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Complexity theory

Pinaki Bhattacharya, Marco Viceconti
More and more frequently, computational biomechanics deals with problems where the portion of physical reality to be modeled spans over such a large range of spatial and temporal dimensions, that it is impossible to represent it as a single space-time continuum. We are forced to consider multiple space-time continua, each representing the phenomenon of interest at a characteristic space-time scale. Multiscale models describe a complex process across multiple scales, and account for how quantities transform as we move from one scale to another...
January 19, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
Goran Kovačević, Branko Pivac
Reaction mechanisms that lead to creation of silicon-nitrogen bonds are studied in detail. These reactions are of fundamental importance for silicon nitride synthesis by plasma enhanced chemical vapour deposition from the gas mixture of silane (SiH4) and ammonia (NH3). All reactions in SiH4-NH3 plasma can be categorised as some of the basic types of reactions: bond dissociation, neutral nucleophilic substitution, radical neutralisation, neutral-radical addition, silylene addition, silylene rearrangement, radical nucleophilic addition or hydrogen abstraction reaction...
January 19, 2017: Physical Chemistry Chemical Physics: PCCP
Sarawoot Impeng, Siwarut Siwaipram, Sareeya Bureekaew, Michael Probst
We first investigate the feasibility of designing a Fe-oxo complex for the activation of alkane C-H bonds by (a) incorporating an Fe ion into a Zn-based cluster derived from a metal-organic framework (MOF) and (b) creating the Fe-oxo complex via decomposition of N2O over a Fe(2+)-substituted Zn-based cluster (Fe-Zn3O(pyrazole)6). From the energy profile, it turns out that both steps should be feasible and that the resulting Fe-oxo complex is stable. In the main step, we then investigate the reactivity of this Fe-oxo cluster for the C-H bond cleavage of ethane by calculating the reaction energy profile and analyzing the electronic structure along the relevant steps...
January 19, 2017: Physical Chemistry Chemical Physics: PCCP
Zhubin Hu, Bin Zhou, Zhenrong Sun, Haitao Sun
A methodology combining the polarizable continuum model and optimally-tuned range-separated (RS) hybrid functional was proposed for the quantitative characterization of the excited-state properties in oligoacene (from anthracene to hexacene) crystals. We show that it provides lowest vertical singlet and triplet excitation energies, singlet-triplet gap, and exciton binding energies in very good agreement with the available experimental data. We further find that it significantly outperforms its non-tuned RS counterpart and the widely used B3LYP functional, and even many-body perturbation theory within the GW approximation (based on a PBE starting point)...
January 19, 2017: Journal of Computational Chemistry
Raphael Hellwig, Tobias Paintner, Zhi Chen, Mario Ruben, Ari P Seitsonen, Florian Klappenberger, Harald Brune, Johannes V Barth
We report on the surface-guided synthesis of an unprecedented dinuclear organocobalt complex, its self-assembly into a complex nanoarchitecture, and a single-molecule level investigation of its switching behavior. Initially, an organic layer is prepared by depositing hexakis((trimethylsilyl)ethynyl)-benzene under ultra-high vacuum conditions onto Ag(111). After Co dosage at 200 Kelvin, low-temperature scanning tunneling microscopy (STM) reveals an epitaxy-mediated organization mechanism of molecules and on-surface formed host-guest complexes...
January 18, 2017: ACS Nano
Wenzhu Zhang, Feiyue Zhang, Yong-Lei Wang, Bo Song, Run Zhang, Jingli Yuan
Transition-metal complexes, ruthenium(II) and iridium(III) complexes in particular, with fascinating triplet emissions are rapidly emerging as important phosphorescent dyes for application in the sensing and imaging of biological makers in live cells and organisms. In this contribution, two red-emitting transition-metal complexes, [Ru(bpy)2(DA-phen)](PF6)2 and [Ir(ppy)2(DA-phen)](PF6) (bpy = 2,2'-bipyridine, DA-phen = 4,5-diamino-1,10-phenanthroline, and ppy = 2-phenylpyridine), were designed and synthesized as phosphorescent probes for the highly sensitive and selective detection of methylglyoxal (MGO), an essential biomarker in the etiopathogenesis of several diseases...
January 18, 2017: Inorganic Chemistry
Petr Lazar, Michal Otyepka
Molybdenum disulfide, in particular its edges, has attracted considerable attention as possible substitute of platinum catalysts for hydrogen evolution reaction. Complex nature of the reaction complicates its detailed experimental investigations, which are mostly indirect and sample dependent. Therefore, we employed density functional theory calculations to study how the properties of MoS2 Mo-edge influence the thermodynamics of hydrogen adsorption onto the edge. We discuss the effect of the computational model (one-dimensional nanostripe), border symmetry imposed by its length, sulfur saturation of the edge, and dimensionality of the material...
