Relevant bibliographies by topics / Complex systems- Molecular dynamics study

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
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Academic literature on the topic 'Complex systems- Molecular dynamics study'

Author: Grafiati
Published: 6 September 2023

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Journal articles on the topic "Complex systems- Molecular dynamics study"

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Borodin, Vladislav, Mikhail Bubenchikov, Alexey Bubenchikov, Dmitriy Mamontov, Sergey Azheev, and Alexandr Azheev. "Study of the Unstable Rotational Dynamics of a Tor-Fullerene Molecular System." Crystals 13, no. 2 (January 20, 2023): 181. http://dx.doi.org/10.3390/cryst13020181.

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This work is devoted to modeling the dynamics of large molecules. The key issue in modeling the dynamics of real molecular systems is to correctly represent the temperature of the system using the available theoretical tools. In most works on molecular dynamics, vibrations of atoms inside a molecule are modeled with enviable persistence, which has nothing to do with physical temperature. These vibrations represent the energy internal to the molecule. Therefore, it should not be present in problems in the dynamics of inert molecular systems. In this work, by means of classical mechanics, it is shown that the simplest system containing only three molecular bodies, due to multiple acts of pair interactions of these bodies, reproduces the temperature even in an extremely complex unstable motion of the system. However, at the same time, it is necessary to separate the stochastic part of the movement from the deterministic one. Calculations also show that translational fluctuations in the motion of molecules make the greatest contribution to temperature. The contribution of rotational energy to the total energy of fluctuation motions is small. It follows from these results that the thermal state of the system is determined only by the translational temperature. The latter, in turn, opens up possibilities for a simplified description of many complex systems composed of carbon molecules such as fullerenes and nanotori.
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Kahana, Amit, and Doron Lancet. "Protobiotic Systems Chemistry Analyzed by Molecular Dynamics." Life 9, no. 2 (May 10, 2019): 38. http://dx.doi.org/10.3390/life9020038.

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Systems chemistry has been a key component of origin of life research, invoking models of life’s inception based on evolving molecular networks. One such model is the graded autocatalysis replication domain (GARD) formalism embodied in a lipid world scenario, which offers rigorous computer simulation based on defined chemical kinetics equations. GARD suggests that the first pre-RNA life-like entities could have been homeostatically-growing assemblies of amphiphiles, undergoing compositional replication and mutations, as well as rudimentary selection and evolution. Recent progress in molecular dynamics has provided an experimental tool to study complex biological phenomena such as protein folding, ligand-receptor interactions, and micellar formation, growth, and fission. The detailed molecular definition of GARD and its inter-molecular catalytic interactions make it highly compatible with molecular dynamics analyses. We present a roadmap for simulating GARD’s kinetic and thermodynamic behavior using various molecular dynamics methodologies. We review different approaches for testing the validity of the GARD model by following micellar accretion and fission events and examining compositional changes over time. Near-future computational advances could provide empirical delineation for further system complexification, from simple compositional non-covalent assemblies towards more life-like protocellular entities with covalent chemistry that underlies metabolism and genetic encoding.
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Rapaport, D. C. "GPU molecular dynamics: Algorithms and performance." Journal of Physics: Conference Series 2241, no. 1 (March 1, 2022): 012007. http://dx.doi.org/10.1088/1742-6596/2241/1/012007.

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Abstract A previous study of MD algorithms designed for GPU use is extended to cover more recent developments in GPU architecture. Algorithm modifications are described, togther with extensions to more complex systems. New measurements include the effects of increased parallelism on GPU performance, as well as comparisons with multiple-core CPUs using multitasking based on CPU threads and message passing. The results show that the GPU retains a significant performance advantage.
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Wang, Xiunan, Yi Liu, Jingcheng Xu, Shengjuan Li, Fada Zhang, Qian Ye, Xiao Zhai, and Xinluo Zhao. "Molecular Dynamics Study of Stability and Diffusion of Graphene-Based Drug Delivery Systems." Journal of Nanomaterials 2015 (2015): 1–14. http://dx.doi.org/10.1155/2015/872079.

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Graphene, a two-dimensional nanomaterial with unique biomedical properties, has attracted great attention due to its potential applications in graphene-based drug delivery systems (DDS). In this work graphene sheets with various sizes and graphene oxide functionalized with polyethylene glycol (GO-PEG) are utilized as nanocarriers to load anticancer drug molecules including CE6, DOX, MTX, and SN38. We carried out molecular dynamics calculations to explore the energetic stabilities and diffusion behaviors of the complex systems with focuses on the effects of the sizes and functionalization of graphene sheets as well as the number and types of drug molecules. Our study shows that the binding of graphene-drug complex is favorable when the drug molecules and finite graphene sheets become comparable in sizes. The boundaries of finite sized graphene sheets restrict the movement of drug molecules. The double-side loading often slows down the diffusion of drug molecules compared with the single-side loading. The drug molecules bind more strongly with GO-PEG than with pristine graphene sheets, demonstrating the advantages of functionalization in improving the stability and biocompatibility of graphene-based DDS.
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Puzyrkov, Dmitry, Sergey Polyakov, Viktoriia Podryga, and Sergey Markizov. "Concept of a Cloud Service for Data Preparation and Computational Control on Custom HPC Systems in Application to Molecular Dynamics." EPJ Web of Conferences 173 (2018): 05014. http://dx.doi.org/10.1051/epjconf/201817305014.

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At the present stage of computer technology development it is possible to study the properties and processes in complex systems at molecular and even atomic levels, for example, by means of molecular dynamics methods. The most interesting are problems related with the study of complex processes under real physical conditions. Solving such problems requires the use of high performance computing systems of various types, for example, GRID systems and HPC clusters. Considering the time consuming computational tasks, the need arises of software for automatic and unified monitoring of such computations. A complex computational task can be performed over different HPC systems. It requires output data synchronization between the storage chosen by a scientist and the HPC system used for computations. The design of the computational domain is also quite a problem. It requires complex software tools and algorithms for proper atomistic data generation on HPC systems. The paper describes the prototype of a cloud service, intended for design of atomistic systems of large volume for further detailed molecular dynamic calculations and computational management for this calculations, and presents the part of its concept aimed at initial data generation on the HPC systems.
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Benton, Tim G., Stewart J. Plaistow, and Tim N. Coulson. "Complex population dynamics and complex causation: devils, details and demography." Proceedings of the Royal Society B: Biological Sciences 273, no. 1591 (March 29, 2006): 1173–81. http://dx.doi.org/10.1098/rspb.2006.3495.

