored but not limited to the coupling challenges of and applications in the coastal ocean. MOSSCO builds on the Earth System Modeling Framework (ESMF) and on the Framework for Aquatic Biogeochemical Models (FABM). It goes beyond existing technologies by creating a unique level of modularity in both domain and process coupling, including a clear separation of component and basic model interfaces, flexible scheduling of several tens of models, and facilitation of iterative development at the lab and the station and on the coastal ocean scale. MOSSCO is rich in metadata and its concepts are also applicable outside the coastal domain. For coastal modelling, it contains dozens of example coupling configurations and tested set-ups for coupled applications. Thus, MOSSCO addresses the technology needs of a growing marine coastal Earth system community that encompasses very different disciplines, numerical tools, and research questions.

New results for exponential synchronization of linearly coupled ordinary differential systems

International Nuclear Information System (INIS)

Tong Ping; Chen Shi-Hua

2017-01-01

This paper investigates the exponential synchronization of linearly coupled ordinary differential systems. The intrinsic nonlinear dynamics may not satisfy the QUAD condition or weak-QUAD condition. First, it gives a new method to analyze the exponential synchronization of the systems. Second, two theorems and their corollaries are proposed for the local or global exponential synchronization of the coupled systems. Finally, an application to the linearly coupled Hopfield neural networks and several simulations are provided for verifying the effectiveness of the theoretical results. (paper)

Systems biology solutions for biochemical production challenges.

Science.gov (United States)

Hansen, Anne Sofie Lærke; Lennen, Rebecca M; Sonnenschein, Nikolaus; Herrgård, Markus J

2017-06-01

There is an urgent need to significantly accelerate the development of microbial cell factories to produce fuels and chemicals from renewable feedstocks in order to facilitate the transition to a biobased society. Methods commonly used within the field of systems biology including omics characterization, genome-scale metabolic modeling, and adaptive laboratory evolution can be readily deployed in metabolic engineering projects. However, high performance strains usually carry tens of genetic modifications and need to operate in challenging environmental conditions. This additional complexity compared to basic science research requires pushing systems biology strategies to their limits and often spurs innovative developments that benefit fields outside metabolic engineering. Here we survey recent advanced applications of systems biology methods in engineering microbial production strains for biofuels and -chemicals. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

GPSR: A Resource for Genomics Proteomics and Systems Biology

Indian Academy of Sciences (India)

GPSR: A Resource for Genomics Proteomics and Systems Biology · Simple Calculation Programs for Biology Immunological Methods · Simple Calculation Programs for Biology Methods in Molecular Biology · Simple Calculation Programs for Biology Other Methods · PowerPoint Presentation · Slide 6 · Slide 7 · Prediction of ...

Advancing metabolic engineering through systems biology of industrial microorganisms

DEFF Research Database (Denmark)

Dai, Zongjie; Nielsen, Jens

2015-01-01

resources. The objective of systems biology is to gain a comprehensive and quantitative understanding of living cells and can hereby enhance our ability to characterize and predict cellular behavior. Systems biology of industrial microorganisms is therefore valuable for metabolic engineering. Here we review......Development of sustainable processes to produce bio-based compounds is necessary due to the severe environmental problems caused by the use of fossil resources. Metabolic engineering can facilitate the development of highly efficient cell factories to produce these compounds from renewable...... the application of systems biology tools for the identification of metabolic engineering targets which may lead to reduced development time for efficient cell factories. Finally, we present some perspectives of systems biology for advancing metabolic engineering further....

Coupling effects of depletion interactions in a three-sphere colloidal system

International Nuclear Information System (INIS)

Chen Ze-Shun; Dai Gang; Gao Hai-Xia; Xiao Chang-Ming

2013-01-01

In a three-sphere system, the middle sphere is acted upon by two opposite depletion forces from the other two spheres. It is found that, in this system, the two depletion forces are coupled with each other and result in a strengthened depletion force. So the difference of the depletion forces of the three-sphere system and its corresponding two two-sphere systems is introduced to describe the coupling effect of the depletion interactions. The numerical results obtained by Monte-Carlo simulations show that this coupling effect is affected by both the concentration of small spheres and the geometrical confinement. Meanwhile, it is also found that the mechanisms of the coupling effect and the effect on the depletion force from the geometry factor are the same. (interdisciplinary physics and related areas of science and technology)

Dietary antioxidant synergy in chemical and biological systems.

Science.gov (United States)

Wang, Sunan; Zhu, Fan

2017-07-24

Antioxidant (AOX) synergies have been much reported in chemical ("test-tube" based assays focusing on pure chemicals), biological (tissue culture, animal and clinical models), and food systems during the past decade. Tentative synergies differ from each other due to the composition of AOX and the quantification methods. Regeneration mechanism responsible for synergy in chemical systems has been discussed. Solvent effects could contribute to the artifacts of synergy observed in the chemical models. Synergy in chemical models may hardly be relevant to biological systems that have been much less studied. Apparent discrepancies exist in understanding the molecular mechanisms in both chemical and biological systems. This review discusses diverse variables associated with AOX synergy and molecular scenarios for explanation. Future research to better utilize the synergy is suggested.

Complex modal properties of coupled moderately light equipment-structure systems

International Nuclear Information System (INIS)

Gupta, A.K.; Jaw Jingwen

1986-01-01

A new improved perturbation method for evaluating complex modal properties of coupled equipment-structure systems is presented. The method is applicable even when the equipment is not very light, and when the secondary system (equipment) introduces static constraint on the primary system (structure). The new method is applied to nine 8DOF coupled multiply connected equipment-structure systems. It is shown that the new method yields results which are in excellent agreement with the corresponding exact results. (orig.)

It's the System, Stupid: How Systems Biology Is Transforming.

Science.gov (United States)

2010-01-01

So far, little is known about systems biology and its potential for changing how we diagnose and treat disease. That will change soon, say the systems experts, who advise payers to begin learning now about how it could make healthcare efficient.

Seasonal allergic rhinitis and systems biology-oriented biomarker discovery

NARCIS (Netherlands)

Baars, E.W.; Nierop, A.F.M.; Savelkoul, H.F.J.

2015-01-01

There is an increasing interest in science and medicine in the systems approach. Instead of the reductionist approach that focuses on the physical and chemical properties of the individual components, systems biology aims to describe, understand, and explain from the complex biological systems

Interactive analysis of systems biology molecular expression data

Directory of Open Access Journals (Sweden)

Prabhakar Sunil

2008-02-01

Full Text Available Abstract Background Systems biology aims to understand biological systems on a comprehensive scale, such that the components that make up the whole are connected to one another and work through dependent interactions. Molecular correlations and comparative studies of molecular expression are crucial to establishing interdependent connections in systems biology. The existing software packages provide limited data mining capability. The user must first generate visualization data with a preferred data mining algorithm and then upload the resulting data into the visualization package for graphic visualization of molecular relations. Results Presented is a novel interactive visual data mining application, SysNet that provides an interactive environment for the analysis of high data volume molecular expression information of most any type from biological systems. It integrates interactive graphic visualization and statistical data mining into a single package. SysNet interactively presents intermolecular correlation information with circular and heatmap layouts. It is also applicable to comparative analysis of molecular expression data, such as time course data. Conclusion The SysNet program has been utilized to analyze elemental profile changes in response to an increasing concentration of iron (Fe in growth media (an ionomics dataset. This study case demonstrates that the SysNet software is an effective platform for interactive analysis of molecular expression information in systems biology.

Tracing organizing principles: Learning from the history of systems biology

DEFF Research Database (Denmark)

Green, Sara; Wolkenhauer, Olaf

2014-01-01

on this historical background in order to increase the understanding of the motivation behind the search for general principles and to clarify different epistemic aims within systems biology. We pinpoint key aspects of earlier approaches that also underlie the current practice. These are i) the focus on relational......With the emergence of systems biology, the identification of organizing principles is being highlighted as a key research aim. Researchers attempt to “reverse engineer” the functional organization of biological systems using methodologies from mathematics, engineering and computer science while...... taking advantage of data produced by new experimental techniques. While systems biology is a relatively new approach, the quest for general principles of biological organization dates back to systems theoretic approaches in early and mid-twentieth century. The aim of this paper is to draw...

An online model composition tool for system biology models.

Science.gov (United States)

Coskun, Sarp A; Cicek, A Ercument; Lai, Nicola; Dash, Ranjan K; Ozsoyoglu, Z Meral; Ozsoyoglu, Gultekin

2013-09-05

There are multiple representation formats for Systems Biology computational models, and the Systems Biology Markup Language (SBML) is one of the most widely used. SBML is used to capture, store, and distribute computational models by Systems Biology data sources (e.g., the BioModels Database) and researchers. Therefore, there is a need for all-in-one web-based solutions that support advance SBML functionalities such as uploading, editing, composing, visualizing, simulating, querying, and browsing computational models. We present the design and implementation of the Model Composition Tool (Interface) within the PathCase-SB (PathCase Systems Biology) web portal. The tool helps users compose systems biology models to facilitate the complex process of merging systems biology models. We also present three tools that support the model composition tool, namely, (1) Model Simulation Interface that generates a visual plot of the simulation according to user's input, (2) iModel Tool as a platform for users to upload their own models to compose, and (3) SimCom Tool that provides a side by side comparison of models being composed in the same pathway. Finally, we provide a web site that hosts BioModels Database models and a separate web site that hosts SBML Test Suite models. Model composition tool (and the other three tools) can be used with little or no knowledge of the SBML document structure. For this reason, students or anyone who wants to learn about systems biology will benefit from the described functionalities. SBML Test Suite models will be a nice starting point for beginners. And, for more advanced purposes, users will able to access and employ models of the BioModels Database as well.

System-Level Coupled Modeling of Piezoelectric Vibration Energy Harvesting Systems by Joint Finite Element and Circuit Analysis

Directory of Open Access Journals (Sweden)

Congcong Cheng

2016-01-01

Full Text Available A practical piezoelectric vibration energy harvesting (PVEH system is usually composed of two coupled parts: a harvesting structure and an interface circuit. Thus, it is much necessary to build system-level coupled models for analyzing PVEH systems, so that the whole PVEH system can be optimized to obtain a high overall efficiency. In this paper, two classes of coupled models are proposed by joint finite element and circuit analysis. The first one is to integrate the equivalent circuit model of the harvesting structure with the interface circuit and the second one is to integrate the equivalent electrical impedance of the interface circuit into the finite element model of the harvesting structure. Then equivalent circuit model parameters of the harvesting structure are estimated by finite element analysis and the equivalent electrical impedance of the interface circuit is derived by circuit analysis. In the end, simulations are done to validate and compare the proposed two classes of system-level coupled models. The results demonstrate that harvested powers from the two classes of coupled models approximate to theoretic values. Thus, the proposed coupled models can be used for system-level optimizations in engineering applications.

