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https://www.readbyqxmd.com/read/28212112/cancer-as-robust-intrinsic-state-shaped-by-evolution-a-key-issues-review
#1
Ruoshi Yuan, Xiaomei Zhu, Gaowei Wang, Site Li, Ping Ao
Cancer is a complex disease: its pathology cannot be properly understood in terms of independent players-genes, proteins, molecular pathways, or their simple combinations. This is similar to many-body physics of a condensed phase that many important properties are not determined by a single atom or molecule. The rapidly accumulating large 'omics' data also require a new mechanistic and global underpinning to organize for rationalizing cancer complexity. A unifying and quantitative theory was proposed by some of the present authors that cancer is a robust state formed by the endogenous molecular-cellular network, which is evolutionarily built for the developmental processes and physiological functions...
February 17, 2017: Reports on Progress in Physics
https://www.readbyqxmd.com/read/28211934/a-computational-assessment-of-the-electronic-thermoelectric-and-defect-properties-of-bournonite-cupbsbs3-and-related-substitutions
#2
Alireza Faghaninia, Guodong Yu, Umut Aydemir, Max Wood, Wei Chen, Gian-Marco Rignanese, G Jeffrey Snyder, Geoffroy Hautier, Anubhav Jain
Bournonite (CuPbSbS3) is an earth-abundant mineral with potential thermoelectric applications. This material has a complex crystal structure (space group Pmn21 #31) and has previously been measured to exhibit a very low thermal conductivity (κ < 1 W m(-1) K(-1) at T ≥ 300 K). In this study, we employ high-throughput density functional theory calculations to investigate how the properties of the bournonite crystal structure change with elemental substitutions. Specifically, we compute the stability and electronic properties of 320 structures generated via substitutions {Na-K-Cu-Ag}{Si-Ge-Sn-Pb}{N-P-As-Sb-Bi}{O-S-Se-Te} in the ABCD3 formula...
February 17, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28211758/life-cycle-host-utilization-and-ecological-fitting-for-invasive-lancet-liver-fluke-dicrocoelium-dendriticum-emerging-in-southern-alberta-canada
#3
Bradley van Paridon, John S Gilleard, Douglas D Colwell, Cameron P Goater
The expansion of parasite distributions outside of their native host and geographical ranges has occurred repeatedly over evolutionary time. Contemporary examples include emerging infectious diseases (EID's), many of which pose threats to human, domestic animal, and wildlife populations. Theory predicts that parasites with complex life cycles will be rare as EID's due to constraints imposed by host specialization at each life-cycle stage. In contrast to predictions of this theory, we report 2 new intermediate hosts in the 3-host life cycle of the liver fluke Dicrocoelium dendriticum in Cypress Hills Provincial Park, Alberta, Canada...
February 17, 2017: Journal of Parasitology
https://www.readbyqxmd.com/read/28211737/poynting-robertson-like-drag-at-the-sun-s-surface
#4
Ian Cunnyngham, Marcelo Emilio, Jeff Kuhn, Isabelle Scholl, Rock Bush
The Sun's internal rotation Ω(r,Θ) has previously been measured using helioseismology techniques and found to be a complex function of colatitude θ and radius r. From helioseismology and observations of apparently "rooted" solar magnetic tracers, we know that the surface rotates more slowly than much of the interior. The cause of this slow-down is not understood, but it is important for understanding stellar rotation generally and any plausible theory of the solar interior. A new analysis using 5-min solar p-mode limb oscillations as a rotation "tracer" finds an even larger velocity gradient in a thin region at the top of the photosphere...
February 3, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28211454/harnessing-catalytic-pumps-for-directional-delivery-of-microparticles-in-microchambers
#5
Sambeeta Das, Oleg E Shklyaev, Alicia Altemose, Henry Shum, Isamar Ortiz-Rivera, Lyanne Valdez, Thomas E Mallouk, Anna C Balazs, Ayusman Sen
The directed transport of microparticles in microfluidic devices is vital for efficient bioassays and fabrication of complex microstructures. There remains, however, a need for methods to propel and steer microscopic cargo that do not require modifying these particles. Using theory and experiments, we show that catalytic surface reactions can be used to deliver microparticle cargo to specified regions in microchambers. Here reagents diffuse from a gel reservoir and react with the catalyst-coated surface. Fluid density gradients due to the spatially varying reagent concentration induce a convective flow, which carries the suspended particles until the reagents are consumed...