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Population dynamics result from the interplay of density-independent and density-dependent processes. Understanding this interplay is important, especially for being able to predict near-term population trajectories for management. In recent years, the study of model systems—experimental, observational and theoretical—has shed considerable light on the way that the both density-dependent and -independent aspects of the environment affect population dynamics via impacting on the organism's life history and therefore demography. These model-based approaches suggest that (i) individuals in different states differ in their demographic performance, (ii) these differences generate structure that can fluctuate independently of current total population size and so can influence the dynamics in important ways, (iii) individuals are strongly affected by both current and past environments, even when the past environments may be in previous generations and (iv) dynamics are typically complex and transient due to environmental noise perturbing complex population structures. For understanding population dynamics of any given system, we suggest that ‘the devil is in the detail’. Experimental dissection of empirical systems is providing important insights into the details of the drivers of demographic responses and therefore dynamics and should also stimulate theory that incorporates relevant biological mechanism.
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Pieroni, Michele, Francesco Madeddu, Jessica Di Martino, Manuel Arcieri, Valerio Parisi, Paolo Bottoni, and Tiziana Castrignanò. "MD–Ligand–Receptor: A High-Performance Computing Tool for Characterizing Ligand–Receptor Binding Interactions in Molecular Dynamics Trajectories." International Journal of Molecular Sciences 24, no. 14 (July 19, 2023): 11671. http://dx.doi.org/10.3390/ijms241411671.

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Molecular dynamics simulation is a widely employed computational technique for studying the dynamic behavior of molecular systems over time. By simulating macromolecular biological systems consisting of a drug, a receptor and a solvated environment with thousands of water molecules, MD allows for realistic ligand–receptor binding interactions (lrbi) to be studied. In this study, we present MD–ligand–receptor (MDLR), a state-of-the-art software designed to explore the intricate interactions between ligands and receptors over time using molecular dynamics trajectories. Unlike traditional static analysis tools, MDLR goes beyond simply taking a snapshot of ligand–receptor binding interactions (lrbi), uncovering long-lasting molecular interactions and predicting the time-dependent inhibitory activity of specific drugs. With MDLR, researchers can gain insights into the dynamic behavior of complex ligand–receptor systems. Our pipeline is optimized for high-performance computing, capable of efficiently processing vast molecular dynamics trajectories on multicore Linux servers or even multinode HPC clusters. In the latter case, MDLR allows the user to analyze large trajectories in a very short time. To facilitate the exploration and visualization of lrbi, we provide an intuitive Python notebook (Jupyter), which allows users to examine and interpret the results through various graphical representations.
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Domínguez, D., A. R. Bishop, and N. Grønbech-Jensen. "Coherence and Complexity in Condensed Matter: Josephson Junction Arrays." International Journal of Bifurcation and Chaos 07, no. 05 (May 1997): 979–88. http://dx.doi.org/10.1142/s0218127497000790.

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The importance of the mesoscopic bridge between microscopic and mesoscopic descriptions of complex, nonlinear-nonequilibrium extended dynamical systems is illustrated in a condensed matter context through three-dimensional Josephson junction arrays. Large-scale Langevin molecular dynamics is used to study novel transformer and melting effects, emphasizing the central roles of topological excitations (flux vortex lines) in determining mesoscopic patterns and dynamics — through flux line creation, annihilation, interaction and statistical mechanics.
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Hordijk, Wim, Mike Steel, and Stuart Kauffman. "Molecular Diversity Required for the Formation of Autocatalytic Sets." Life 9, no. 1 (March 1, 2019): 23. http://dx.doi.org/10.3390/life9010023.

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Systems chemistry deals with the design and study of complex chemical systems. However, such systems are often difficult to investigate experimentally. We provide an example of how theoretical and simulation-based studies can provide useful insights into the properties and dynamics of complex chemical systems, in particular of autocatalytic sets. We investigate the issue of the required molecular diversity for autocatalytic sets to exist in random polymer libraries. Given a fixed probability that an arbitrary polymer catalyzes the formation of other polymers, we calculate this required molecular diversity theoretically for two particular models of chemical reaction systems, and then verify these calculations by computer simulations. We also argue that these results could be relevant to an origin of life scenario proposed recently by Damer and Deamer.
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Cassone, Giuseppe, Adriano Sofia, Jiri Sponer, A. Marco Saitta, and Franz Saija. "Ab Initio Molecular Dynamics Study of Methanol-Water Mixtures under External Electric Fields." Molecules 25, no. 15 (July 24, 2020): 3371. http://dx.doi.org/10.3390/molecules25153371.

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Intense electric fields applied on H-bonded systems are able to induce molecular dissociations, proton transfers, and complex chemical reactions. Nevertheless, the effects induced in heterogeneous molecular systems such as methanol-water mixtures are still elusive. Here we report on a series of state-of-the-art ab initio molecular dynamics simulations of liquid methanol-water mixtures at different molar ratios exposed to static electric fields. If, on the one hand, the presence of water increases the proton conductivity of methanol-water mixtures, on the other, it hinders the typical enhancement of the chemical reactivity induced by electric fields. In particular, a sudden increase of the protonic conductivity is recorded when the amount of water exceeds that of methanol in the mixtures, suggesting that important structural changes of the H-bond network occur. By contrast, the field-induced multifaceted chemistry leading to the synthesis of e.g., hydrogen, dimethyl ether, formaldehyde, and methane observed in neat methanol, in 75:25, and equimolar methanol-water mixtures, completely disappears in samples containing an excess of water and in pure water. The presence of water strongly inhibits the chemical reactivity of methanol.
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Dissertations / Theses on the topic "Complex systems- Molecular dynamics study"

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Haughney, Michael Francis. "A molecular dynamics study of selected polar liquids and their aqueous mixtures." Thesis, University of Cambridge, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.254062.

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MICELI, GIACOMO FRANCESCO LEONARDO. "Fist principles study of the LINH2/LI2NH hydrogen storage system." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2011. http://hdl.handle.net/10281/19693.