Toward mechanical systems biology in bone.

Science.gov (United States)

Trüssel, Andreas; Müller, Ralph; Webster, Duncan

2012-11-01

Cyclic mechanical loading is perhaps the most important physiological factor regulating bone mass and shape in a way which balances optimal strength with minimal weight. This bone adaptation process spans multiple length and time scales. Forces resulting from physiological exercise at the organ scale are sensed at the cellular scale by osteocytes, which reside inside the bone matrix. Via biochemical pathways, osteocytes orchestrate the local remodeling action of osteoblasts (bone formation) and osteoclasts (bone resorption). Together these local adaptive remodeling activities sum up to strengthen bone globally at the organ scale. To resolve the underlying mechanisms it is required to identify and quantify both cause and effect across the different scales. Progress has been made at the different scales experimentally. Computational models of bone adaptation have been developed to piece together various experimental observations at the different scales into coherent and plausible mechanisms. However additional quantitative experimental validation is still required to build upon the insights which have already been achieved. In this review we discuss emerging as well as state of the art experimental and computational techniques and how they might be used in a mechanical systems biology approach to further our understanding of the mechanisms governing load induced bone adaptation, i.e., ways are outlined in which experimental and computational approaches could be coupled, in a quantitative manner to create more reliable multiscale models of bone.

Partial synchronization in a system of coupled logistic maps

DEFF Research Database (Denmark)

Taborov, A.V.; Maistrenko, Y.L; Mosekilde, Erik

1999-01-01

The phenomenon of clustering (or partial synchronization) in a system of globqally coupled chaotic oscillators is studied by means of a model of three coupled logistic maps. We determine the regions in parameter space where total and partial synchronization take place, examine the bifurcations...

SEEK: a systems biology data and model management platform.

Science.gov (United States)

Wolstencroft, Katherine; Owen, Stuart; Krebs, Olga; Nguyen, Quyen; Stanford, Natalie J; Golebiewski, Martin; Weidemann, Andreas; Bittkowski, Meik; An, Lihua; Shockley, David; Snoep, Jacky L; Mueller, Wolfgang; Goble, Carole

2015-07-11

Systems biology research typically involves the integration and analysis of heterogeneous data types in order to model and predict biological processes. Researchers therefore require tools and resources to facilitate the sharing and integration of data, and for linking of data to systems biology models. There are a large number of public repositories for storing biological data of a particular type, for example transcriptomics or proteomics, and there are several model repositories. However, this silo-type storage of data and models is not conducive to systems biology investigations. Interdependencies between multiple omics datasets and between datasets and models are essential. Researchers require an environment that will allow the management and sharing of heterogeneous data and models in the context of the experiments which created them. The SEEK is a suite of tools to support the management, sharing and exploration of data and models in systems biology. The SEEK platform provides an access-controlled, web-based environment for scientists to share and exchange data and models for day-to-day collaboration and for public dissemination. A plug-in architecture allows the linking of experiments, their protocols, data, models and results in a configurable system that is available 'off the shelf'. Tools to run model simulations, plot experimental data and assist with data annotation and standardisation combine to produce a collection of resources that support analysis as well as sharing. Underlying semantic web resources additionally extract and serve SEEK metadata in RDF (Resource Description Format). SEEK RDF enables rich semantic queries, both within SEEK and between related resources in the web of Linked Open Data. The SEEK platform has been adopted by many systems biology consortia across Europe. It is a data management environment that has a low barrier of uptake and provides rich resources for collaboration. This paper provides an update on the functions and

Advancing metabolic engineering through systems biology of industrial microorganisms.

Science.gov (United States)

Dai, Zongjie; Nielsen, Jens

2015-12-01

Development of sustainable processes to produce bio-based compounds is necessary due to the severe environmental problems caused by the use of fossil resources. Metabolic engineering can facilitate the development of highly efficient cell factories to produce these compounds from renewable resources. The objective of systems biology is to gain a comprehensive and quantitative understanding of living cells and can hereby enhance our ability to characterize and predict cellular behavior. Systems biology of industrial microorganisms is therefore valuable for metabolic engineering. Here we review the application of systems biology tools for the identification of metabolic engineering targets which may lead to reduced development time for efficient cell factories. Finally, we present some perspectives of systems biology for advancing metabolic engineering further. Copyright © 2015 Elsevier Ltd. All rights reserved.

Mediterranea Forecasting System: a focus on wave-current coupling

Science.gov (United States)

Clementi, Emanuela; Delrosso, Damiano; Pistoia, Jenny; Drudi, Massimiliano; Fratianni, Claudia; Grandi, Alessandro; Pinardi, Nadia; Oddo, Paolo; Tonani, Marina

2016-04-01

The Mediterranean Forecasting System (MFS) is a numerical ocean prediction system that produces analyses, reanalyses and short term forecasts for the entire Mediterranean Sea and its Atlantic Ocean adjacent areas. MFS became operational in the late 90's and has been developed and continuously improved in the framework of a series of EU and National funded programs and is now part of the Copernicus Marine Service. The MFS is composed by the hydrodynamic model NEMO (Nucleus for European Modelling of the Ocean) 2-way coupled with the third generation wave model WW3 (WaveWatchIII) implemented in the Mediterranean Sea with 1/16 horizontal resolution and forced by ECMWF atmospheric fields. The model solutions are corrected by the data assimilation system (3D variational scheme adapted to the oceanic assimilation problem) with a daily assimilation cycle, using a background error correlation matrix varying seasonally and in different sub-regions of the Mediterranean Sea. The focus of this work is to present the latest modelling system upgrades and the related achieved improvements. In order to evaluate the performance of the coupled system a set of experiments has been built by coupling the wave and circulation models that hourly exchange the following fields: the sea surface currents and air-sea temperature difference are transferred from NEMO model to WW3 model modifying respectively the mean momentum transfer of waves and the wind speed stability parameter; while the neutral drag coefficient computed by WW3 model is passed to NEMO that computes the turbulent component. In order to validate the modelling system, numerical results have been compared with in-situ and remote sensing data. This work suggests that a coupled model might be capable of a better description of wave-current interactions, in particular feedback from the ocean to the waves might assess an improvement on the prediction capability of wave characteristics, while suggests to proceed toward a fully

Synchronization of coupled stochastic oscillators: The effect of ...

Indian Academy of Sciences (India)

as an approximate means of accounting for a separation of time-scales between ... phase relationships between coupled oscillator systems as well as to effect a variety ... ations are often termed as internal noise since their origin is in the very ..... design and control of synthetic biological networks where synchronous ...

Genome Scale Modeling in Systems Biology: Algorithms and Resources

Science.gov (United States)

Najafi, Ali; Bidkhori, Gholamreza; Bozorgmehr, Joseph H.; Koch, Ina; Masoudi-Nejad, Ali

2014-01-01

In recent years, in silico studies and trial simulations have complemented experimental procedures. A model is a description of a system, and a system is any collection of interrelated objects; an object, moreover, is some elemental unit upon which observations can be made but whose internal structure either does not exist or is ignored. Therefore, any network analysis approach is critical for successful quantitative modeling of biological systems. This review highlights some of most popular and important modeling algorithms, tools, and emerging standards for representing, simulating and analyzing cellular networks in five sections. Also, we try to show these concepts by means of simple example and proper images and graphs. Overall, systems biology aims for a holistic description and understanding of biological processes by an integration of analytical experimental approaches along with synthetic computational models. In fact, biological networks have been developed as a platform for integrating information from high to low-throughput experiments for the analysis of biological systems. We provide an overview of all processes used in modeling and simulating biological networks in such a way that they can become easily understandable for researchers with both biological and mathematical backgrounds. Consequently, given the complexity of generated experimental data and cellular networks, it is no surprise that researchers have turned to computer simulation and the development of more theory-based approaches to augment and assist in the development of a fully quantitative understanding of cellular dynamics. PMID:24822031

Systems Biology Knowledgebase for a New Era in Biology A Genomics:GTL Report from the May 2008 Workshop

Energy Technology Data Exchange (ETDEWEB)

Gregurick, S.; Fredrickson, J. K.; Stevens, R.

2009-03-01

Biology has entered a systems-science era with the goal to establish a predictive understanding of the mechanisms of cellular function and the interactions of biological systems with their environment and with each other. Vast amounts of data on the composition, physiology, and function of complex biological systems and their natural environments are emerging from new analytical technologies. Effectively exploiting these data requires developing a new generation of capabilities for analyzing and managing the information. By revealing the core principles and processes conserved in collective genomes across all biology and by enabling insights into the interplay between an organism's genotype and its environment, systems biology will allow scientific breakthroughs in our ability to project behaviors of natural systems and to manipulate and engineer managed systems. These breakthroughs will benefit Department of Energy (DOE) missions in energy security, climate protection, and environmental remediation.

Imaging quality evaluation method of pixel coupled electro-optical imaging system

Science.gov (United States)

He, Xu; Yuan, Li; Jin, Chunqi; Zhang, Xiaohui

2017-09-01

With advancements in high-resolution imaging optical fiber bundle fabrication technology, traditional photoelectric imaging system have become ;flexible; with greatly reduced volume and weight. However, traditional image quality evaluation models are limited by the coupling discrete sampling effect of fiber-optic image bundles and charge-coupled device (CCD) pixels. This limitation substantially complicates the design, optimization, assembly, and evaluation image quality of the coupled discrete sampling imaging system. Based on the transfer process of grayscale cosine distribution optical signal in the fiber-optic image bundle and CCD, a mathematical model of coupled modulation transfer function (coupled-MTF) is established. This model can be used as a basis for following studies on the convergence and periodically oscillating characteristics of the function. We also propose the concept of the average coupled-MTF, which is consistent with the definition of traditional MTF. Based on this concept, the relationships among core distance, core layer radius, and average coupled-MTF are investigated.

Modular System for Shelves and Coasts (MOSSCO v1.0 – a flexible and multi-component framework for coupled coastal ocean ecosystem modelling

Directory of Open Access Journals (Sweden)

C. Lemmen

2018-03-01

Full Text Available Shelf and coastal sea processes extend from the atmosphere through the water column and into the seabed. These processes reflect intimate interactions between physical, chemical, and biological states on multiple scales. As a consequence, coastal system modelling requires a high and flexible degree of process and domain integration; this has so far hardly been achieved by current model systems. The lack of modularity and flexibility in integrated models hinders the exchange of data and model components and has historically imposed the supremacy of specific physical driver models. We present the Modular System for Shelves and Coasts (MOSSCO; http://www.mossco.de, a novel domain and process coupling system tailored but not limited to the coupling challenges of and applications in the coastal ocean. MOSSCO builds on the Earth System Modeling Framework (ESMF and on the Framework for Aquatic Biogeochemical Models (FABM. It goes beyond existing technologies by creating a unique level of modularity in both domain and process coupling, including a clear separation of component and basic model interfaces, flexible scheduling of several tens of models, and facilitation of iterative development at the lab and the station and on the coastal ocean scale. MOSSCO is rich in metadata and its concepts are also applicable outside the coastal domain. For coastal modelling, it contains dozens of example coupling configurations and tested set-ups for coupled applications. Thus, MOSSCO addresses the technology needs of a growing marine coastal Earth system community that encompasses very different disciplines, numerical tools, and research questions.