February 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/28211194/a-field-reciprocal-transplant-experiment-reveals-asymmetric-costs-of-migration-between-lake-and-river-ecotypes-of-three-spined-sticklebacks-gasterosteus-aculeatus
#6
Joshka Kaufmann, Tobias L Lenz, Martin Kalbe, Manfred Milinski, Christophe Eizaguirre
Theory of local adaptation predicts that non-adapted migrants will suffer increased costs compared to local residents. Ultimately this process can result in the reduction of gene flow and culminate in speciation. Here, we experimentally investigated the relative fitness of migrants in foreign habitats, focusing on diverging lake and river ecotypes of three-spined sticklebacks. A reciprocal transplant experiment performed in the field revealed asymmetric costs of migration: while mortality of river fish was increased under lake conditions, lake migrants suffered from reduced growth relative to river residents...
February 17, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/28211036/unconscious-phantasy-as-a-structural-principle-and-organizer-of-mental-life-the-evolution-of-a-concept-from-freud-to-klein-and-some-of-her-successors
#7
Heinz Weiss
Starting with Freud's discovery of unconscious phantasy as a means of accessing his patients' internal world, the author discusses the evolution of the concept in the work of Melanie Klein and some of her successors. Whereas Freud sees phantasy as a wish fulfilling imagination, dominated by primary process functioning and kept apart from reality testing, Klein understands phantasies as a structural function and organizer of mental life. From their very beginnings they involve object relations and gradually evolve from primitive body-near experiences to images and symbolic representations...
February 17, 2017: International Journal of Psycho-analysis
https://www.readbyqxmd.com/read/28210878/the-role-of-weak-interactions-in-lignin-polymerization
#8
Ángel Sánchez-González, Francisco J Martín-Martínez, J A Dobado
Lignin is the most abundant natural polymer composed by aromatic moieties. Its chemical composition and its abundance have focused efforts to unlock its potential as a source of aromatic compounds for many years. The lack of a proper way for lignin de-polymerization has hampered its success as a natural solution for commodity aromatic chemicals, which is also due to the lack of understanding of the underlying mechanisms of lignin polymerization. A fuller fundamental understanding of polymerization mechanisms could lead to improvements in de-polymerization strategies, and therefore a proper methodology and a predictive theoretical framework are required for such purpose...
March 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28210726/exploring-the-interaction-of-phenothiazinium-dyes-methylene-blue-new-methylene-blue-azure-a-and-azure-b-with-trna-phe-spectroscopic-thermodynamic-voltammetric-and-molecular-modeling-approach
#9
Puja Paul, Soumya Sundar Mati, Subhash Chandra Bhattacharya, Gopinatha Suresh Kumar
This study focuses on the understanding of the interaction of phenothiazinium dyes methylene blue (MB), new methylene blue (NMB), azure A (AZA) and azure B (AZB) with tRNA(Phe) with particular emphasis on deciphering the mode and energetics of the binding. Strong intercalative binding to tRNA(Phe) was observed for MB, NMB and AZB, bound by a partial intercalative mode. AZA has shown groove binding characteristics. From spectroscopic studies binding affinity values of the order of 10(5) M(-1) were deduced for these dyes; the trend varied as MB > NMB > AZB > AZA...
February 17, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28209066/determination-of-the-relative-configuration-of-terminal-and-spiroepoxides-by-computational-methods-advantages-of-the-inclusion-of-unscaled-data
#10
María M Zanardi, Alejandra G Suárez, Ariel M Sarotti
The assignment of the relative configuration of spiroepoxides or related quaternary carbon-containing oxiranes can be troublesome and difficult to achieve. The use of GIAO NMR shift calculations can provide helpful assistance in challenging cases of structural elucidation. In this regard, the DP4 probability is one of the most popular methods to be employed when only one set of experimental data is available, though modest results were obtained when dealing with spiroepoxides. Recently, we introduced an improved probability (DP4+) that includes the use of both scaled and unscaled NMR data computed at higher levels of theory...