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In this work we focused our attention on the lithium amide/imide, LiNH2/Li2NH, a very important system for hydrogen storage. By means of ab initio simulations we have resolved the structure of the two crystalline phases of Li2NH stable below and above 356 K and provide a comprehensive description of the elementary steps in the dehydrogenation and rehydrogenation processes. We performed molecular dynamics simulations based on density-functional theory and optimizations of the reaction pathways of elementary steps to provide estimates of reaction rates within the harmonic transition state theory.
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Singh, Vidisha. "Integrative analysis and modeling of molecular pathways dysregulated in rheumatoid arthritis Computational systems biology approach for the study of rheumatoid arthritis: from a molecular map to a dynamical model RA-map: building a state-of-the-art interactive knowledge base for rheumatoid arthritis Automated inference of Boolean models from molecular interaction maps using CaSQ." Thesis, université Paris-Saclay, 2020. http://www.theses.fr/2020UPASL039.

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La polyarthrite rhumatoïde (PR) est unemaladie auto-immune complexe qui entraîne uneinflammation synoviale et une hyperplasie pouvantprovoquer une érosion osseuse et une destruction ducartilage dans les articulations. L'étiologie de la PR restepartiellement inconnue, mais elle implique de multiplescascades de signalisation croisées et l'expression demédiateurs pro-inflammatoires. Dans la première partie demon projet de doctorat, nous présentons un effortsystématique pour construire une base de connaissancessur la PR, entièrement annotée et validée par des experts.Cette carte de la PR illustre les voies moléculaires et designalisation importantes impliquées dans la maladie. Latransduction du signal est systématiquement représentéedes récepteurs au noyau en utilisant la représentationstandard de notation graphique en biologie des systèmes(SBGN). La curation manuelle est basée sur des critèresstricts et spécifique aux études sur l'homme, limitantl'apparition de faux positifs sur la carte. Cette carte peutservir de base de connaissances interactive pour la maladiemais aussi de tableau pour la visualisation des donnéesomiques. De plus, c’est une excellente base pour ledéveloppement d'un modèle informatique. La naturestatique de la carte PR pourrait fournir une compréhensionrelativement limitée du comportement émergeant dusystème dans différentes conditions. La modélisationinformatique pourra révéler les propriétés dynamiques duréseau par le biais de perturbations in silico et peut êtreutilisée pour tester et prédire des hypothèses.Dans la deuxième partie du projet, nous présentons unpipeline permettant la construction automatisée d'un grandmodèle booléen, à partir d'une carte d'interactionsmoléculaires. Pour cela, nous avons développé l'outilCaSQ (CellDesigner as SBML-qual), qui automatise laconversion des cartes moléculaires en modèles booléensexécutables basés sur la topologie et la sémantique descartes. Le modèle booléen résultant pourrait être utilisépour des simulations in silico afin de reproduire lecomportement biologique connu du système et de prédirede nouvelles cibles thérapeutiques. Pour l'analyse deperformance de l’outil, nous avons utilisé différentescartes et modèles de maladies en mettant l'accent sur lagrande carte moléculaire de la PR.Dans la troisième partie du projet, nous présentons nosefforts pour créer un modèle dynamique (booléen) àgrande échelle pour les synoviocytes de type fibroblastede polyarthrite rhumatoïde (RA-FLS). Parmi denombreuses cellules de l'articulation et du systèmeimmunitaire impliquées dans la pathogenèse de la PR, lesRA-FLS joue un rôle important dans l'initiation et laperpétuation de l'inflammation articulaire destructrice.Les RA-FLS expriment des cytokinesimmunomodulatrices, des molécules d'adhésion et desenzymes de modélisation matricielle. De plus, les RAFLSprésentent des taux de prolifération élevés et unphénotype résistant à l'apoptose. Les RA-FLS peuventégalement se comporter comme les principaux moteurs del'inflammation, et les thérapies dirigées contre les RA FLSpourraient devenir une approche complémentaire auximmunothérapies. Le défi est de prédire les conditionsoptimales qui favoriseraient l'apoptose des RA FLS,limiteraient l'inflammation, ralentiraient le taux deprolifération et minimiseraient l'érosion osseuse et ladestruction du cartilage
Rheumatoid arthritis (RA) is a complexautoimmune disease that results in synovial inflammationand hyperplasia leading to bone erosion and cartilagedestruction in the joints. The aetiology of RA remainspartially unknown, yet, it involves a variety of intertwinedsignalling cascades and the expression of pro-inflammatorymediators. In the first part of my PhD project, we present asystematic effort to construct a fully annotated, expertvalidated, state of the art knowledge-base for RA. The RAmap illustrates significant molecular and signallingpathways implicated in the disease. Signal transduction isdepicted from receptors to the nucleus systematically usingthe systems biology graphical notation (SBGN) standardrepresentation. Manual curation based on strict criteria andrestricted to only human-specific studies limits theoccurrence of false positives in the map. The RA map canserve as an interactive knowledge base for the disease butalso as a template for omic data visualization and as anexcellent base for the development of a computationalmodel. The static nature of the RA map could provide arelatively limited understanding of the emerging behaviorof the system under different conditions. Computationalmodeling can reveal dynamic network properties throughin silico perturbations and can be used to test and predictassumptions.In the second part of the project, we present a pipelineallowing the automated construction of a large Booleanmodel, starting from a molecular interaction map. For thispurpose, we developed the tool CaSQ (CellDesigner asSBML-qual), which automates the conversion ofmolecular maps to executable Boolean models based ontopology and map semantics. The resulting Booleanmodel could be used for in silico simulations to reproduceknown biological behavior of the system and to furtherpredict novel therapeutic targets. For benchmarking, weused different disease maps and models with a focus onthe large molecular map for RA.In the third part of the project we present our efforts tocreate a large scale dynamical (Boolean) model forrheumatoid arthritis fibroblast-like synoviocytes (RAFLS).Among many cells of the joint and of the immunesystem involved in the pathogenesis of RA, RA FLS playa significant role in the initiation and perpetuation ofdestructive joint inflammation. RA-FLS are shown toexpress immuno-modulating cytokines, adhesionmolecules, and matrix-modelling enzymes. Moreover,RA-FLS display high proliferative rates and an apoptosisresistantphenotype. RA-FLS can also behave as primarydrivers of inflammation, and RA FLS-directed therapiescould become a complementary approach to immunedirectedtherapies. The challenge is to predict the optimalconditions that would favour RA FLS apoptosis, limitinflammation, slow down the proliferation rate andminimize bone erosion and cartilage destruction
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Ouyang, Jian. "Molecular dynamics studies of interfacial properties of complex liquid systems." Diss., Georgia Institute of Technology, 1995. http://hdl.handle.net/1853/30494.