Exploring Synthetic and Systems Biology at the University of Edinburgh.

Science.gov (United States)

Fletcher, Liz; Rosser, Susan; Elfick, Alistair

2016-06-15

The Centre for Synthetic and Systems Biology ('SynthSys') was originally established in 2007 as the Centre for Integrative Systems Biology, funded by the Biotechnology and Biological Sciences Research Council (BBSRC) and the Engineering and Physical Sciences Research Council (EPSRC). Today, SynthSys embraces an extensive multidisciplinary community of more than 200 researchers from across the University with a common interest in synthetic and systems biology. Our research is broad and deep, addressing a diversity of scientific questions, with wide ranging impact. We bring together the power of synthetic biology and systems approaches to focus on three core thematic areas: industrial biotechnology, agriculture and the environment, and medicine and healthcare. In October 2015, we opened a newly refurbished building as a physical hub for our new U.K. Centre for Mammalian Synthetic Biology funded by the BBSRC/EPSRC/MRC as part of the U.K. Research Councils' Synthetic Biology for Growth programme. © 2016 The Author(s). published by Portland Press Limited on behalf of the Biochemical Society.

Coupled Immunological and Biomechanical Model of Emphysema Progression

Directory of Open Access Journals (Sweden)

Mario Ceresa

2018-04-01

Full Text Available Chronic Obstructive Pulmonary Disease (COPD is a disabling respiratory pathology, with a high prevalence and a significant economic and social cost. It is characterized by different clinical phenotypes with different risk profiles. Detecting the correct phenotype, especially for the emphysema subtype, and predicting the risk of major exacerbations are key elements in order to deliver more effective treatments. However, emphysema onset and progression are influenced by a complex interaction between the immune system and the mechanical properties of biological tissue. The former causes chronic inflammation and tissue remodeling. The latter influences the effective resistance or appropriate mechanical response of the lung tissue to repeated breathing cycles. In this work we present a multi-scale model of both aspects, coupling Finite Element (FE and Agent Based (AB techniques that we would like to use to predict the onset and progression of emphysema in patients. The AB part is based on existing biological models of inflammation and immunological response as a set of coupled non-linear differential equations. The FE part simulates the biomechanical effects of repeated strain on the biological tissue. We devise a strategy to couple the discrete biological model at the molecular /cellular level and the biomechanical finite element simulations at the tissue level. We tested our implementation on a public emphysema image database and found that it can indeed simulate the evolution of clinical image biomarkers during disease progression.

Generating Systems Biology Markup Language Models from the Synthetic Biology Open Language.

Science.gov (United States)

Roehner, Nicholas; Zhang, Zhen; Nguyen, Tramy; Myers, Chris J

2015-08-21

In the context of synthetic biology, model generation is the automated process of constructing biochemical models based on genetic designs. This paper discusses the use cases for model generation in genetic design automation (GDA) software tools and introduces the foundational concepts of standards and model annotation that make this process useful. Finally, this paper presents an implementation of model generation in the GDA software tool iBioSim and provides an example of generating a Systems Biology Markup Language (SBML) model from a design of a 4-input AND sensor written in the Synthetic Biology Open Language (SBOL).

Noninvasive biological sensor system for detection of drunk driving.

Science.gov (United States)

Murata, Kohji; Fujita, Etsunori; Kojima, Shigeyuki; Maeda, Shinitirou; Ogura, Yumi; Kamei, Tsutomu; Tsuji, Toshio; Kaneko, Shigehiko; Yoshizumi, Masao; Suzuki, Nobutaka

2011-01-01

Systems capable of monitoring the biological condition of a driver and issuing warnings during instances of drowsiness have recently been studied. Moreover, many researchers have reported that biological signals, such as brain waves, pulsation waves, and heart rate, are different between people who have and have not consumed alcohol. Currently, we are developing a noninvasive system to detect individuals driving under the influence of alcohol by measuring biological signals. We used the frequency time series analysis to attempt to distinguish between normal and intoxicated states of a person as the basis of the sensing system.

Evaluation of hydrogen production system coupling with HTTR using dynamic analysis code

International Nuclear Information System (INIS)

Sato, Hiroyuki; Ohashi, Hirofumi; Inaba, Yoshitomo; Nishihara, Tetsuo; Hayashi, Koji; Inagaki, Yoshiyuki

2006-01-01

The Japan Atomic Energy Agency (JAEA) was entrusted 'Development of Nuclear Heat Utilization Technology' by Ministry of Education, Culture, Sports, Science and Technology. In this development, the JAEA investigated the system integration technology to couple the hydrogen production system by steam reforming with the High Temperature Engineering Test Reactor (HTTR). Prior to the construction of the hydrogen production system coupling with the HTTR, a dynamic analysis code had to be developed to evaluate the system transient behaviour of the hydrogen production system because there are no examples of chemical facilities coupled with nuclear reactor in the world. This report describes the evaluation of the hydrogen production system coupling with HTTR using analysis code, N-HYPAC, which can estimate transient behaviour of the hydrogen production system by steam reforming. The results of this investigation provide that the influence of the thermal disturbance caused by the hydrogen production system on the HTTR can be estimated well. (author)

Coupled Dynamic Modeling of Floating Wind Turbine Systems: Preprint

Energy Technology Data Exchange (ETDEWEB)

Wayman, E. N.; Sclavounos, P. D.; Butterfield, S.; Jonkman, J.; Musial, W.

2006-03-01

This article presents a collaborative research program that the Massachusetts Institute of Technology (MIT) and the National Renewable Energy Laboratory (NREL) have undertaken to develop innovative and cost-effective floating and mooring systems for offshore wind turbines in water depths of 10-200 m. Methods for the coupled structural, hydrodynamic, and aerodynamic analysis of floating wind turbine systems are presented in the frequency domain. This analysis was conducted by coupling the aerodynamics and structural dynamics code FAST [4] developed at NREL with the wave load and response simulation code WAMIT (Wave Analysis at MIT) [15] developed at MIT. Analysis tools were developed to consider coupled interactions between the wind turbine and the floating system. These include the gyroscopic loads of the wind turbine rotor on the tower and floater, the aerodynamic damping introduced by the wind turbine rotor, the hydrodynamic damping introduced by wave-body interactions, and the hydrodynamic forces caused by wave excitation. Analyses were conducted for two floater concepts coupled with the NREL 5-MW Offshore Baseline wind turbine in water depths of 10-200 m: the MIT/NREL Shallow Drafted Barge (SDB) and the MIT/NREL Tension Leg Platform (TLP). These concepts were chosen to represent two different methods of achieving stability to identify differences in performance and cost of the different stability methods. The static and dynamic analyses of these structures evaluate the systems' responses to wave excitation at a range of frequencies, the systems' natural frequencies, and the standard deviations of the systems' motions in each degree of freedom in various wind and wave environments. This article in various wind and wave environments. This article explores the effects of coupling the wind turbine with the floating platform, the effects of water depth, and the effects of wind speed on the systems' performance. An economic feasibility analysis of

A techno-economic comparison of ground-coupled and air-coupled heat pump system for space cooling

Energy Technology Data Exchange (ETDEWEB)

Esen, Hikmet; Esen, Mehmet [Department of Mechanical Education, Faculty of Technical Education, University of Firat, 23119 Elazig (Turkey); Inalli, Mustafa [Department of Mechanical Engineering, Faculty of Engineering, University of Firat, 23119 Elazig (Turkey)

2007-05-15

This paper reports a techno-economic comparison between a ground-coupled heat pump (GCHP) system and an air-coupled heat pump (ACHP) system. The systems connected to a test room in Firat University, Elazig (38.41{sup o}N, 39.14{sup o}E), Turkey, were designed and constructed for space cooling. The performances of the GCHP and the ACHP system were experimentally determined. The experimental results were obtained from June to September in cooling season of 2004. The average cooling performance coefficients (COP{sub sys}) of the GCHP system for horizontal ground heat exchanger (HGHE) in the different trenches, at 1 and 2m depths, were obtained to be 3.85 and 4.26, respectively and the COP{sub sys} of the ACHP system was determined to be 3.17. The test results indicate that system parameters can have an important effect on performance, and that GCHP systems are economically preferable to ACHP systems for the purpose of space cooling. (author)

Matrix separation by chelation to prepare biological materials for isotopic zinc analysis by inductively coupled plasma mass spectrometry

International Nuclear Information System (INIS)

Durrant, S.F.; Krushevska, A.; Amarasiriwardena, D.; Argentine, M.D.; Romon-Guesnier, S.; Barnes, R.M.

1994-01-01

Following an evaluation of three chelating resins [Chelex-100, poly(dithiocarbamate) (PDTC) and carboxymethylated poly(ethyleneimine)-poly(methylenepolyphenylene) isocyanate (CPPI)], a procedure was established with the last of these for the separation of Zn from biological matrix elements prior to 70 Zn: 68 Zn isotopic analysis by inductively coupled plasma mass spectrometry (ICP-MS). The method was verified by establishing Zn recoveries and by determining its effectiveness in removing Cl and Na from buffered test solutions. Calcium, Na, and Zn concentration data were determined by inductively coupled plasma atomic emission spectrometry. Chlorine was measured by electrothermal vaporization ICP-MS. The efficacy of the technique was demonstrated by the determination of zinc isotope ratios in bovine milk and human urine. (Author)

Plasmons in Dimensionally Mismatched Coulomb Coupled Graphene Systems.

Science.gov (United States)

Badalyan, S M; Shylau, A A; Jauho, A P

2017-09-22

We calculate the plasmon dispersion relation for Coulomb coupled metallic armchair graphene nanoribbons and doped monolayer graphene. The crossing of the plasmon curves, which occurs for uncoupled 1D and 2D systems, is split by the interlayer Coulomb coupling into a lower and an upper plasmon branch. The upper branch exhibits an unusual behavior with end points at finite q. Accordingly, the structure factor shows either a single or a double peak behavior, depending on the plasmon wavelength. The new plasmon structure is relevant to recent experiments, its properties can be controlled by varying the system parameters and be used in plasmonic applications.