February 17, 2017: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/28208832/mitigating-multipath-bias-using-a-dual-polarization-antenna-theoretical-performance-algorithm-design-and-simulation
#11
Lin Xie, Xiaowei Cui, Sihao Zhao, Mingquan Lu
It is well known that multipath effect remains a dominant error source that affects the positioning accuracy of Global Navigation Satellite System (GNSS) receivers. Significant efforts have been made by researchers and receiver manufacturers to mitigate multipath error in the past decades. Recently, a multipath mitigation technique using dual-polarization antennas has become a research hotspot for it provides another degree of freedom to distinguish the line-of-sight (LOS) signal from the LOS and multipath composite signal without extensively increasing the complexity of the receiver...
February 13, 2017: Sensors
https://www.readbyqxmd.com/read/28208480/transverse-vibration-of-nematic-elastomer-timoshenko-beams
#12
Dong Zhao, Ying Liu, Chuang Liu
Being a rubber-like liquid crystalline elastomer, a nematic elastomer (NE) is anisotropic viscoelastic, and displays dynamic soft elasticity. In this paper, the transverse vibration of a NE Timoshenko beam is studied based on the linear viscoelasticity theory of nematic elastomers. The governing equation of motion for the transverse vibration of a NE Timoshenko beam is derived. A complex modal analysis method is used to obtain the natural frequencies and decrement coefficients of NE beams. The influences of the nematic director rotation, the rubber relaxation time, and the director rotation time on the vibration characteristic of NE Timoshenko beams are discussed in detail...
January 2017: Physical Review. E
https://www.readbyqxmd.com/read/28208471/analysis-of-thermodiffusive-cellular-instabilities-in-continuum-combustion-fronts
#13
Hossein Azizi, Sebastian Gurevich, Nikolas Provatas
We explore numerically the morphological patterns of thermodiffusive instabilities in combustion fronts with a continuum fuel source, within a range of Lewis numbers and ignition temperatures, focusing on the cellular regime. For this purpose, we generalize the recent model of Brailovsky et al. to include distinct process kinetics and reactant heterogeneity. The generalized model is derived analytically and validated with other established models in the limit of infinite Lewis number for zero-order and first-order kinetics...
January 2017: Physical Review. E
https://www.readbyqxmd.com/read/28208446/effective-distances-for-epidemics-spreading-on-complex-networks
#14
Flavio Iannelli, Andreas Koher, Dirk Brockmann, Philipp Hövel, Igor M Sokolov
We show that the recently introduced logarithmic metrics used to predict disease arrival times on complex networks are approximations of more general network-based measures derived from random walks theory. Using the daily air-traffic transportation data we perform numerical experiments to compare the infection arrival time with this alternative metric that is obtained by accounting for multiple walks instead of only the most probable path. The comparison with direct simulations reveals a higher correlation compared to the shortest-path approach used previously...
January 2017: Physical Review. E
https://www.readbyqxmd.com/read/28208340/scaling-features-of-the-tribology-of-polymer-brushes-of-increasing-grafting-density-around-the-mushroom-to-brush-transition
#15
E Mayoral, J Klapp, A Gama Goicochea
Nonequilibrium coarse-grained, dissipative particle dynamics simulations of complex fluids, made up of polymer brushes tethered to planar surfaces immersed in a solvent yield nonmonotonic behavior of the friction coefficient as a function of the polymer grating density on the substrates, Γ, while the viscosity shows a monotonically increasing dependence on Γ. This effect is shown to be independent of the degree of polymerization, N, and the size of the system. It arises from the composition and the structure of the first particle layer adjacent to each surface that results from the confinement of the fluid...