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Kenway, O. A. "Molecular dynamics simulations of complex systems including HIV-1 protease." Thesis, University College London (University of London), 2010. http://discovery.ucl.ac.uk/19485/.

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Advances in supercomputer architectures have resulted in a situation where many scientific codes are used on systems whose performance characteristics differ considerably from the platform they were developed and optimised for. This is particularly apparent in the realm of Grid computing, where new technologies such as MPIg allow researchers to connect geographically disparate resources together into virtual parallel machines. Finding ways to exploit these new resources efficiently is necessary both to extract the maximum benefit from them, and to provide the enticing possibility of enabling new science. In this thesis, an existing general purpose molecular dynamics code (LAMMPS) is extended to allow it to perform more efficiently in a geographically distributed Grid environment showing considerable performance gains as a result. The technique of replica exchange molecular dynamics is discussed along with its applicability to the Grid model and its benefits with respect to increasing sampling of configurational space. The dynamics of two sub-structures of the HIV-1 protease (known as the flaps) are investigated using replica exchange molecular dynamics in LAMMPS showing considerable movement that would have been difficult to investigate by traditional methods. To complement this, a study was carried out investigating the use of computational tools to calculate binding affinity between HIV-1 protease mutants and the drug lopinavir in comparison with results derived experimentally by other research groups. The results demonstrate some promise for computational methods in helping to determine the most effective course of treatment for patients in the future.
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Ding, Xiaoyan. "Increasingly Complex Systems in Intense Laser Fields." Thesis, Université d'Ottawa / University of Ottawa, 2018. http://hdl.handle.net/10393/38504.

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With more atoms in a system, coupling between quantum states complicates the system dynamics. We shine intense laser pulses on three systems with increasing complexity: a molecule, a dimer, and a solid. For single molecules, a 400 nm photon excites NO_2 and initiates a dissociation process. We probe the dynamics using a strong laser pulse to ionize the molecule, and detect the resulting electrons and ions. The evolution of the NO-O molecular bond was directly measured in our experiment. For dimers, a laser pulse removes three electrons from (CO)_2. The dimer breaks up into C^+, O^+ and CO^+. Compared to a monomer, CO^{2+} in the dimer has a new prompt dissociation pathway that produces fragments with higher kinetic energy. Calculation shows that the Coulomb field of the neighboring CO^+ modifies the electronic state of the dimer, giving rise to a prompt channel. Coupling between different charge state configurations results in a new dimer electronic state, which leads to dissociation with higher kinetic energy. For solids, coupling among many atoms creates bands and a bandgap that plays the role of the ionization potential and reduces the threshold for electron-hole pair generation. Thus, solids are a good medium for high-order harmonic generation at the high repetition rates needed for frequency combs. We generate up to the 7th harmonic in silicon and zinc oxide with femtosecond pulses from a thulium fiber laser.
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Shim, Sangwoo. "Quantum Dynamics in Biological Systems." Thesis, Harvard University, 2012. http://dissertations.umi.com/gsas.harvard:10125.

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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.
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Vanga, Amulya. "A Molecular Dynamics Study of Systems of Hard Ellipses." Kent State University / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=kent149849408801736.

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Iuchi, Satoru. "Theoretical study on dynamics of molecular systems in solution." 京都大学 (Kyoto University), 2005. http://hdl.handle.net/2433/145101.

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Megerle, Uwe. "Photoinduced molecular dynamics in increasingly complex systems: From ultrafast transient absorption spectroscopy to nanoscopic models." Diss., lmu, 2011. http://nbn-resolving.de/urn:nbn:de:bvb:19-130444.

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Books on the topic "Complex systems- Molecular dynamics study"

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Micha, David A., and Irene Burghardt, eds. Quantum Dynamics of Complex Molecular Systems. Berlin, Heidelberg: Springer Berlin Heidelberg, 2007. http://dx.doi.org/10.1007/978-3-540-34460-5.

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David, Micha, and Burghardt Irene, eds. Quantum dynamics of complex molecular systems. Berlin: Springer, 2007.

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Saksaganskiĭ, G. L. Molecular flow in complex vacuum systems. New York: Gordon and Breach Science Publishers, 1988.

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Jim, De Yoreo, ed. Morphology and dynamics of crystal surfaces in complex molecular systems. Warrendale, Pa: Materials Research Society, 2001.

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The evolutionary dynamics of complex systems: A study in biosocial complexity. New York: Oxford University Press, 1988.

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Komatsuzaki, Tamiki, David M. Leitner, and R. Stephen Berry. Advancing theory for kinetics and dynamics of complex, many-dimensional systems: Clusters and proteins. Hoboken, NJ: John Wiley & Sons, 2011.

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Zeiske, Tim. Understanding complex biomolecular systems through the synergy of molecular dynamics simulations, NMR spectroscopy and X-Ray crystallography. [New York, N.Y.?]: [publisher not identified], 2016.

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Peter, Entel, and Wolf Dietrich E, eds. International Symposium on Structure and Dynamics of Heterogeneous Systems: From atoms, molecules and clusters in complex environment to thin films and multilayers : Duisburg, Germany, 24-26 February 1999. Singapore: World Scientific, 2000.

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Collins, Michael W. Micro and Nano Flow Systems for Bioanalysis. New York, NY: Springer New York, 2013.

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Nitzan, Abraham. Chemical Dynamics in Condensed Phases. Oxford University Press, 2006. http://dx.doi.org/10.1093/oso/9780198529798.001.0001.

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This text provides a uniform and consistent approach to diversified problems encountered in the study of dynamical processes in condensed phase molecular systems. Given the broad interdisciplinary aspect of this subject, the book focuses on three themes: coverage of needed background material, in-depth introduction of methodologies, and analysis of several key applications. The uniform approach and common language used in all discussions help to develop general understanding and insight on condensed phases chemical dynamics. The applications discussed are among the most fundamental processes that underlie physical, chemical and biological phenomena in complex systems. The first part of the book starts with a general review of basic mathematical and physical methods (Chapter 1) and a few introductory chapters on quantum dynamics (Chapter 2), interaction of radiation and matter (Chapter 3) and basic properties of solids (chapter 4) and liquids (Chapter 5). In the second part the text embarks on a broad coverage of the main methodological approaches. The central role of classical and quantum time correlation functions is emphasized in Chapter 6. The presentation of dynamical phenomena in complex systems as stochastic processes is discussed in Chapters 7 and 8. The basic theory of quantum relaxation phenomena is developed in Chapter 9, and carried on in Chapter 10 which introduces the density operator, its quantum evolution in Liouville space, and the concept of reduced equation of motions. The methodological part concludes with a discussion of linear response theory in Chapter 11, and of the spin-boson model in chapter 12. The third part of the book applies the methodologies introduced earlier to several fundamental processes that underlie much of the dynamical behaviour of condensed phase molecular systems. Vibrational relaxation and vibrational energy transfer (Chapter 13), Barrier crossing and diffusion controlled reactions (Chapter 14), solvation dynamics (Chapter 15), electron transfer in bulk solvents (Chapter 16) and at electrodes/electrolyte and metal/molecule/metal junctions (Chapter 17), and several processes pertaining to molecular spectroscopy in condensed phases (Chapter 18) are the main subjects discussed in this part.
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Book chapters on the topic "Complex systems- Molecular dynamics study"