Observation of Fano-Type Interference in a Coupled Cavity-Atom System

International Nuclear Information System (INIS)

Cheng Yong; Tan Zheng; Wang Jin; Zhan Ming-Sheng; Zhu Yi-Fu

2016-01-01

We present the experimental observation of the Fano-type interference in a coupled cavity-atom system by confining the laser-cooled "8"5Rb atoms in an optical cavity. The asymmetric Fano profile is obtained through quantum interference in a three-level atomic system coherently coupled to a single mode cavity field. The observed Fano profile can be explained by the interference between the intra-cavity dark state and the polariton state of the coupled cavity-atom system. The possible applications of our observations include all-optical switching, optical sensing and narrow band optical filters. (paper)

Amplitude death induced by mixed attractive and repulsive coupling in the relay system

Science.gov (United States)

Zhao, Nannan; Sun, Zhongkui; Xu, Wei

2018-01-01

The amplitude death (AD) phenomenon is found in the relay system in the presence of the mixed couplings composed of attractive coupling and repulsive coupling. The generation mechanism of AD is revealed and shows that the middle oscillator achieving AD is a prerequisite to further suppress oscillation of the outermost oscillators for the paradigmatic Stuart-Landau and Rössler models. Moreover, regarding the Stuart-Landau relay system as a small motif of star network, we also observe that the mixed couplings can facilitate AD state of the whole network system. Particularly, the threshold of coupling strength is invariable with the change of network size. Our findings may shed a new insight to explore the effects of hybrid coupling on complex systems, also provide a new strategy to control dynamic behaviors in engineering science and neuroscience fields.

Synchronizing spiral waves in a coupled Rössler system

International Nuclear Information System (INIS)

Gao Jia-Zhen; Yang Shu-Xin; Xie Ling-Ling; Gao Ji-Hua

2011-01-01

The synchronisation of spiral patterns in a drive-response Rössler system is studied. The existence of three types of synchronisation is revealed by inspecting the coupling parameter space. Two transient stages of phase synchronisation and partial synchronisation are observed in a comparatively weak feedback coupling parameter regime, whilst complete synchronisation of spirals is found with strong negative couplings. Detailed observations of the synchronous process, such as oscillatory frequencies, parameters mismatches and amplitude variations, etc, are investigated via numerical simulations. (general)

Set membership experimental design for biological systems

Directory of Open Access Journals (Sweden)

Marvel Skylar W

2012-03-01

Full Text Available Abstract Background Experimental design approaches for biological systems are needed to help conserve the limited resources that are allocated for performing experiments. The assumptions used when assigning probability density functions to characterize uncertainty in biological systems are unwarranted when only a small number of measurements can be obtained. In these situations, the uncertainty in biological systems is more appropriately characterized in a bounded-error context. Additionally, effort must be made to improve the connection between modelers and experimentalists by relating design metrics to biologically relevant information. Bounded-error experimental design approaches that can assess the impact of additional measurements on model uncertainty are needed to identify the most appropriate balance between the collection of data and the availability of resources. Results In this work we develop a bounded-error experimental design framework for nonlinear continuous-time systems when few data measurements are available. This approach leverages many of the recent advances in bounded-error parameter and state estimation methods that use interval analysis to generate parameter sets and state bounds consistent with uncertain data measurements. We devise a novel approach using set-based uncertainty propagation to estimate measurement ranges at candidate time points. We then use these estimated measurements at the candidate time points to evaluate which candidate measurements furthest reduce model uncertainty. A method for quickly combining multiple candidate time points is presented and allows for determining the effect of adding multiple measurements. Biologically relevant metrics are developed and used to predict when new data measurements should be acquired, which system components should be measured and how many additional measurements should be obtained. Conclusions The practicability of our approach is illustrated with a case study. This

Biocellion: accelerating computer simulation of multicellular biological system models.

Science.gov (United States)

Kang, Seunghwa; Kahan, Simon; McDermott, Jason; Flann, Nicholas; Shmulevich, Ilya

2014-11-01

Biological system behaviors are often the outcome of complex interactions among a large number of cells and their biotic and abiotic environment. Computational biologists attempt to understand, predict and manipulate biological system behavior through mathematical modeling and computer simulation. Discrete agent-based modeling (in combination with high-resolution grids to model the extracellular environment) is a popular approach for building biological system models. However, the computational complexity of this approach forces computational biologists to resort to coarser resolution approaches to simulate large biological systems. High-performance parallel computers have the potential to address the computing challenge, but writing efficient software for parallel computers is difficult and time-consuming. We have developed Biocellion, a high-performance software framework, to solve this computing challenge using parallel computers. To support a wide range of multicellular biological system models, Biocellion asks users to provide their model specifics by filling the function body of pre-defined model routines. Using Biocellion, modelers without parallel computing expertise can efficiently exploit parallel computers with less effort than writing sequential programs from scratch. We simulate cell sorting, microbial patterning and a bacterial system in soil aggregate as case studies. Biocellion runs on x86 compatible systems with the 64 bit Linux operating system and is freely available for academic use. Visit http://biocellion.com for additional information. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Existence of solutions to second-order nonlinear coupled systems with nonlinear coupled boundary conditions

Directory of Open Access Journals (Sweden)

Imran Talib

2015-12-01

Full Text Available In this article, study the existence of solutions for the second-order nonlinear coupled system of ordinary differential equations $$\\displaylines{ u''(t=f(t,v(t,\\quad t\\in [0,1],\\cr v''(t=g(t,u(t,\\quad t\\in [0,1], }$$ with nonlinear coupled boundary conditions $$\\displaylines{ \\phi(u(0,v(0,u(1,v(1,u'(0,v'(0=(0,0, \\cr \\psi(u(0,v(0,u(1,v(1,u'(1,v'(1=(0,0, }$$ where $f,g:[0,1]\\times \\mathbb{R}\\to \\mathbb{R}$ and $\\phi,\\psi:\\mathbb{R}^6\\to \\mathbb{R}^2$ are continuous functions. Our main tools are coupled lower and upper solutions, Arzela-Ascoli theorem, and Schauder's fixed point theorem.

SEEK: a systems biology data and model management platform.

NARCIS (Netherlands)

Wolstencroft, K.J.; Owen, S.; Krebs, O.; Nguyen, Q.; Stanford, N.J.; Golebiewski, M.; Weidemann, A.; Bittkowski, M.; An, L.; Shockley, D.; Snoep, J.L.; Mueller, W.; Goble, C.

2015-01-01

Background: Systems biology research typically involves the integration and analysis of heterogeneous data types in order to model and predict biological processes. Researchers therefore require tools and resources to facilitate the sharing and integration of data, and for linking of data to systems

Coupled solar photo-Fenton and biological treatment for the degradation of diuron and linuron herbicides at pilot scale.

Science.gov (United States)

Farré, Maria José; Maldonado, Manuel Ignacio; Gernjak, Wolfgang; Oller, Isabel; Malato, Sixto; Domènech, Xavier; Peral, José

2008-06-01

A coupled solar photo-Fenton (chemical) and biological treatment has been used to remove biorecalcitrant diuron (42 mg l(-1)) and linuron (75 mg l(-1)) herbicides from water at pilot plant scale. The chemical process has been carried out in a 82 l solar pilot plant made up by four compound parabolic collector units, and it was followed by a biological treatment performed in a 40 l sequencing batch reactor. Two Fe(II) doses (2 and 5 mg l(-1)) and sequential additions of H2O2 (20 mg l(-1)) have been used to chemically degrade the initially polluted effluent. Next, biodegradability at different oxidation states has been assessed by means of BOD/COD ratio. A reagent dose of Fe=5 mg l(-1) and H2O2=100 mg l(-1) has been required to obtain a biodegradable effluent after 100 min of irradiation time. Finally, the organic content of the photo-treated solution has been completely assimilated by a biomass consortium in the sequencing batch reactor using a total suspended solids concentration of 0.2 g l(-1) and a hydraulic retention time of 24h. Comparison between the data obtained at pilot plant scale (specially the one corresponding to the chemical step) and previously published data from a similar system performing at laboratory scale, has been carried out.

Coupled fermion-kink system in Jackiw-Rebbi model

International Nuclear Information System (INIS)

Amado, A.; Mohammadi, A.

2017-01-01

In this paper, we study Jackiw-Rebbi model, in which a massless fermion is coupled to the kink of λφ"4 theory through a Yukawa interaction. In the original Jackiw-Rebbi model, the soliton is prescribed. However, we are interested in the back-reaction of the fermion on the soliton besides the effect of the soliton on the fermion. Also, as a particular example, we consider a minimal supersymmetric kink model in (1 + 1) dimensions. In this case, the bosonic self-coupling, λ, and the Yukawa coupling between fermion and soliton, g, have a specific relation, g = √(λ/2). As the set of coupled equations of motion of the system is not analytically solvable, we use a numerical method to solve it self-consistently. We obtain the bound energy spectrum, bound states of the system and the corresponding shape of the soliton using a relaxation method, except for the zero mode fermionic state and threshold energies which are analytically solvable. With the aid of these results, we are able to show how the soliton is affected in general and supersymmetric cases. The results we obtain are consistent with the ones in the literature, considering the soliton as background. (orig.)

Sustained currents in coupled diffusive systems

International Nuclear Information System (INIS)

Larralde, Hernán; Sanders, David P

2014-01-01

Coupling two diffusive systems may give rise to a nonequilibrium stationary state (NESS) with a non-trivial persistent, circulating current. We study a simple example that is exactly soluble, consisting of random walkers with different biases towards a reflecting boundary, modelling, for example, Brownian particles with different charge states in an electric field. We obtain analytical expressions for the concentrations and currents in the NESS for this model, and exhibit the main features of the system by numerical simulation. (paper)

Synchronization of Coupled Nonidentical Fractional-Order Hyperchaotic Systems

Directory of Open Access Journals (Sweden)

Zhouchao Wei

2011-01-01

Full Text Available Synchronization of coupled nonidentical fractional-order hyperchaotic systems is addressed by the active sliding mode method. By designing an active sliding mode controller and choosing proper control parameters, the master and slave systems are synchronized. Furthermore, synchronizing fractional-order hyperchaotic Lorenz system and fractional-order hyperchaotic Chen system is performed to show the effectiveness of the proposed controller.

Coupling of biologically active steroids to conjugating arms through ether linkages for use in immunochemistry.

