scholarly journals The Compressed Vocabulary of Microbial Life

2021 ◽  
Vol 12 ◽  
Author(s):  
Gustavo Caetano-Anollés
Keyword(s):  
Evolutionary Strategies ◽  
Module Structure ◽  
Microbial World ◽  
Scale Free ◽  
Microbial Life ◽  
Size Dependent ◽  
Cellular Life ◽  
Universal Common Ancestor ◽  
Evolutionary Genomic ◽  
The Impact

Communication is an undisputed central activity of life that requires an evolving molecular language. It conveys meaning through messages and vocabularies. Here, I explore the existence of a growing vocabulary in the molecules and molecular functions of the microbial world. There are clear correspondences between the lexicon, syntax, semantics, and pragmatics of language organization and the module, structure, function, and fitness paradigms of molecular biology. These correspondences are constrained by universal laws and engineering principles. Macromolecular structure, for example, follows quantitative linguistic patterns arising from statistical laws that are likely universal, including the Zipf’s law, a special case of the scale-free distribution, the Heaps’ law describing sublinear growth typical of economies of scales, and the Menzerath–Altmann’s law, which imposes size-dependent patterns of decreasing returns. Trade-off solutions between principles of economy, flexibility, and robustness define a “triangle of persistence” describing the impact of the environment on a biological system. The pragmatic landscape of the triangle interfaces with the syntax and semantics of molecular languages, which together with comparative and evolutionary genomic data can explain global patterns of diversification of cellular life. The vocabularies of proteins (proteomes) and functions (functionomes) revealed a significant universal lexical core supporting a universal common ancestor, an ancestral evolutionary link between Bacteria and Eukarya, and distinct reductive evolutionary strategies of language compression in Archaea and Bacteria. A “causal” word cloud strategy inspired by the dependency grammar paradigm used in catenae unfolded the evolution of lexical units associated with Gene Ontology terms at different levels of ontological abstraction. While Archaea holds the smallest, oldest, and most homogeneous vocabulary of all superkingdoms, Bacteria heterogeneously apportions a more complex vocabulary, and Eukarya pushes functional innovation through mechanisms of flexibility and robustness.

R&D Heterogeneity and the Impact of R&D Subsidies*

2021 ◽  
Author(s):  
Sigurd M⊘lster Galaasen ◽  
Alfonso Irarrazabal
Keyword(s):  
Economic Impact ◽  
Growth Model ◽  
Relative Size ◽  
Schumpeterian Growth ◽  
Size Dependent ◽  
Investment Growth ◽  
The Impact ◽  
D Investment ◽  
Model Fits

Abstract This paper studies the determinants of R&D heterogeneity and the economic impact of R&D subsidies. We estimate a Schumpeterian growth model featuring firms with heterogeneous innovation efficiencies. The model fits well the R&D investment distribution, and the frequency and relative size of R&D performers. Using the model we study the impact of a Norwegian R&D reform targeting firms with R&D spending below a certain threshold. The size-dependent subsidy increases aggregate R&D investment by 11.7%, but reduces growth and welfare. In contrast, a uniform subsidy stimulates investment, growth and welfare.

scholarly journals Nonlocal and Size-Dependent Dielectric Function for Plasmonic Nanoparticles

2019 ◽  
Vol 9 (15) ◽  
pp. 3083
Author(s):  
Kai-Jian Huang ◽  
Shui-Jie Qin ◽  
Zheng-Ping Zhang ◽  
Zhao Ding ◽  
Zhong-Chen Bai
Keyword(s):  
Metallic Nanoparticles ◽  
High Efficiency ◽  
Finite Size ◽  
Plasmonic Nanostructures ◽  
Accurate Analysis ◽  
Finite Size Effects ◽  
Size Dependent ◽  
Quantum Size ◽  
The Impact ◽  
Electron Energy Loss

We develop a theoretical approach to investigate the impact that nonlocal and finite-size effects have on the dielectric response of plasmonic nanostructures. Through simulations, comprehensive comparisons of the electron energy loss spectroscopy (EELS) and the optical performance are discussed for a gold spherical dimer system in terms of different dielectric models. Our study offers a paradigm of high efficiency compatible dielectric theoretical framework for accounting the metallic nanoparticles behavior combining local, nonlocal and size-dependent effects in broader energy and size ranges. The results of accurate analysis and simulation for these effects unveil the weight and the evolution of both surface and bulk plasmons vibrational mechanisms, which are important for further understanding the electrodynamics properties of structures at the nanoscale. Particularly, our method can be extended to other plasmonic nanostructures where quantum-size or strongly interacting effects are likely to play an important role.

scholarly journals Localisation determines the optimal noise rate for quantum transport

2021 ◽  
Author(s):  
Alexandre Coates ◽  
Brendon W Lovett ◽  
Erik Gauger
Keyword(s):  
Energy Transport ◽  
Optimal Transport ◽  
Detailed Balance ◽  
Finite Size ◽  
Temperature Limit ◽  
Transport Efficiency ◽  
Size Dependent ◽  
Noise Rate ◽  
Pure Dephasing ◽  
The Impact