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Poghosyan, Armen, Levon Arsenyan, and Hrachya Astsatryan. "Dynamic Features of Complex Systems: A Molecular Simulation Study." In High-Performance Computing Infrastructure for South East Europe's Research Communities, 117–21. Cham: Springer International Publishing, 2014. http://dx.doi.org/10.1007/978-3-319-01520-0_14.

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Kantardjiev, Alexander, and Pavletta Shestakova. "Coarse-Grained Molecular Dynamics for Copolymer-Vesicle Self-Assembly. Case Study: Sterically Stabilized Liposomes." In First Complex Systems Digital Campus World E-Conference 2015, 255–60. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-45901-1_28.

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Sprik, M. "Molecular Dynamics Techniques for Complex Molecular Systems." In Observation, Prediction and Simulation of Phase Transitions in Complex Fluids, 421–61. Dordrecht: Springer Netherlands, 1995. http://dx.doi.org/10.1007/978-94-011-0065-6_10.

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Mansour, M. Malek, M. Mareschal, G. Sonnino, and E. Kestemont. "Molecular Dynamic Study of Density Fluctuation in a Non-equilibrium system." In Microscopic Simulations of Complex Hydrodynamic Phenomena, 87–99. Boston, MA: Springer US, 1992. http://dx.doi.org/10.1007/978-1-4899-2314-1_6.

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Wang, Qifan, Zhiping Yao, and Guangle Yan. "Chaos Study in System Dynamics." In Computer-Based Management of Complex Systems, 543–48. Berlin, Heidelberg: Springer Berlin Heidelberg, 1989. http://dx.doi.org/10.1007/978-3-642-74946-9_59.

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Brüggemann, B., D. Tsivlin, and V. May. "Ultrafast Exciton Dynamics in Molecular Systems." In Quantum Dynamics of Complex Molecular Systems, 31–55. Berlin, Heidelberg: Springer Berlin Heidelberg, 2007. http://dx.doi.org/10.1007/978-3-540-34460-5_2.

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Prezhdo, O. V., W. R. Duncan, C. F. Craig, S. V. Kilina, and B. F. Habenicht. "Photoexcitation Dynamics on the Nanoscale." In Quantum Dynamics of Complex Molecular Systems, 5–30. Berlin, Heidelberg: Springer Berlin Heidelberg, 2007. http://dx.doi.org/10.1007/978-3-540-34460-5_1.

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Ciccotti, G., D. F. Coker, and Raymond Kapral. "Quantum Statistical Dynamics with Trajectories." In Quantum Dynamics of Complex Molecular Systems, 275–93. Berlin, Heidelberg: Springer Berlin Heidelberg, 2007. http://dx.doi.org/10.1007/978-3-540-34460-5_12.

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Öhrn, Y., and E. Deumens. "Time-Dependent, Direct, Nonadiabatic, Molecular Reaction Dynamics." In Quantum Dynamics of Complex Molecular Systems, 245–58. Berlin, Heidelberg: Springer Berlin Heidelberg, 2007. http://dx.doi.org/10.1007/978-3-540-34460-5_10.

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Nandi, Champa, Somudeep Bhattacharjee, and Samrat Chakraborty. "Climate Change and Energy Dynamics with Solutions: A Case Study in Egypt." In Understanding Complex Systems, 225–57. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-11202-8_8.

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Conference papers on the topic "Complex systems- Molecular dynamics study"

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Huang, Ching-I., Wei-Zen Cheng, Yong-Ting Chung, Michio Tokuyama, Irwin Oppenheim, and Hideya Nishiyama. "Structure and Dynamics of Water Surrounding the Poly (Methacrylic Acid):A Molecular Dynamics Study." In COMPLEX SYSTEMS: 5th International Workshop on Complex Systems. AIP, 2008. http://dx.doi.org/10.1063/1.2897908.

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Affouard, F., A. Lerbret, A. Hédoux, Y. Guinet, M. Descamps, Michio Tokuyama, Irwin Oppenheim, and Hideya Nishiyama. "Biopreservative Capabilities of Disaccharides on Proteins: A Study by Molecular Dynamics Simulations." In COMPLEX SYSTEMS: 5th International Workshop on Complex Systems. AIP, 2008. http://dx.doi.org/10.1063/1.2897879.

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Nagao, Hidemi, Shuhei Kawamoto, Micke Rusmerryani, Acep Purqon, Kazutomo Kawaguchi, and Hiroaki Saito. "Molecular dynamics study on entrainment phenomenon in model molecular systems." In 4TH INTERNATIONAL SYMPOSIUM ON SLOW DYNAMICS IN COMPLEX SYSTEMS: Keep Going Tohoku. American Institute of Physics, 2013. http://dx.doi.org/10.1063/1.4794669.

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Baumketner, A. "Molecular Dynamics Study of Protein Folding: Potentials and Mechanisms." In MODELING OF COMPLEX SYSTEMS: Seventh Granada Lectures. AIP, 2003. http://dx.doi.org/10.1063/1.1571312.

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Isobe, Masaharu. "Molecular Dynamics Study on a Self-organized Shock Wave in an Inelastic Hard Disk System." In SLOW DYNAMICS IN COMPLEX SYSTEMS: 3rd International Symposium on Slow Dynamics in Complex Systems. AIP, 2004. http://dx.doi.org/10.1063/1.1764102.

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Shinoda, W. "Molecular dynamics study of the Lipid Bilayers: Effects of the Chain Branching on the Structure and Dynamics." In SLOW DYNAMICS IN COMPLEX SYSTEMS: 3rd International Symposium on Slow Dynamics in Complex Systems. AIP, 2004. http://dx.doi.org/10.1063/1.1764171.