Science.gov (United States)

Kohl, Michel J; Lejeune, Robert G

2002-01-01

Conjugation of haptens through ether linkages avoids leakage problems in immunoassays, but this procedure is not easily applied to most steroids that bear low reacting hydroxyls. A new technique allowing the ether coupling of biologically active steroids with conjugating arms in mild conditions compatible with thermosensitive protecting groups is presented. In the first step, the solvent (an aromatic hydrocarbon) was dehydrated by azeotropic distillation in a soxhlet apparatus using a cartridge filled with 0.3 nm and 0.4 nm molecular sieves. In this protected medium, a thallium steroid alkoxide was completely formed by reaction of the steroid with thallium ethoxide and by the continuous elimination of ethanol. The halogenated chain was then introduced into the same medium and reacted in the absence of moisture to give the ether. 17beta-Hydroxy and 11alpha-hydroxy derivatives were involved in this reaction. The coupling was effective for all of the compounds tested after 2-36 h of reaction time and at temperatures between 80 and 140 degrees C. The conjugates were at least 95% pure, and yields ranged from 15 to 95%.

Virtual lesions of the IFG abolish response facilitation for biological and non-biological cues

Directory of Open Access Journals (Sweden)

Roger D Newman-Norlund

2010-03-01

Full Text Available Humans are faster to perform a given action following observation of that same action. Converging evidence suggests that the human mirror neuron system (MNS plays an important role in this phenomenon. However, the specificity of the neural mechanisms governing this effect remain controversial. Specialist theories of imitation suggest that biological cues are maximally capable of eliciting imitative facilitation. Generalist models, on the other hand, posit a broader role for the MNS in linking visual stimuli with appropriate responses. In the present study, we investigated the validity of these two theoretical approaches by disrupting the left and right inferior frontal gyrus (IFG during the preparation of congruent (imitative and incongruent (complementary actions cued by either biological (hand or non-biological (static dot stimuli. Delivery of TMS over IFG abolished imitative response facilitation. Critically, this effect was identical whether actions were cued by biological or non-biological stimuli. This finding argues against theories of imitation in which biological stimuli are treated preferentially and stresses the notion of the IFG as a vital center of general perception-action coupling in the human brain.

The FLUKA Monte Carlo code coupled with the local effect model for biological calculations in carbon ion therapy

Energy Technology Data Exchange (ETDEWEB)

Mairani, A [University of Pavia, Department of Nuclear and Theoretical Physics, and INFN, via Bassi 6, 27100 Pavia (Italy); Brons, S; Parodi, K [Heidelberg Ion Beam Therapy Center and Department of Radiation Oncology, Im Neuenheimer Feld 450, 69120 Heidelberg (Germany); Cerutti, F; Ferrari, A; Sommerer, F [CERN, 1211 Geneva 23 (Switzerland); Fasso, A [SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States); Kraemer, M; Scholz, M, E-mail: Andrea.Mairani@mi.infn.i [GSI Biophysik, Planck-Str. 1, D-64291 Darmstadt (Germany)

2010-08-07

Clinical Monte Carlo (MC) calculations for carbon ion therapy have to provide absorbed and RBE-weighted dose. The latter is defined as the product of the dose and the relative biological effectiveness (RBE). At the GSI Helmholtzzentrum fuer Schwerionenforschung as well as at the Heidelberg Ion Therapy Center (HIT), the RBE values are calculated according to the local effect model (LEM). In this paper, we describe the approach followed for coupling the FLUKA MC code with the LEM and its application to dose and RBE-weighted dose calculations for a superimposition of two opposed {sup 12}C ion fields as applied in therapeutic irradiations. The obtained results are compared with the available experimental data of CHO (Chinese hamster ovary) cell survival and the outcomes of the GSI analytical treatment planning code TRiP98. Some discrepancies have been observed between the analytical and MC calculations of absorbed physical dose profiles, which can be explained by the differences between the laterally integrated depth-dose distributions in water used as input basic data in TRiP98 and the FLUKA recalculated ones. On the other hand, taking into account the differences in the physical beam modeling, the FLUKA-based biological calculations of the CHO cell survival profiles are found in good agreement with the experimental data as well with the TRiP98 predictions. The developed approach that combines the MC transport/interaction capability with the same biological model as in the treatment planning system (TPS) will be used at HIT to support validation/improvement of both dose and RBE-weighted dose calculations performed by the analytical TPS.

Tunable promoters in systems biology

DEFF Research Database (Denmark)

Mijakovic, Ivan; Petranovic, Dina; Jensen, Peter Ruhdal

2005-01-01

The construction of synthetic promoter libraries has represented a major breakthrough in systems biology, enabling the subtle tuning of enzyme activities. A number of tools are now available that allow the modulation of gene expression and the detection of changes in expression patterns. But, how...

The role of mechanics in biological and bio-inspired systems.

Science.gov (United States)

Egan, Paul; Sinko, Robert; LeDuc, Philip R; Keten, Sinan

2015-07-06

Natural systems frequently exploit intricate multiscale and multiphasic structures to achieve functionalities beyond those of man-made systems. Although understanding the chemical make-up of these systems is essential, the passive and active mechanics within biological systems are crucial when considering the many natural systems that achieve advanced properties, such as high strength-to-weight ratios and stimuli-responsive adaptability. Discovering how and why biological systems attain these desirable mechanical functionalities often reveals principles that inform new synthetic designs based on biological systems. Such approaches have traditionally found success in medical applications, and are now informing breakthroughs in diverse frontiers of science and engineering.

Complex biological and bio-inspired systems

Energy Technology Data Exchange (ETDEWEB)

Ecke, Robert E [Los Alamos National Laboratory

2009-01-01

The understanding and characterization ofthe fundamental processes of the function of biological systems underpins many of the important challenges facing American society, from the pathology of infectious disease and the efficacy ofvaccines, to the development of materials that mimic biological functionality and deliver exceptional and novel structural and dynamic properties. These problems are fundamentally complex, involving many interacting components and poorly understood bio-chemical kinetics. We use the basic science of statistical physics, kinetic theory, cellular bio-chemistry, soft-matter physics, and information science to develop cell level models and explore the use ofbiomimetic materials. This project seeks to determine how cell level processes, such as response to mechanical stresses, chemical constituents and related gradients, and other cell signaling mechanisms, integrate and combine to create a functioning organism. The research focuses on the basic physical processes that take place at different levels ofthe biological organism: the basic role of molecular and chemical interactions are investigated, the dynamics of the DNA-molecule and its phylogenetic role are examined and the regulatory networks of complex biochemical processes are modeled. These efforts may lead to early warning algorithms ofpathogen outbreaks, new bio-sensors to detect hazards from pathomic viruses to chemical contaminants. Other potential applications include the development of efficient bio-fuel alternative-energy processes and the exploration ofnovel materials for energy usages. Finally, we use the notion of 'coarse-graining,' which is a method for averaging over less important degrees of freedom to develop computational models to predict cell function and systems-level response to disease, chemical stress, or biological pathomic agents. This project supports Energy Security, Threat Reduction, and the missions of the DOE Office of Science through its efforts to

Heavy-ion microbeam system at JAEA-Takasaki for microbeam biology

International Nuclear Information System (INIS)

Funayama, Tomoo; Wada, Seiichi; Yokota, Yuichiro

2008-01-01

Research concerning cellular responses to low dose irradiation, radiation-induced bystander effects, and the biological track structure of charged particles has recently received particular attention in the field of radiation biology. Target irradiation employing a microbeam represents a useful means of advancing this research by obviating some of the disadvantages associated with the conventional irradiation strategies. The heavy-ion microbeam system at Japan Atomic Energy Agency (JAEA)-Takasaki, which was planned in 1987 and started in the early 1990's, can provide target irradiation of heavy charged particles to biological material at atmospheric pressure using a minimum beam size 5 μm in diameter. A variety of biological material has been irradiated using this microbeam system including cultured mammalian and higher plant cells, isolated fibers of mouse skeletal muscle, silkworm (Bombyx mori) embryos and larvae, Arabidopsis thaliana roots, and the nematode Caenorhabditis elegans. The system can be applied to the investigation of mechanisms within biological organisms not only in the context of radiation biology, but also in the fields of general biology such as physiology, developmental biology and neurobiology, and should help to establish and contribute to the field of 'microbeam biology'. (author)

Evaluation of biological hydrogen sulfide oxidation coupled with two-stage upflow filtration for groundwater treatment.

Science.gov (United States)

Levine, Audrey D; Raymer, Blake J; Jahn, Johna

2004-01-01

Hydrogen sulfide in groundwater can be oxidized by aerobic bacteria to form elemental sulfur and biomass. While this treatment approach is effective for conversion of hydrogen sulfide, it is important to have adequate control of the biomass exiting the biological treatment system to prevent release of elemental sulfur into the distribution system. Pilot scale tests were conducted on a Florida groundwater to evaluate the use of two-stage upflow filtration downstream of biological sulfur oxidation. The combined biological and filtration process was capable of excellent removal of hydrogen sulfide and associated turbidity. Additional benefits of this treatment approach include elimination of odor generation, reduction of chlorine demand, and improved stability of the finished water.

Toxin detection using a tyrosinase-coupled oxygen electrode.

Science.gov (United States)

Smit, M H; Rechnitz, G A

1993-02-15

An enzyme-based "electrochemical canary" is described for the detection of cyanide. The sensing system imitates cyanide's site of toxicity in the mitochondria. The terminal sequence of electron transfer in aerobic respiration is mimicked by mediator coupling of tyrosinase catalysis to an electro-chemical system. An enzyme-coupled oxygen electrode is created which is sensitive to selective poisoning. Biocatalytic reduction of oxygen is promoted by electrochemically supplying tyrosinase with electrons. Thus, ferrocyanide is generated at a cathode and mediates the enzymatic reduction of oxygen to water. An enzyme-dependent reductive current can be monitored which is inhibited by cyanide in a concentration-dependent manner. Oxygen depletion in the reaction layer can be minimized by addressing enzyme activity using a potential pulsing routine. Enzyme activity is electrochemically initiated and terminated and the sensor becomes capable of continuous monitoring. Cyanide poisoning of the biological component is reversible, and it can be reused after rinsing. The resulting sensor detects cyanide based on its biological activity rather than its physical or chemical properties.

Holarchical Systems and Emotional Holons : Biologically-Inspired System Designs for Control of Autonomous Aerial Vehicles

Science.gov (United States)

Ippolito, Corey; Plice, Laura; Pisanich, Greg

2003-01-01

The BEES (Bio-inspired Engineering for Exploration Systems) for Mars project at NASA Ames Research Center has the goal of developing bio-inspired flight control strategies to enable aerial explorers for Mars scientific investigations. This paper presents a summary of our ongoing research into biologically inspired system designs for control of unmanned autonomous aerial vehicle communities for Mars exploration. First, we present cooperative design considerations for robotic explorers based on the holarchical nature of biological systems and communities. Second, an outline of an architecture for cognitive decision making and control of individual robotic explorers is presented, modeled after the emotional nervous system of cognitive biological systems. Keywords: Holarchy, Biologically Inspired, Emotional UAV Flight Control

Enhancing the Relationship Adjustment of South Asian Canadian Couples Using a Systemic-Constructivist Approach to Couple Therapy.