Abstract Environmental noise plays a key role in determining the efficiency of transport in quantum systems. However, disorder and localisation alter the impact of such noise on energy transport. To provide a deeper understanding of this relationship we perform a systematic study of the connection between eigenstate localisation and the optimal dephasing rate in 1D chains. The effects of energy gradients and disorder on chains of various lengths are evaluated and we demonstrate how optimal transport efficiency is determined by both size-independent, as well as size-dependent factors. By discussing how size-dependent influences emerge from finite size effects we establish when these effects are suppressed, and show that a simple power law captures the interplay between size-dependent and size-independent responses. Moving beyond phenomenological pure dephasing, we implement a finite temperature Bloch-Redfield model that captures detailed balance. We show that the relationship between localisation and optimal environmental coupling strength continues to apply at intermediate and high temperature but breaks down in the low temperature limit.

scholarly journals GAME THEORY BASED MULTI CRITERIA DECISION MAKING PROBLEM UNDER UNCERTAINTY: A CASE STUDY ON INDIAN TEA INDUSTRY

2018 ◽  
Vol 19 (1) ◽  
pp. 154-175 ◽  
Author(s):  
Animesh DEBNATH ◽  
Abhirup BANDYOPADHYAY ◽  
Jagannath ROY ◽  
Samarjit KAR
Keyword(s):  
Game Theory ◽  
Decision Making ◽  
Evolutionary Game ◽  
Market Volatility ◽  
Evolutionary Strategies ◽  
Multi Criteria Decision Making ◽  
Tea Industry ◽  
Multi Agent ◽  
The Impact ◽  
Indian Tea

The long-term evolution of multi agent multi criteria decision making (MCDM) and to obtain sustainable decision a novel methodology is proposed based on evolutionary game theory. In this paper multi agent MCDM is represented as an evolutionary game and the evolutionary strategies are defined as sustainable decisions. Here we consider the problem of decision making in Indian Tea Industry. The agents in this game are essentially Indian Tea Estate owner and Indian Tea board. The replicator dynamics of the evolutionary game are studied to obtain evolutionary strategies which could be defined as sustainable strategies. The multi agent MCDM in Indian Tea Industry is considered under different socio-political and Corporate Social Responsibility scenario and groups of Indian Tea Industry. Again, the impacts of imprecision and market volatility on the outcome of some strategies (decisions) are studied. In this paper the imprecision on the impact of the strategies are modelled as fuzzy numbers whereas the market volatility is taken into account as white noise. Hence the MCDM problem for Indian Tea Industry is modelled as a hybrid evolutionary game. The probabilities of strategies are obtained by solving hybrid evolutionary game and could be represented as a Dempster-Shafer belief structure. The simulation results facilitate the Decision Makers to choose the strategies (decisions) under different type of uncertainty.

scholarly journals Aminophosphine Reduction Mechanisms and the Synthesis of Indium Phosphide Nanomaterials

2021 ◽  
Author(s):  
◽  
Geoffry Laufersky
Keyword(s):  
Indium Phosphide ◽  
Density Functional ◽  
Large Scale ◽  
Visible Spectrum ◽  
Size Dependent ◽  
Reduction Mechanisms ◽  
Highly Sensitive ◽  
Dependent Absorption ◽  
Entire Visible Spectrum ◽  
The Impact

<p>Indium phosphide (InP) nanomaterials are attractive for countless technological applications due to their well-placed band gap energies. The quantum confinement of these semiconductors can give rise to size-dependent absorption and emission features throughout the entire visible spectrum. Therefore, InP materials can be employed as low-toxicity fluorophores that can be implemented in high value avenues such as biological probes, lighting applications, and lasing technologies. However, large scale development of these quantum dots (QDs) has been stymied by the lack of affordable and safe phosphorus precursors. Syntheses have largely been restricted to the use of dangerous chemicals such as tris(trimethylsilyl)phosphine ((TMS)₃P), which is costly and highly sensitive to oxygen and water. Recently, less-hazardous tris(dialkylamino)phosphines have been introduced to produce InP QDs on par with those utilizing (TMS)₃P. However, a poor understanding of the reaction mechanics has resulted in difficulties tuning and optimizing this method.  In this work, density functional theory (DFT) is used to identify the mechanism of this aminophosphine precursor conversion. This understanding is then implemented to design an improved InP QD synthesis, allowing for the production of high-quality materials outside of glovebox conditions. Time is spent understanding the impact of different precursor salts on the reaction mechanisms and discerning their subsequent effects on nanoparticle size and quality. The motivation of this work is to formulate safer and less technical indium phosphide quantum dot syntheses to foster non-specialist and industrial implementation of these materials.</p>

scholarly journals Viruses of Polar Aquatic Environments

Viruses ◽  
2019 ◽  
Vol 11 (2) ◽  
pp. 189 ◽  
Author(s):  
Sheree Yau ◽  
Mansha Seth-Pasricha
Keyword(s):  
Community Dynamics ◽  
Spatial Scales ◽  
Extreme Environments ◽  
Cold Climate ◽  
Polar Regions ◽  
Microbial Life ◽  
The North ◽  
Cellular Life ◽  
Antarctic Continent ◽  
Cycling Of Nutrients