January 18, 2017: Chemistry: a European Journal
Peter T Campbell, Timothy R Rebbeck, Reiko Nishihara, Andrew H Beck, Colin B Begg, Alexei A Bogdanov, Yin Cao, Helen G Coleman, Gordon J Freeman, Yujing J Heng, Curtis Huttenhower, Rafael A Irizarry, N Sertac Kip, Franziska Michor, Daniel Nevo, Ulrike Peters, Amanda I Phipps, Elizabeth M Poole, Zhi Rong Qian, John Quackenbush, Harlan Robins, Peter K Rogan, Martha L Slattery, Stephanie A Smith-Warner, Mingyang Song, Tyler J VanderWeele, Daniel Xia, Emily C Zabor, Xuehong Zhang, Molin Wang, Shuji Ogino
Molecular pathological epidemiology (MPE) is a transdisciplinary and relatively new scientific discipline that integrates theory, methods, and resources from epidemiology, pathology, biostatistics, bioinformatics, and computational biology. The underlying objective of MPE research is to better understand the etiology and progression of complex and heterogeneous human diseases with the goal of informing prevention and treatment efforts in population health and clinical medicine. Although MPE research has been commonly applied to investigating breast, lung, and colorectal cancers, its methodology can be used to study most diseases...
January 17, 2017: Cancer Causes & Control: CCC
Yiding Lu, Yufan Guo, Anna Korhonen
BACKGROUND: In silico drug-target interaction (DTI) prediction plays an integral role in drug repositioning: the discovery of new uses for existing drugs. One popular method of drug repositioning is network-based DTI prediction, which uses complex network theory to predict DTIs from a drug-target network. Currently, most network-based DTI prediction is based on machine learning - methods such as Restricted Boltzmann Machines (RBM) or Support Vector Machines (SVM). These methods require additional information about the characteristics of drugs, targets and DTIs, such as chemical structure, genome sequence, binding types, causes of interactions, etc...
January 17, 2017: BMC Bioinformatics
Nicola Pedroni, Enrico Zio, Alberto Pasanisi, Mathieu Couplet
Models for the assessment of the risk of complex engineering systems are affected by uncertainties due to the randomness of several phenomena involved and the incomplete knowledge about some of the characteristics of the system. The objective of this article is to provide operative guidelines to handle some conceptual and technical issues related to the treatment of uncertainty in risk assessment for engineering practice. In particular, the following issues are addressed: (1) quantitative modeling and representation of uncertainty coherently with the information available on the system of interest; (2) propagation of the uncertainty from the input(s) to the output(s) of the system model; (3) (Bayesian) updating as new information on the system becomes available; and (4) modeling and representation of dependences among the input variables and parameters of the system model...
January 17, 2017: Risk Analysis: An Official Publication of the Society for Risk Analysis
Leon Freitag, Stefan Knecht, Celestino Angeli, Markus Reiher
We present a second-order N-electron valence state perturbation theory (NEVPT2) based on a density matrix renormalization group (DMRG) reference wave function that exploits a Cholesky decomposition of the two-electron repulsion integrals (CD-DMRG-NEVPT2). With a parameter-free multireference perturbation theory approach at hand, the latter allows us to efficiently describe static and dynamic correlation in large molecular systems. We demonstrate the applicability of CD-DMRG-NEVPT2 for spin-state energetics of spin-crossover complexes involving calculations with more than 1000 atomic basis functions...
January 17, 2017: Journal of Chemical Theory and Computation
Toshiaki Enoki, Keishi Matsuo, Joji Ohshita, Yousuke Ooyama
The julolidine-structured pyrido[3,4-b]indole dye ET-1 has been newly designed and developed as a small D-A fluorescent dye. ET-1 showed bathochromic shifts of the fluorescence band upon changing from aprotic solvents to protic solvents, as well as positive fluorescence solvatochromism. Moreover, it was found that ET-1 can form a 1 : 1 Py(N)-B complex with boron trifluoride and a hydrogen-bonded proton transfer (Py(N)-H) complex with trifluoroacetic acid, which exhibit photoabsorption and fluorescence bands at a longer wavelength region than the pristine ET-1...
January 17, 2017: Physical Chemistry Chemical Physics: PCCP
Ricardo Rozzi
The biocultural ethic recovers an understanding of the vital links between the life habits of the coinhabitants (humans and other-than-human) that share a habitat. The ″3Hs″ formal framework of the biocultural ethics provides a conceptual and methodological tool to understand and to better manage complex eco-social or biocultural systems in heterogeneous regions of the planet. From the global bioethics originally proposed by V.R. Potter, the integration of theory and praxis promoted by Alfredo Pradenas in the Bioethics Society of Chile, and the conceptual framework of biocultural ethics (including traditions of philosophical thought, scientific and Amerindians), I develop a comparative analysis of: 1...