Science.gov (United States)

Ahmad, Saunia; Reid, David W

2016-10-01

The effectiveness of systemic-constructivist couple therapy (SCCT) in improving the relationship adjustment of South Asian Canadian couples in ways that attend to their culture was evaluated. The SCCT interventions engage partners in reflexive processing of both their own and their partner's ways of construing, and the reciprocity between these two. A core change mechanism of SCCT, couple identity ("we-ness"), that connotes the ability for thinking and experiencing relationally, was coded from verbatim transcripts of partners' within-session dialogue. As predicted, South Asian partners' relationship adjustment improved significantly from the first to final session of SCCT, and concurrent increases in each partner's couple identity mediated such improvements. The implications for considering culture and couple identity in couple therapy are discussed. Video Abstract is found in the online version of the article. © 2016 American Association for Marriage and Family Therapy.

Simulation of the 1979 spring bloom in the Mid-Atlantic Bight - A coupled physical/biological/optical model

Science.gov (United States)

Gregg, Watson W.; Walsh, John J.

1992-01-01

A coupled physical/biological/optical model is developed for studies of phytoplankton variability in the spring 1979 Mid-Atlantic Bight, as observed by CZCS imagery. The model incorporates advection, mixing, sinking, growth as a function of light, temperature, nutrient availability, and death as a function of ingestion. It produced chlorophyll concentrations within the first attenuated depth within 1 standard deviation of CZCS imagery on large scale. The primary production estimates obtained using this model were within reasonable agreement with those measured in situ.

Collaborative Systems Biology Projects for the Military Medical Community.

Science.gov (United States)

Zalatoris, Jeffrey J; Scheerer, Julia B; Lebeda, Frank J

2017-09-01

This pilot study was conducted to examine, for the first time, the ongoing systems biology research and development projects within the laboratories and centers of the U.S. Army Medical Research and Materiel Command (USAMRMC). The analysis has provided an understanding of the breadth of systems biology activities, resources, and collaborations across all USAMRMC subordinate laboratories. The Systems Biology Collaboration Center at USAMRMC issued a survey regarding systems biology research projects to the eight U.S.-based USAMRMC laboratories and centers in August 2016. This survey included a data call worksheet to gather self-identified project and programmatic information. The general topics focused on the investigators and their projects, on the project's research areas, on omics and other large data types being collected and stored, on the analytical or computational tools being used, and on identifying intramural (i.e., USAMRMC) and extramural collaborations. Among seven of the eight laboratories, 62 unique systems biology studies were funded and active during the final quarter of fiscal year 2016. Of 29 preselected medical Research Task Areas, 20 were associated with these studies, some of which were applicable to two or more Research Task Areas. Overall, studies were categorized among six general types of objectives: biological mechanisms of disease, risk of/susceptibility to injury or disease, innate mechanisms of healing, diagnostic and prognostic biomarkers, and host/patient responses to vaccines, and therapeutic strategies including host responses to therapies. We identified eight types of omics studies and four types of study subjects. Studies were categorized on a scale of increasing complexity from single study subject/single omics technology studies (23/62) to studies integrating results across two study subject types and two or more omics technologies (13/62). Investigators at seven USAMRMC laboratories had collaborations with systems biology experts

Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2

Directory of Open Access Journals (Sweden)

Sorokin Anatoly

2015-06-01

Full Text Available The Systems Biological Graphical Notation (SBGN is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD, Entity Relationship (ER and Activity Flow (AF, allow for the representation of different aspects of biological and biochemical systems at different levels of detail.

Impact of systems biology on metabolic engineering of Saccharomyces cerevisiae

DEFF Research Database (Denmark)

Nielsen, Jens; Jewett, Michael Christopher

2008-01-01

in the industrial application of this yeast. Developments in genomics and high-throughput systems biology tools are enhancing one's ability to rapidly characterize cellular behaviour, which is valuable in the field of metabolic engineering where strain characterization is often the bottleneck in strain development...... programmes. Here, the impact of systems biology on metabolic engineering is reviewed and perspectives on the role of systems biology in the design of cell factories are given....

EURASIP journal on bioinformatics & systems biology

National Research Council Canada - National Science Library

2006-01-01

"The overall aim of "EURASIP Journal on Bioinformatics and Systems Biology" is to publish research results related to signal processing and bioinformatics theories and techniques relevant to a wide...

Indirect Inverse Substructuring Method for Multibody Product Transport System with Rigid and Flexible Coupling

Directory of Open Access Journals (Sweden)

Jun Wang

2015-01-01

Full Text Available The aim of this paper is to develop a new frequency response function- (FRF- based indirect inverse substructuring method without measuring system-level FRFs in the coupling DOFs for the analysis of the dynamic characteristics of a three-substructure coupled product transport system with rigid and flexible coupling. By enforcing the dynamic equilibrium conditions at the coupling coordinates and the displacement compatibility conditions, a closed-form analytical solution to inverse substructuring analysis of multisubstructure coupled product transport system is derived based on the relationship of easy-to-monitor component-level FRFs and the system-level FRFs at the coupling coordinates. The proposed method is validated by a lumped mass-spring-damper model, and the predicted coupling dynamic stiffness is compared with the direct computation, showing exact agreement. The method developed offers an approach to predict the unknown coupling dynamic stiffness from measured FRFs purely. The suggested method may help to obtain the main controlling factors and contributions from the various structure-borne paths for product transport system.

Agent-Based Modeling in Molecular Systems Biology.

Science.gov (United States)

Soheilypour, Mohammad; Mofrad, Mohammad R K

2018-06-08

Molecular systems orchestrating the biology of the cell typically involve a complex web of interactions among various components and span a vast range of spatial and temporal scales. Computational methods have advanced our understanding of the behavior of molecular systems by enabling us to test assumptions and hypotheses, explore the effect of different parameters on the outcome, and eventually guide experiments. While several different mathematical and computational methods are developed to study molecular systems at different spatiotemporal scales, there is still a need for methods that bridge the gap between spatially-detailed and computationally-efficient approaches. In this review, we summarize the capabilities of agent-based modeling (ABM) as an emerging molecular systems biology technique that provides researchers with a new tool in exploring the dynamics of molecular systems/pathways in health and disease. © 2018 WILEY Periodicals, Inc.

Study on hybrid ground-coupled heat pump systems

Energy Technology Data Exchange (ETDEWEB)

Yi, Man; Hongxing, Yang [Renewable Energy Research Group, The Hong Kong Polytechnic University, Hong Kong (China); Zhaohong, Fang [School of Thermal Energy Engineering, Shandong Architecture University, Jinan (China)

2008-07-01

Although ground-coupled heat pump (GCHP) systems are becoming attractive air-conditioning systems in some regions, the significant drawback for their wider application is the high initial cost. Besides, more energy is rejected into ground by the GCHP system installed in cooling-dominated buildings than the energy extracted from ground on an annual basis and this imbalance can result in the degradation of system performance. One of the available options that can resolve these problems is to apply the hybrid ground-coupled heat pump (HGCHP) systems, with supplemental heat rejecters for rejecting extra thermal energy when they are installed in cooling-dominated buildings. This paper presents a practical hourly simulation model of the HGCHP system by modeling the heat transfer of its main components. The computer program developed on this hourly simulation model can be used to calculate the operating data of the HGCHP system according to the building load. The design methods and running control strategies of the HGCHP system for a sample building are investigated. The simulation results show that proper HGCHP system can effectively reduce both the initial cost and the operating cost of an air-conditioning system compared with the traditional GCHP system used in cooling-dominated buildings. (author)

Marine biological data and information management system

Digital Repository Service at National Institute of Oceanography (India)

Sarupria, J.S.

Indian National Oceanographic Data Centre (INODC) is engaged in developing a marine biological data and information management system (BIODIMS). This system will contain the information on zooplankton in the water column, zoobenthic biomass...

Coalescence and Interaction of Solitons in the Coupled Korteweg-de Vries System

Science.gov (United States)

Chung, Wai Choi; Chow, Kwok Wing

2017-11-01

There are many physical systems which are governed by the classical Korteweg-de Vries equation. One of the prominent examples is the shallow water wave in fluid dynamics. In recent years, a coupled Korteweg-de Vries system has been proposed to describe fluids in a two-layer flow, and coherent structures in terms of solitons are found. We studied the coupled Korteweg-de Vries system by means of the Hirota bilinear method. Soliton and breather solutions are constructed. Localized pulses which result from the coupling of waves can be formed. The structure of the localized pulses becomes asymmetric as the control parameter varies. The coalescence and interaction of solitons in the coupled Korteweg-de Vries system will be discussed. Partial financial support has been provided by the Research Grants Council contract HKU 17200815.

Predictive modelling of complex agronomic and biological systems.

Science.gov (United States)

Keurentjes, Joost J B; Molenaar, Jaap; Zwaan, Bas J

2013-09-01

Biological systems are tremendously complex in their functioning and regulation. Studying the multifaceted behaviour and describing the performance of such complexity has challenged the scientific community for years. The reduction of real-world intricacy into simple descriptive models has therefore convinced many researchers of the usefulness of introducing mathematics into biological sciences. Predictive modelling takes such an approach another step further in that it takes advantage of existing knowledge to project the performance of a system in alternating scenarios. The ever growing amounts of available data generated by assessing biological systems at increasingly higher detail provide unique opportunities for future modelling and experiment design. Here we aim to provide an overview of the progress made in modelling over time and the currently prevalent approaches for iterative modelling cycles in modern biology. We will further argue for the importance of versatility in modelling approaches, including parameter estimation, model reduction and network reconstruction. Finally, we will discuss the difficulties in overcoming the mathematical interpretation of in vivo complexity and address some of the future challenges lying ahead. © 2013 John Wiley & Sons Ltd.

Desynchronization in coupled systems with quasiperiodic driving

DEFF Research Database (Denmark)

Vadivasova; Sosnovtseva, Olga; Balanov

2000-01-01

We describe the development of coexisting attractors in coupled quasiperiodically forced maps. The process of loss of complete synchronization in the systems, which individually demonstrates strange nonchaotic behavior, is studied. With this process, the complex structure of the basin of attraction...