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Varnik, Fathollah, Michio Tokuyama, Irwin Oppenheim, and Hideya Nishiyama. "Diffusion, Structural Relaxation and Rheological Properties of a Simple Glass Forming Model: A Molecular Dynamics Study." In COMPLEX SYSTEMS: 5th International Workshop on Complex Systems. AIP, 2008. http://dx.doi.org/10.1063/1.2897774.

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Hagiwara, Shoko, Yoko Iwama, Hiroki Fujimori, Michio Tokuyama, Irwin Oppenheim, and Hideya Nishiyama. "Study of Molecular Dynamics in Liquid-Crystalline Phases of CBOOA by High-Resolution [sup 13]C NMR." In COMPLEX SYSTEMS: 5th International Workshop on Complex Systems. AIP, 2008. http://dx.doi.org/10.1063/1.2897887.

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Hibino, M. "Study of Fluidity of Lipid Membranes Using Single Molecule Microscopy." In SLOW DYNAMICS IN COMPLEX SYSTEMS: 3rd International Symposium on Slow Dynamics in Complex Systems. AIP, 2004. http://dx.doi.org/10.1063/1.1764158.

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Nishimura, Megumi, Hiroaki Saito, Kazutomo Kawaguchi, and Hidemi Nagao. "Conformational stability of Met20 loop of DHFR: A molecular dynamics study." In 4TH INTERNATIONAL SYMPOSIUM ON SLOW DYNAMICS IN COMPLEX SYSTEMS: Keep Going Tohoku. American Institute of Physics, 2013. http://dx.doi.org/10.1063/1.4794654.

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Reports on the topic "Complex systems- Molecular dynamics study"

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Bar-Joseph, Moshe, William O. Dawson, and Munir Mawassi. Role of Defective RNAs in Citrus Tristeza Virus Diseases. United States Department of Agriculture, September 2000. http://dx.doi.org/10.32747/2000.7575279.bard.

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This program focused on citrus tristeza virus (CTV), the largest and one of the most complex RNA-plant-viruses. The economic importance of this virus to the US and Israeli citrus industries, its uniqueness among RNA viruses and the possibility to tame the virus and eventually turn it into a useful tool for the protection and genetic improvement of citrus trees justify these continued efforts. Although the overall goal of this project was to study the role(s) of CTV associated defective (d)-RNAs in CTV-induced diseases, considerable research efforts had to be devoted to the engineering of the helper virus which provides the machinery to allow dRNA replication. Considerable progress was made through three main lines of complementary studies. For the first time, the generation of an engineered CTV genetic system that is capable of infecting citrus plants with in vitro modified virus was achieved. Considering that this RNA virus consists of a 20 kb genome, much larger than any other previously developed similar genetic system, completing this goal was an extremely difficult task that was accomplished by the effective collaboration and complementarity of both partners. Other full-length genomic CTV isolates were sequenced and populations examined, resulting in a new level of understanding of population complexities and dynamics in the US and Israel. In addition, this project has now considerably advanced our understanding and ability to manipulate dRNAs, a new class of genetic elements of closteroviruses, which were first found in the Israeli VT isolate and later shown to be omnipresent in CTV populations. We have characterized additional natural dRNAs and have shown that production of subgenomic mRNAs can be involved in the generation of dRNAs. We have molecularly cloned natural dRNAs and directly inoculated citrus plants with 35S-cDNA constructs and have shown that specific dRNAs are correlated with specific disease symptoms. Systems to examine dRNA replication in protoplasts were developed and the requirements for dRNA replication were defined. Several artificial dRNAs that replicate efficiently with a helper virus were created from infectious full-genomic cDNAs. Elements that allow the specific replication of dRNAs by heterologous helper viruses also were defined. The T36-derived dRNAs were replicated efficiently by a range of different wild CTV isolates and hybrid dRNAs with heterologous termini are efficiently replicated with T36 as helper. In addition we found: 1) All CTV genes except of the p6 gene product from the conserved signature block of the Closteroviridae are obligate for assembly, infectivity, and serial protoplast passage; 2) The p20 protein is a major component of the amorphous inclusion bodies of infected cells; and 3) Novel 5'-Co-terminal RNAs in CTV infected cells were characterized. These results have considerably advanced our basic understanding of the molecular biology of CTV and CTV-dRNAs and form the platform for the future manipulation of this complicated virus. As a result of these developments, the way is now open to turn constructs of this viral plant pathogen into new tools for protecting citrus against severe CTV terms and development of virus-based expression vectors for other citrus improvement needs. In conclusion, this research program has accomplished two main interconnected missions, the collection of basic information on the molecular and biological characteristics of the virus and its associated dRNAs toward development of management strategies against severe diseases caused by the virus and building of novel research tools to improve citrus varieties. Reaching these goals will allow us to advance this project to a new phase of turning the virus from a pathogen to an ally.
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Ilachinski, Andrew. Land Warfare and Complexity, Part II: An Assessment of the Applicability of Nonlinear Dynamics and Complex Systems Theory to the Study of Land Warfare. Fort Belvoir, VA: Defense Technical Information Center, July 1996. http://dx.doi.org/10.21236/ada362621.

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Lamont, Susan J., E. Dan Heller, and Avigdor Cahaner. Prediction of Immunocompetence and Resistance to Disease by Using Molecular Markers of the Major Histocompatibility Complex. United States Department of Agriculture, September 1994. http://dx.doi.org/10.32747/1994.7568780.bard.

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This project utilized two live-animal populations in an integrated research program to identify molecular markers for immune response and disease resistance. The populations each had their foundation from meat-type commercial breeder chicken lines of their respective countries. Investigations effectively used unique availability of resources in each country to study commercial-type environments in Israel and line-crosses with diverse inbred lines in the US. Two bacterial systems were investigated to cover both respiratory and gastrointestinal, and primary and secondary, infections. Individual experimental groups of animals were evaluated for combinations of vaccine antibody levels, response to pathogen challenge, growth parameters, genetic background and molecular markers. The positive association of antibody level with resistance to disease was confirmed. Effectiveness of genetic selection for vaccine antibody response level was demonstrated. Molecular markers, both inside and outside the MHC region, were associated with antibody response and resistance to disease. Markers were shown to have a generalized effect, by association with multiple traits of immune response and disease resistance. The impact of genetic background on marker effect was shown to be important. The overall results demonstrate the effectiveness of selection on vaccine antibody response and the potential of molecular marker-assisted selection to improve efficiency of production of meat-type chickens by reducing genetic susceptibility to disease.
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Pichersky, Eran, Alexander Vainstein, and Natalia Dudareva. Scent biosynthesis in petunia flowers under normal and adverse environmental conditions. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7699859.bard.