January 2017: Physical Review. E
https://www.readbyqxmd.com/read/28207956/application-of-network-methods-for-understanding-evolutionary-dynamics-in-discrete-habitats
#16
Gili Greenbaum, Nina H Fefferman
In populations occupying discrete habitat patches, gene flow between habitat patches may form an intricate population structure. In such structures, the evolutionary dynamics resulting from interaction of gene flow patterns with other evolutionary forces may be exceedingly complex. Several models describing gene flow between discrete habitat patches have been presented in the population genetics literature; however, these models have usually addressed relatively simple settings of habitable patches, and have stopped short of providing general methodologies for addressing non-trivial gene flow patterns...
February 16, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28207024/-ru-co-x-core-complexes-with-benzimidazole-ligands-synthesis-x-ray-structure-and-evaluation-of-anticancer-activity-in-vivo
#17
Gabriella Tamasi, Antonello Merlino, Federica Scaletti, Petra Heffeter, Anton A Legin, Michael A Jakupec, Walter Berger, Luigi Messori, Bernhard K Keppler, Renzo Cini
The reaction of [Ru(CO)6Cl2], 1, with N[combining low line](3)-methylbenzimidazole (MBI) and 5,6-dimethylbenzimidazole (DMBI) afforded two new complexes with the general formula fac-[Ru(II)(CO)3Cl2L], L = MBI (2) or DMBI (4). Crystals of cis,trans-[Ru(II)(CO)2Cl2(N[combining low line](3)-MBI)2], 3, were also obtained from the mother liquor that produced 2. In the presence of water, the dissociation of Ru-N, Ru-Cl and Ru-CO bonds occurred as a function of time, water content and pH. Density functional theory structure simulations/optimizations were carried out at the Becke3LYP level of theory for evaluating the relative stability of possible conformers...
February 16, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28205402/quantum-chemistry-descriptors-for-photosensitizers-based-on-macrocycles
#18
Fernanda Bettanin, Felipe C T Antonio, Kathia M Honorio, Paula Homem-de-Mello
Phthalocyanines, porphyrins, and chlorins have been widely studied as photosensitizers. Both experimental and computational strategies are employed in order to propose new and more active molecules derived from those macrocycles. In this context, there are two main strategies used: (i) the addition of different substituents and (ii) the complexation of the macrocycle with different metallic ions. In this work, we present selected descriptors based on quantum chemistry calculations for forty macrocycles, including some approved drugs...
February 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28204941/microscopic-progression-in-the-free-radical-addition-reaction-modeling-geometry-energy-and-kinetics
#19
Yun Zhang, Hong Huang, Zhiling Liang, Houhe Liu, Ling Yi, Jinhong Zhang, Zhiqiang Zhang, Cheng Zhong, Yugang Huang, Guodong Ye
The free radical addition reaction is very important in UV curing. The benzoyl radical is the most commonly observed radical. In the addition process, the benzoyl radical adds to an acrylate monomer, forming a primary radical that has great value for subsequent research. In this article, a quantum chemical method was used to study the microscopic progression from the reactive complex to the saddle point. The reactions of three monomers (amylene, allyl methyl ether and methyl acrylate) with a benzoyl radical were evaluated in terms of geometry and energy...
March 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28204939/metadynamics-combined-with-auxiliary-density-functional-and-density-functional-tight-binding-methods-alanine-dipeptide-as-a-case-study
#20
Jerome Cuny, Kseniia Korchagina, Chemseddine Menakbi, Tzonka Mineva
Application of ab initio molecular dynamics to study free energy surfaces (FES) is still not commonly performed because of the extensive sampling required. Indeed, it generally necessitates computationally costly simulations of more than several hundreds of picoseconds. To achieve such studies, efficient density functional theory (DFT) formalisms, based on various levels of approximate computational schemes, have been developed, and provide a good alternative to commonly used DFT implementations. We report benchmark results on the conformational change FES of alanine dipeptide obtained with auxiliary density functional theory (ADFT) and second- and third-order density functional tight-binding (DFTB) methods coupled to metadynamics simulations...
March 2017: Journal of Molecular Modeling
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