Carbon nanomaterials in biological systems

Energy Technology Data Exchange (ETDEWEB)

Pu Chun Ke [Laboratory of Single-Molecule Biophysics and Polymer Physics, Department of Physics and Astronomy, Clemson University, Clemson, SC 29634 (United States); Qiao Rui [Department of Mechanical Engineering, Clemson University, Clemson, SC 29634 (United States)

2007-09-19

This paper intends to reflect, from the biophysical viewpoint, our current understanding on interfacing nanomaterials, such as carbon nanotubes and fullerenes, with biological systems. Strategies for improving the solubility, and therefore, the bioavailability of nanomaterials in aqueous solutions are summarized. In particular, the underlining mechanisms of attaching biomacromolecules (DNA, RNA, proteins) and lysophospholipids onto carbon nanotubes and gallic acids onto fullerenes are analyzed. The diffusion and the cellular delivery of RNA-coated carbon nanotubes are characterized using fluorescence microscopy. The translocation of fullerenes across cell membranes is simulated using molecular dynamics to offer new insight into the complex issue of nanotoxicity. To assess the fate of nanomaterials in the environment, the biomodification of lipid-coated carbon nanotubes by the aquatic organism Daphnia magna is discussed. The aim of this paper is to illuminate the need for adopting multidisciplinary approaches in the field study of nanomaterials in biological systems and in the environment. (topical review)

Systems Biology of the Fluxome

Directory of Open Access Journals (Sweden)

Miguel A. Aon

2015-07-01

Full Text Available The advent of high throughput -omics has made the accumulation of comprehensive data sets possible, consisting of changes in genes, transcripts, proteins and metabolites. Systems biology-inspired computational methods for translating metabolomics data into fluxomics provide a direct functional, dynamic readout of metabolic networks. When combined with appropriate experimental design, these methods deliver insightful knowledge about cellular function under diverse conditions. The use of computational models accounting for detailed kinetics and regulatory mechanisms allow us to unravel the control and regulatory properties of the fluxome under steady and time-dependent behaviors. This approach extends the analysis of complex systems from description to prediction, including control of complex dynamic behavior ranging from biological rhythms to catastrophic lethal arrhythmias. The powerful quantitative metabolomics-fluxomics approach will help our ability to engineer unicellular and multicellular organisms evolve from trial-and-error to a more predictable process, and from cells to organ and organisms.

Carbon nanomaterials in biological systems

International Nuclear Information System (INIS)

Pu Chun Ke; Qiao Rui

2007-01-01

This paper intends to reflect, from the biophysical viewpoint, our current understanding on interfacing nanomaterials, such as carbon nanotubes and fullerenes, with biological systems. Strategies for improving the solubility, and therefore, the bioavailability of nanomaterials in aqueous solutions are summarized. In particular, the underlining mechanisms of attaching biomacromolecules (DNA, RNA, proteins) and lysophospholipids onto carbon nanotubes and gallic acids onto fullerenes are analyzed. The diffusion and the cellular delivery of RNA-coated carbon nanotubes are characterized using fluorescence microscopy. The translocation of fullerenes across cell membranes is simulated using molecular dynamics to offer new insight into the complex issue of nanotoxicity. To assess the fate of nanomaterials in the environment, the biomodification of lipid-coated carbon nanotubes by the aquatic organism Daphnia magna is discussed. The aim of this paper is to illuminate the need for adopting multidisciplinary approaches in the field study of nanomaterials in biological systems and in the environment. (topical review)

From noise to synthetic nucleoli: can synthetic biology achieve new insights?

Science.gov (United States)

Ciechonska, Marta; Grob, Alice; Isalan, Mark

2016-04-18

Synthetic biology aims to re-organise and control biological components to make functional devices. Along the way, the iterative process of designing and testing gene circuits has the potential to yield many insights into the functioning of the underlying chassis of cells. Thus, synthetic biology is converging with disciplines such as systems biology and even classical cell biology, to give a new level of predictability to gene expression, cell metabolism and cellular signalling networks. This review gives an overview of the contributions that synthetic biology has made in understanding gene expression, in terms of cell heterogeneity (noise), the coupling of growth and energy usage to expression, and spatiotemporal considerations. We mainly compare progress in bacterial and mammalian systems, which have some of the most-developed engineering frameworks. Overall, one view of synthetic biology can be neatly summarised as "creating in order to understand."

Biological-Physical Coupling in the Gulf of Maine: Satellite and Model Studies of Phytoplankton Variability

Science.gov (United States)

Thomas, Andrew C.; Chai, F.; Townsend, D. W.; Xue, H.

2002-01-01

The goals of this project were to acquire, process, QC, archive and analyze SeaWiFS chlorophyll fields over the Gulf of Maine and Scotia Shelf region. The focus of the analysis effort was to calculate and quantify seasonality and interannual. variability of SeaWiFS-measured phytoplankton biomass in the study area and compare these to physical forcing and hydrography. An additional focus within this effort was on regional differences within the heterogeneous biophysical regions of the Gulf of Maine / Scotia Shelf. Overall goals were approached through the combined use of SeaWiFS and AVHRR data and the development of a coupled biology-physical numerical model.

Synchronization and Control of Linearly Coupled Singular Systems

Directory of Open Access Journals (Sweden)

Fang Qingxiang

2013-01-01

Full Text Available The synchronization and control problem of linearly coupled singular systems is investigated. The uncoupled dynamical behavior at each node is general and can be chaotic or, otherwise the coupling matrix is not assumed to be symmetrical. Some sufficient conditions for globally exponential synchronization are derived based on Lyapunov stability theory. These criteria, which are in terms of linear matrix inequality (LMI, indicate that the left and right eigenvectors corresponding to eigenvalue zero of the coupling matrix play key roles in the stability analysis of the synchronization manifold. The controllers are designed for state feedback control and pinning control, respectively. Finally, a numerical example is provided to illustrate the effectiveness of the proposed conditions.

Quantitative computational models of molecular self-assembly in systems biology.

Science.gov (United States)

Thomas, Marcus; Schwartz, Russell

2017-05-23

Molecular self-assembly is the dominant form of chemical reaction in living systems, yet efforts at systems biology modeling are only beginning to appreciate the need for and challenges to accurate quantitative modeling of self-assembly. Self-assembly reactions are essential to nearly every important process in cell and molecular biology and handling them is thus a necessary step in building comprehensive models of complex cellular systems. They present exceptional challenges, however, to standard methods for simulating complex systems. While the general systems biology world is just beginning to deal with these challenges, there is an extensive literature dealing with them for more specialized self-assembly modeling. This review will examine the challenges of self-assembly modeling, nascent efforts to deal with these challenges in the systems modeling community, and some of the solutions offered in prior work on self-assembly specifically. The review concludes with some consideration of the likely role of self-assembly in the future of complex biological system models more generally.

COSMOS: A System-Level Modelling and Simulation Framework for Coprocessor-Coupled Reconfigurable Systems

DEFF Research Database (Denmark)

Wu, Kehuai; Madsen, Jan

2007-01-01

and resource management, and iii) present a SystemC based framework to model and simulate coprocessor-coupled reconfigurable systems. We illustrate how COSMOS may be used to capture the dynamic behavior of such systems and emphasize the need for capturing the system aspects of such systems in order to deal...

Central- and autonomic nervous system coupling in schizophrenia

Science.gov (United States)

Schulz, Steffen; Bolz, Mathias; Bär, Karl-Jürgen

2016-01-01

The autonomic nervous system (ANS) dysfunction has been well described in schizophrenia (SZ), a severe mental disorder. Nevertheless, the coupling between the ANS and central brain activity has been not addressed until now in SZ. The interactions between the central nervous system (CNS) and ANS need to be considered as a feedback–feed-forward system that supports flexible and adaptive responses to specific demands. For the first time, to the best of our knowledge, this study investigates central–autonomic couplings (CAC) studying heart rate, blood pressure and electroencephalogram in paranoid schizophrenic patients, comparing them with age–gender-matched healthy subjects (CO). The emphasis is to determine how these couplings are composed by the different regulatory aspects of the CNS–ANS. We found that CAC were bidirectional, and that the causal influence of central activity towards systolic blood pressure was more strongly pronounced than such causal influence towards heart rate in paranoid schizophrenic patients when compared with CO. In paranoid schizophrenic patients, the central activity was a much stronger variable, being more random and having fewer rhythmic oscillatory components. This study provides a more in-depth understanding of the interplay of neuronal and autonomic regulatory processes in SZ and most likely greater insights into the complex relationship between psychotic stages and autonomic activity. PMID:27044986

Resolved sidebands in a strain-coupled hybrid spin-oscillator system

OpenAIRE

Teissier, Jean; Barfuss, Arne; Appel, Patrick; Neu, Elke; Maletinsky, P.

2014-01-01

We report on single electronic spins coupled to the motion of mechanical resonators by a novel mechanism based on crystal strain. Our device consists of single-crystalline diamond cantilevers with embedded Nitrogen-Vacancy center spins. Using optically detected electron spin resonance, we determine the unknown spin-strain coupling constants and demonstrate that our system resides well within the resolved sideband regime. We realize coupling strengths exceeding ten MHz under mechanical driving...

Inverse Problems in Systems Biology: A Critical Review.

Science.gov (United States)

Guzzi, Rodolfo; Colombo, Teresa; Paci, Paola

2018-01-01

Systems Biology may be assimilated to a symbiotic cyclic interplaying between the forward and inverse problems. Computational models need to be continuously refined through experiments and in turn they help us to make limited experimental resources more efficient. Every time one does an experiment we know that there will be some noise that can disrupt our measurements. Despite the noise certainly is a problem, the inverse problems already involve the inference of missing information, even if the data is entirely reliable. So the addition of a certain limited noise does not fundamentally change the situation but can be used to solve the so-called ill-posed problem, as defined by Hadamard. It can be seen as an extra source of information. Recent studies have shown that complex systems, among others the systems biology, are poorly constrained and ill-conditioned because it is difficult to use experimental data to fully estimate their parameters. For these reasons was born the concept of sloppy models, a sequence of models of increasing complexity that become sloppy in the limit of microscopic accuracy. Furthermore the concept of sloppy models contains also the concept of un-identifiability, because the models are characterized by many parameters that are poorly constrained by experimental data. Then a strategy needs to be designed to infer, analyze, and understand biological systems. The aim of this work is to provide a critical review to the inverse problems in systems biology defining a strategy to determine the minimal set of information needed to overcome the problems arising from dynamic biological models that generally may have many unknown, non-measurable parameters.

Integration of ecological-biological thresholds in conservation decision making.