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The ability of flowering plants to prosper throughout evolution, and for many crop plants to set fruit, is strongly dependent on their ability to attract pollinators. To that end many plants synthesize a spectrum of volatile compounds in their flowers. Scent is a highly dynamic trait that is strongly influenced by the environment. However, with high temperature conditions becoming more common, the molecular interplay between this type of stress and scent biosynthesis need to be investigated. Using petunia as a model system, our project had three objectives: (1) Determine the expression patterns of genes encoding biosynthetic scent genes (BSGs) and of several genes previously identified as encoding transcription factors involved in scent regulation under normal and elevated temperature conditions. (2) Examine the function of petunia transcription factors and a heterologous transcription factor, PAPl, in regulating genes of the phenylpropanoid/benzenoid scent pathway. (3) Study the mechanism of transcriptional regulation by several petunia transcription factors and PAPl of scent genes under normal and elevated temperature conditions by examining the interactions between these transcription factors and the promoters of target genes. Our work accomplished the first two goals but was unable to complete the third goal because of lack of time and resources. Our general finding was that when plants grew at higher temperatures (28C day/22C night, vs. 22C/16C), their scent emission decreased in general, with the exception of a few volatiles such as vanillin. To understand why, we looked at gene transcription levels, and saw that generally there was a good correlation between levels of transcriptions of gene specifying enzymes for specific scent compounds and levels of emission of the corresponding scent compounds. Enzyme activity levels, however, showed little difference between plants growing at different temperature regimes. Plants expressing the heterologous gene PAPl showed general increase in scent emission in control temperature conditions but emission decreased at the higher temperature conditions, as seen for control plants. Finally, expression of several transcription factor genes decreased at high temperature, but expression of new transcription factor, EOB-V, increased, implicating it in the decrease of transcription of BSGs. The major conclusion of this work is that high temperature conditions negatively affect scent emission from plants, but that some genetic engineering approaches could ameliorate this problem.
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Montville, Thomas J., and Roni Shapira. Molecular Engineering of Pediocin A to Establish Structure/Function Relationships for Mechanistic Control of Foodborne Pathogens. United States Department of Agriculture, August 1993. http://dx.doi.org/10.32747/1993.7568088.bard.

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This project relates the structure of the bacteriocin molecule (which is genetically determined) to its antimicrobial function. We have sequenced the 19,542 bp pediocin plasmid pMD136 and developed a genetic transfer system for pediococci. The pediocin A operon is complex, containing putative structural, immunity, processing, and transport genes. The deduced sequence of the pediocin A molecule contains 44 amino acids and has a predicted PI of 9.45. Mechanistic studies compared the interaction of pediocin PA-1 and nisin with Listeria monocytgenes cells and model lipid systems. While significant nisin-induced intracellular ATP depletion is caused by efflux, pediocin-induced depletion is caused exclusively by hydrolysis. Liposomes derived from L. monocytogenes phospholipids were used to study the physical chemistry of pediocin and nisin interactions with lipids. Their different pH optima are the results of different specific ionizable amino acids. We generated a predicted 3-D structural model for pediocin PA-1 and used a variety of mutant pediocins to demonstrate that the "positive patch" at residues 11 and 12 (and not the YGNGV consensus sequence) is responsible for the binding step of pediocin action. This structure/function understanding gained here provides necessary prerequisites to the more efficacious use of bacteriocins to control foodborne pathogens.
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Chamovitz, Daniel, and Xing-Wang Deng. Morphogenesis and Light Signal Transduction in Plants: The p27 Subunit of the COP9-Complex. United States Department of Agriculture, 1997. http://dx.doi.org/10.32747/1997.7580666.bard.

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Plants monitor environmental signals and modulate their growth and development in a manner optimal for the prevailing light conditions. The mechanisms by which plants transduce light signals and integrate them with other environmental and developmental signals to regulate plant pattern development are beginning to be unraveled. A large body of knowledge has accumulated regarding the roles of specific photoreceptors in perceiving light signals, and about the downstream developmental responses responding to light (Batschauer, 1999; Chamovitz and Deng, 1996; Deng and Quail, 1999). Still, little is know about the molecular mechanisms connecting the photoreceptors to development, and how these developmental pathways are integrated with additional developmental regulatory pathways to modulate growth. The multi-subunit protein complex COP9 signalosome (previously referred to as the "COP9 complex") has a central role in mediating the light control of plant development, and in general developmental regulation. Arabidopsis mutants that lack this complex develop photomorphogenically even in the absence of light signals (reviewed in Chamovitz and Deng 1996, 1997). Various genetic studies have indicated that the COP9 signalosome acts at the nexus of upstream signals transduced from the individual photoreceptors, and specific downstream signaling pathways. Thus the COP9 signalosome was hypothesized to be a master repressor of photomorphogenesis, and that light acts to abrogate this repression. However, the COP9 signalosome has roles beyond the regulation of photomorphogenesis as all mutants lacking this complex die following early seedling development, and an essentially identical complex has also been detected in animal systems (Chamovitz and Deng, 1995; Seeger et al., 1998; Wei et al., 1998). Our long term objective is to determine the role of the COP9 signalosome in controlling plant development. In this research project we showed that this complex contains at least eight subunits (Karniol et al., 1998; Serino et al., 1999) and that the 27 kD subunit is encoded by the FUS5 locus (Karniol et al., 1999). The FUS5 subunit also has a role extraneous to the COP9 signalosome, and differential kinase activity has been implicated in regulating FUSS and the COP9 signalosome (Karniol et al., 1999). We have also shown that the COP9 signalosome may work together with the translational-regulator eIF3. Our study of the COP9 signalosome is one of the exciting examples of plant science leading the way to discoveries in basic animal science (Chamovitz and Deng, 1995; Karniol and Chamovitz, 2000; Wei and Deng, 1999).
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Lers, Amnon, and Gan Susheng. Study of the regulatory mechanism involved in dark-induced Postharvest leaf senescence. United States Department of Agriculture, January 2009. http://dx.doi.org/10.32747/2009.7591734.bard.