September 2016: Cuadernos de Bioética: Revista Oficial de la Asociación Española de Bioética y Ética Médica
Uri Rogers, Min-Sung Koh
This paper explores the in vivo distributed detection of an undesired biological agent's (BAs) biomarkers by a group of biological sized nanomachines in an aqueous medium under drift. The term distributed, indicates that the system information relative to the BAs presence is dispersed across the collection of nanomachines, where each nanomachine possesses limited communication, computation, and movement capabilities. Using Brownian motion with drift, a probabilistic detection and optimal data fusion framework, coined molecular distributed detection, will be introduced that combines theory from both molecular communication and distributed detection...
December 2016: IEEE Transactions on Nanobioscience
Benjamin Brown, Daniel J Green, Matthew Wilson, Jonathan Drezner, Keith George, David Oxborough
Pre-participation screening is vital to exclude inherited cardiac conditions which have the potential to cause sudden cardiac death in seemingly healthy athletes. Recent research has questioned traditional theories of load-induced, dichotomous cardiac adaptation. We therefore considered whether a "one-size-fits-all" approach to screening can account for inter-individual differences brought about by sporting discipline, training volume, ethnicity, body size, sex and age.
January 13, 2017: Exercise and Sport Sciences Reviews
Jürgen Heck, Alejandra Escribano, Torben Steenbock, Carmen Herrmann, Conrad Stork
Attaching an organometallic unit to a dithienylethene (DTE) molecular switch can allow to vary its switching and spectroscopic properties, and to create switchable magnetic properties. In this work, two different dithienylethene molecular switches were used as a bridge between two cobalt sandwich units. The only difference between the switching cores was in the size of the cycloalkene ring connecting both thiophene rings. The complexes present different oxidation states for the cobalt atoms, which were demonstrated to determine the switching reaction...
January 16, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
Yongho Kim, Binh Khanh Mai, Sumin Park
High-valent Cu and Fe species, which are generated from dioxygen activation in metalloenzymes, carry out the functionalization of strong C-H bonds. Understanding the atomic details of the catalytic mechanism has long been one of the main objectives of bioinorganic chemistry. Large H/D kinetic isotope effects (KIEs) were observed in the C-H activation by high-valent non-heme Cu or Fe complexes in enzymes and their synthetic models. The H/D KIE depends significantly on the transition state properties, such as structure, energies, frequencies, and shape of the potential energy surface, when the tunneling effect is large...
January 16, 2017: Journal of Biological Inorganic Chemistry: JBIC
Michael Kühn, Sergei Lebedkin, Florian Weigend, Andreas Eichhöfer
The optical properties of four isostructural trinuclear chalcogenolato bridged metal complexes [Cu2Sn(SPh)6(PPh3)2], [Cu2Sn(SePh)6(PPh3)2], [Ag2Sn(SPh)6(PPh3)2] and [Cu2Ti(SPh)6(PPh3)2] have been investigated by absorption and photoluminescence spectroscopy and time-dependent density functional theory (TDDFT) calculations. All copper-tin compounds demonstrate near-infrared (NIR) phosphorescence at ∼900-1100 nm in the solid state at low temperature, which is nearly absent at ambient temperature. Stokes shifts of these emissions are found to be unusually large with values of about 1...
January 16, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
Shi Gu, Richard F Betzel, Marcelo G Mattar, Matthew Cieslak, Philip R Delio, Scott T Grafton, Fabio Pasqualetti, Danielle S Bassett
The complexity of neural dynamics stems in part from the complexity of the underlying anatomy. Yet how white matter structure constrains how the brain transitions from one cognitive state to another remains unknown. Here we address this question by drawing on recent advances in network control theory to model the underlying mechanisms of brain state transitions as elicited by the collective control of region sets. We find that previously identified attention and executive control systems are poised to affect a broad array of state transitions that cannot easily be classified by traditional engineering-based notions of control...
January 11, 2017: NeuroImage
Thomas J Lampo, Stella Stylianidou, Mikael P Backlund, Paul A Wiggins, Andrew J Spakowitz
The cellular cytoplasm is a complex, heterogeneous environment (both spatially and temporally) that exhibits viscoelastic behavior. To further develop our quantitative insight into cellular transport, we analyze data sets of mRNA molecules fluorescently labeled with MS2-GFP tracked in real time in live Escherichia coli and Saccharomyces cerevisiae cells. As shown previously, these RNA-protein particles exhibit subdiffusive behavior that is viscoelastic in its origin. Examining the ensemble of particle displacements reveals a Laplace distribution at all observed timescales rather than the Gaussian distribution predicted by the central limit theorem...
January 11, 2017: Biophysical Journal
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