Science.gov (United States)

Mavrommati, Georgia; Bithas, Kostas; Borsuk, Mark E; Howarth, Richard B

2016-12-01

In the Anthropocene, coupled human and natural systems dominate and only a few natural systems remain relatively unaffected by human influence. On the one hand, conservation criteria based on areas of minimal human impact are not relevant to much of the biosphere. On the other hand, conservation criteria based on economic factors are problematic with respect to their ability to arrive at operational indicators of well-being that can be applied in practice over multiple generations. Coupled human and natural systems are subject to economic development which, under current management structures, tends to affect natural systems and cross planetary boundaries. Hence, designing and applying conservation criteria applicable in real-world systems where human and natural systems need to interact and sustainably coexist is essential. By recognizing the criticality of satisfying basic needs as well as the great uncertainty over the needs and preferences of future generations, we sought to incorporate conservation criteria based on minimal human impact into economic evaluation. These criteria require the conservation of environmental conditions such that the opportunity for intergenerational welfare optimization is maintained. Toward this end, we propose the integration of ecological-biological thresholds into decision making and use as an example the planetary-boundaries approach. Both conservation scientists and economists must be involved in defining operational ecological-biological thresholds that can be incorporated into economic thinking and reflect the objectives of conservation, sustainability, and intergenerational welfare optimization. © 2016 Society for Conservation Biology.

Synchronous behavior of two coupled electronic neurons

International Nuclear Information System (INIS)

Pinto, R. D.; Varona, P.; Volkovskii, A. R.; Szuecs, A.; Abarbanel, Henry D. I.; Rabinovich, M. I.

2000-01-01

We report on experimental studies of synchronization phenomena in a pair of analog electronic neurons (ENs). The ENs were designed to reproduce the observed membrane voltage oscillations of isolated biological neurons from the stomatogastric ganglion of the California spiny lobster Panulirus interruptus. The ENs are simple analog circuits which integrate four-dimensional differential equations representing fast and slow subcellular mechanisms that produce the characteristic regular/chaotic spiking-bursting behavior of these cells. In this paper we study their dynamical behavior as we couple them in the same configurations as we have done for their counterpart biological neurons. The interconnections we use for these neural oscillators are both direct electrical connections and excitatory and inhibitory chemical connections: each realized by analog circuitry and suggested by biological examples. We provide here quantitative evidence that the ENs and the biological neurons behave similarly when coupled in the same manner. They each display well defined bifurcations in their mutual synchronization and regularization. We report briefly on an experiment on coupled biological neurons and four-dimensional ENs, which provides further ground for testing the validity of our numerical and electronic models of individual neural behavior. Our experiments as a whole present interesting new examples of regularization and synchronization in coupled nonlinear oscillators. (c) 2000 The American Physical Society

Dielectric relaxation in biological systems physical principles, methods, and applications

CERN Document Server

Feldman, Yuri

2015-01-01

This title covers the theoretical basis and practical aspects of the study of dielectric properties of biological systems, such as water, electrolyte and polyelectrolytes, solutions of biological macromolecules, cells suspensions and cellular systems.

Systems-biology dissection of eukaryotic cell growth

Directory of Open Access Journals (Sweden)

Andrews Justen

2010-05-01

Full Text Available Abstract A recent article in BMC Biology illustrates the use of a systems-biology approach to integrate data across the transcriptome, proteome and metabolome of budding yeast in order to dissect the relationship between nutrient conditions and cell growth. See research article http://jbiol.com/content/6/2/4 and http://www.biomedcentral.com/1741-7007/8/68

It’s the System, Stupid: How Systems Biology Is Transforming

Science.gov (United States)

2010-01-01

So far, little is known about systems biology and its potential for changing how we diagnose and treat disease. That will change soon, say the systems experts, who advise payers to begin learning now about how it could make healthcare efficient. PMID:22478806

A dedicated database system for handling multi-level data in systems biology

OpenAIRE

Pornputtapong, Natapol; Wanichthanarak, Kwanjeera; Nilsson, Avlant; Nookaew, Intawat; Nielsen, Jens

2014-01-01

Background Advances in high-throughput technologies have enabled extensive generation of multi-level omics data. These data are crucial for systems biology research, though they are complex, heterogeneous, highly dynamic, incomplete and distributed among public databases. This leads to difficulties in data accessibility and often results in errors when data are merged and integrated from varied resources. Therefore, integration and management of systems biological data remain very challenging...

Energy eigenvalues and squeezing properties of general systems of coupled quantum anharmonic oscillators

International Nuclear Information System (INIS)

Chung, N. N.; Chew, L. Y.

2007-01-01

We have generalized the two-step approach to the solution of systems of N coupled quantum anharmonic oscillators. By using the squeezed vacuum state of each individual oscillator, we construct the tensor product state, and obtain the optimal squeezed vacuum product state through energy minimization. We then employ this optimal state and its associated bosonic operators to define a basis set to construct the Heisenberg matrix. The diagonalization of the matrix enables us to obtain the energy eigenvalues of the coupled oscillators. In particular, we have applied our formalism to determine the eigenenergies of systems of two coupled quantum anharmonic oscillators perturbed by a general polynomial potential, as well as three and four coupled systems. Furthermore, by performing a first-order perturbation analysis about the optimal squeezed vacuum product state, we have also examined into the squeezing properties of two coupled oscillator systems

Transient chaos in a globally coupled system of nearly conservative Hamiltonian Duffing oscillators

International Nuclear Information System (INIS)

Sabarathinam, S.; Thamilmaran, K.

2015-01-01

Highlights: •We have examined transient chaos in globally coupled oscillators. •We analyze transient chaos using new techniques. •We give experimental confirmation of transient chaos. -- Abstract: In this work, transient chaos in a ring and globally coupled system of nearly conservative Hamiltonian Duffing oscillators is reported. The networks are formed by coupling of three, four and six Duffing oscillators. The nearly conservative Hamiltonian nature of the coupled system is proved by stability analysis. The transient phenomenon is confirmed through various numerical investigations such as recurrence analysis, 0–1 test and Finite Time Lyapunov Exponents. Further, the effect of damping and the average transient lifetime of three, four and six coupled schemes for randomly generated initial conditions have been analyzed. The experimental confirmation of transient chaos in an illustrative system of three ringly coupled Duffing oscillators is also presented

Fully coupled thermal-mechanical-fluid flow model for nonliner geologic systems

International Nuclear Information System (INIS)

Hart, R.D.

1981-01-01

A single model is presented which describes fully coupled thermal-mechanical-fluid flow behavior of highly nonlinear, dynamic or quasistatic, porous geologic systems. The mathematical formulation for the model utilizes the continuum theory of mixtures to describe the multiphase nature of the system, and incremental linear constitutive theory to describe the path dependency of nonlinear material behavior. The model, incorporated in an explicit finite difference numerical procedure, was implemented in two different computer codes. A special-purpose one-dimensional code, SNEAKY, was written for initial validation of the coupling mechanisms and testing of the coupled model logic. A general purpose commercially available code, STEALTH, developed for modeling dynamic nonlinear thermomechanical processes, was modified to include fluid flow behavior and the coupling constitutive model. The fully explicit approach in the coupled calculation facilitated the inclusion of the coupling mechanisms and complex constitutive behavior. Analytical solutions pertaining to consolidation theory for soils, thermoelasticity for solids, and hydrothermal convection theory provided verification of stress and fluid flow, stress and conductive heat transfer, and heat transfer and fluid flow couplings, respectively, in the coupled model. A limited validation of the adequacy of the coupling constitutive assumptions was also performed by comparison with the physical response from two laboratory tests. Finally, the full potential of the coupled model is illustrated for geotechnical applications in energy-resource related areas. Examples in the areas of nuclear waste isolation and cut-and-fill mining are cited

Dynamics and non-equilibrium steady state in a system of coupled harmonic oscillators

Energy Technology Data Exchange (ETDEWEB)

Ghesquière, Anne, E-mail: Anne.Ghesquiere@nithep.ac.za; Sinayskiy, Ilya, E-mail: sinayskiy@ukzn.ac.za; Petruccione, Francesco, E-mail: petruccione@ukzn.ac.za

2013-10-15

A system of two coupled oscillators, each of them coupled to an independent reservoir, is analysed. The analytical solution of the non-rotating wave master equation is obtained in the high-temperature and weak coupling limits. No thermal entanglement is found in the high-temperature limit. In the weak coupling limit the system converges to an entangled non-equilibrium steady state. A critical temperature for the appearance of quantum correlations is found.

Dynamic characteristic of electromechanical coupling effects in motor-gear system

Science.gov (United States)

Bai, Wenyu; Qin, Datong; Wang, Yawen; Lim, Teik C.

2018-06-01

Dynamic characteristics of an electromechanical model which combines a nonlinear permeance network model (PNM) of a squirrel-cage induction motor and a coupled lateral-torsional dynamic model of a planetary geared rotor system is analyzed in this study. The simulations reveal the effects of internal excitations or parameters like machine slotting, magnetic saturation, time-varying mesh stiffness and shaft stiffness on the system dynamics. The responses of the electromechanical system with PNM motor model are compared with those responses of the system with dynamic motor model. The electromechanical coupling due to the interactions between the motor and gear system are studied. Furthermore, the frequency analysis of the electromechanical system dynamic characteristics predicts an efficient way to detect work condition of unsymmetrical voltage sag.

The Met Office Coupled Atmosphere/Land/Ocean/Sea-Ice Data Assimilation System

Science.gov (United States)

Lea, Daniel; Mirouze, Isabelle; King, Robert; Martin, Matthew; Hines, Adrian

2015-04-01

The Met Office has developed a weakly-coupled data assimilation (DA) system using the global coupled model HadGEM3 (Hadley Centre Global Environment Model, version 3). At present the analysis from separate ocean and atmosphere DA systems are combined to produced coupled forecasts. The aim of coupled DA is to produce a more consistent analysis for coupled forecasts which may lead to less initialisation shock and improved forecast performance. The HadGEM3 coupled model combines the atmospheric model UM (Unified Model) at 60 km horizontal resolution on 85 vertical levels, the ocean model NEMO (Nucleus for European Modelling of the Ocean) at 25 km (at the equator) horizontal resolution on 75 vertical levels, and the sea-ice model CICE at the same resolution as NEMO. The atmosphere and the ocean/sea-ice fields are coupled every 1-hour using the OASIS coupler. The coupled model is corrected using two separate 6-hour window data assimilation systems: a 4D-Var for the atmosphere with associated soil moisture content nudging and snow analysis schemes on the one hand, and a 3D-Var FGAT for the ocean and sea-ice on the other hand. The background information in the DA systems comes from a previous 6-hour forecast of the coupled model. To isolate the impact of the coupled DA, 13-month experiments have been carried out, including 1) a full atmosphere/land/ocean/sea-ice coupled DA run, 2) an atmosphere-only run forced by OSTIA SSTs and sea-ice with atmosphere and land DA, and 3) an ocean-only run forced by atmospheric fields from run 2 with ocean and sea-ice DA. In addition, 5-day and 10-day forecast runs, have been produced from initial conditions generated by either run 1 or a combination of runs 2 and 3. The different results have been compared to each other and, whenever possible, to other references such as the Met Office atmosphere and ocean operational analyses or the OSTIA SST data. The performance of the coupled DA is similar to the existing separate ocean and atmosphere