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Postharvest leaf senescence contributes to quality losses in flowers and leafy vegetables. The general goal of this research project was to investigate the regulatory mechanisms involved in dark-induced leaf senescence. The regulatory system involved in senescence induction and control is highly complex and possibly involves a network of senescence promoting pathways responsible for activation of the senescence-associated genes. Pathways involving different internal signals and environmental factors may have distinctive importance in different leaf senescence systems. Darkness is known to have a role in enhancement of postharvest leaf senescence and for getting an insight into its regulatory mechanism/s we have applied molecular genetics and functional genomics approaches. The original objectives were: 1. Identification of dark-induced SAGs in Arabidopsis using enhancer/promoter trap lines and microarray approaches; 2. Molecular and functional characterization of the identified genes by analyzing their expression and examining the phenotypes in related knockout mutant plants; 3. Initial studies of promoter sequences for selected early dark-induced SAGs. Since genomic studies of senescence, with emphasis on dark-induced senescence, were early-on published which included information on potential regulatory genes we decided to use this new information. This is instead of using the uncharacterized enhancer/promoter trap lines as originally planned. We have also focused on specific relevant genes identified in the two laboratories. Based on the available genomic analyses of leaf senescence 10 candidate genes hypothesized to have a regulatory role in dark-induced senescence were subjected to both expression as well as functional analyses. For most of these genes senescence-specific regulation was confirmed, however, functional analyses using knock-out mutants indicated no consequence to senescence progression. The transcription factor WARK75 was found to be specifically expressed during natural and dark-induced leaf senescence. Functional analysis demonstrated that in detached leaves senescence under darkness was significantly delayed while no phenotypic consequences could be observed on growth and development, including no effect on natural leaf senescence,. Thus, WARKY75 is suggested to have a role in dark-induced senescence, but not in natural senescence. Another regulatory gene identified to have a role in senescence is MKK9 encoding for a Mitogen-Activated Protein Kinase Kinase 9 which is upregulated during senescence in harvested leaves as well as in naturally senescing leaves. MKK9 can specifically phosphorylate another kinase, MPK6. Both knockouts of MKK9 and MPK6 displayed a significantly senescence delay in harvested leaves and possibly function as a phosphorelay that regulates senescence. To our knowledge, this is the first report that clearly demonstrates the involvement of a MAP kinase pathway in senescence. This research not only revealed a new signal transduction pathway, but more important provided significant insights into the regulatory mechanisms underlying senescence in harvested leaves. In an additional line of research we have employed the promoter of the senescence-induced BFN1 gene as a handle for identifying components of the regulatory mechanism. This gene was shown to be activated during darkinduced senescence of detached leaves, as well as natural senescence. This was shown by following protein accumulation and promoter activity which demonstrated that this promoter is activated during dark-induced senescence. Analysis of the promoter established that, at least some of the regulatory sequences reside in an 80 bps long fragment of the promoter. Overall, progress was made in identification of components with a role in dark-induced senescence in this project. Further studies should be done in order to better understand the function of these components and develop approaches for modulating the progress of senescence in crop plants for the benefit of agriculture.
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Соловйов, В. М., and О. С. Лук’янчук. Фолксономія соціально-економічних об’єктів в складних мережах засобами CorrRank. Брама-Україна, 2014. http://dx.doi.org/10.31812/0564/1307.

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The financial and economic crisis 2007-2009 shown that economic institutions are closely linked and the behavior of complex systems is difficult predictable. There is an urgent need to develop new quantitative methods that adequately describe the dynamic changes in complex systems during normal conditions and during the crisis. There is a need for methods that describe the topology of the interaction between economic institutions, using the tools developed in the theory of networks. The paper used a method of investigation of nonlinear dynamics, as the random matrices theory, which when combined with network methods are adequate means for the study of complex systems. The given technique we have implemented the study in the real time series of global stock markets.
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Soloviev, Vladimir, Andrii Bielinskyi, and Viktoria Solovieva. Entropy Analysis of Crisis Phenomena for DJIA Index. [б. в.], June 2019. http://dx.doi.org/10.31812/123456789/3179.

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The Dow Jones Industrial Average (DJIA) index for the 125-year-old (since 1896) history has experienced many crises of different nature and, reflecting the dynamics of the world stock market, is an ideal model object for the study of quantitative indicators and precursors of crisis phenomena. In this paper, the classification and periodization of crisis events for the DJIA index have been carried out; crashes and critical events have been highlighted. Based on the modern paradigm of the theory of complexity, a spectrum of entropy indicators and precursors of crisis phenomena have been proposed. The entropy of a complex system is not only a measure of uncertainty (like Shannon's entropy) but also a measure of complexity (like the permutation and Tsallis entropy). The complexity of the system in a crisis changes significantly. This fact can be used as an indicator, and in the case of a proactive change as a precursor of a crisis. Complex systems also have the property of scale invariance, which can be taken into account by calculating the Multiscale entropy. The calculations were carried out within the framework of the sliding window algorithm with the subsequent comparison of the entropy measures of complexity with the dynamics of the DJIA index itself. It is shown that Shannon's entropy is an indicator, and the permutation and Tsallis entropy are the precursors of crisis phenomena to the same extent for both crashes and critical events.
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Brodie, Katherine, Ian Conery, Nicholas Cohn, Nicholas Spore, and Margaret Palmsten. Spatial variability of coastal foredune evolution, part A : timescales of months to years. Engineer Research and Development Center (U.S.), July 2021. http://dx.doi.org/10.21079/11681/41322.

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Coastal foredunes are topographically high features that can reduce vulnerability to storm-related flooding hazards. While the dominant aeolian, hydrodynamic, and ecological processes leading to dune growth and erosion are fairly well-understood, predictive capabilities of spatial variations in dune evolution on management and engineering timescales (days to years) remain relatively poor. In this work, monthly high-resolution terrestrial lidar scans were used to quantify topographic and vegetation changes over a 2.5 year period along a micro-tidal intermediate beach and dune. Three-dimensional topographic changes to the coastal landscape were used to investigate the relative importance of environmental, ecological, and morphological factors in controlling spatial and temporal variability in foredune growth patterns at two 50 m alongshore stretches of coast. Despite being separated by only 700 m in the alongshore, the two sites evolved differently over the study period. The northern dune retreated landward and lost volume, whereas the southern dune prograded and vertically accreted. The largest differences in dune response between the two sections of dunes occurred during the fall storm season, when each of the systems’ geomorphic and ecological properties modulated dune growth patterns. These findings highlight the complex eco-morphodynamic feedback controlling dune dynamics across a range of spatial scales.
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