The poles constitute 14% of the Earth’s biosphere: The aquatic Arctic surrounded by land in the north, and the frozen Antarctic continent surrounded by the Southern Ocean. In spite of an extremely cold climate in addition to varied topographies, the polar aquatic regions are teeming with microbial life. Even in sub-glacial regions, cellular life has adapted to these extreme environments where perhaps there are traces of early microbes on Earth. As grazing by macrofauna is limited in most of these polar regions, viruses are being recognized for their role as important agents of mortality, thereby influencing the biogeochemical cycling of nutrients that, in turn, impact community dynamics at seasonal and spatial scales. Here, we review the viral diversity in aquatic polar regions that has been discovered in the last decade, most of which has been revealed by advances in genomics-enabled technologies, and we reflect on the vast extent of the still-to-be explored polar microbial diversity and its “enigmatic virosphere”.

scholarly journals Benefits and Costs of Animal Virulence for Microbes

mBio ◽  
2019 ◽  
Vol 10 (3) ◽  
Author(s):  
Arturo Casadevall ◽  
Liise-anne Pirofski
Keyword(s):  
Infectious Diseases ◽  
Vantage Point ◽  
Animal Disease ◽  
Microbial Pathogenesis ◽  
Costs And Benefits ◽  
Microbial World ◽  
Microbial Survival ◽  
The Impact ◽  
Benefits And Costs

ABSTRACT This essay is written from the vantage point of the microbial world. While the focus of much thought in the microbial pathogenesis and infectious diseases fields has been on the impact of host-microbe interaction on the host, here we ask questions about what happens to the microbe. What are the costs and benefits for microbes of having the capacity for virulence? Our exploration of this topic leads us to conclude that virulence confers very few benefits for microbes, unless disease is necessary for microbial survival through host-to-host spread. In fact, the capacity for virulence is often fraught with risk for microbes, including host dependence and the threat of extinction. The costs of virulence may explain why, relative to their enormous numbers in nature, very few microbes are actually associated with human and animal disease.

SE2IR Invest Market Rumor Spreading Model Considering Hesitating Mechanism

2019 ◽  
Vol 7 (1) ◽  
pp. 54-69 ◽  
Author(s):  
Hongxing Yao ◽  
Xiangyang Gao
Keyword(s):  
Mean Field ◽  
Basic Reproductive Number ◽  
Reproductive Number ◽  
Field Equations ◽  
Rumor Spreading ◽  
Immunization Strategy ◽  
Scale Free ◽  
Spreading Model ◽  
Mean Field Equations ◽  
The Impact

Abstract According to the actual situation of investor network, a SE2IR rumor spreading model with hesitating mechanism is proposed, and the corresponding mean-field equations is obtained on scale-free network. In this paper, we first combine the theory of spreading dynamics and find out the basic reproductive number R0. And then analyzes the stability of the rumor-free equilibrium and the final rumor size. Finally, we discuss random immune strategies and target immune strategies for the rumor spreading, respectively. Through numerical simulation, we can draw the following conclusions: Reducing the fuzziness and attractiveness of invest market rumor can effectively reduce the impact of rumor. And the target immunization strategy is more effective than the random immunization strategy for the communicators in the invest investor network.

scholarly journals OHNOLOGS v2: a comprehensive resource for the genes retained from whole genome duplication in vertebrates

2019 ◽  
Author(s):  
Param Priya Singh ◽  
Hervé Isambert
Keyword(s):  
Teleost Fish ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Genetic Diseases ◽  
Genomic Analysis ◽  
Biased Sampling ◽  
Whole Genome ◽  
Genome Duplications ◽  
Evolutionary Genomic ◽  
The Impact

Abstract All vertebrates including human have evolved from an ancestor that underwent two rounds of whole genome duplication (2R-WGD). In addition, teleost fish underwent an additional third round of genome duplication (3R-WGD). The genes retained from these genome duplications, so-called ohnologs, have been instrumental in the evolution of vertebrate complexity, development and susceptibility to genetic diseases. However, the identification of vertebrate ohnologs has been challenging, due to lineage specific genome rearrangements since 2R- and 3R-WGD. We previously identified vertebrate ohnologs using a novel synteny comparison across multiple genomes. Here, we refine and apply this approach on 27 vertebrate genomes to identify ohnologs from both 2R- and 3R-WGD, while taking into account the phylogenetically biased sampling of available species. We assemble vertebrate ohnolog pairs and families in an expanded OHNOLOGS v2 database. We find that teleost fish have retained more 2R-WGD ohnologs than mammals and sauropsids, and that these 2R-ohnologs have retained significantly more ohnologs from the subsequent 3R-WGD than genes without 2R-ohnologs. Interestingly, species with fewer extant genes, such as sauropsids, have retained similar or higher proportions of ohnologs. OHNOLOGS v2 should allow deeper evolutionary genomic analysis of the impact of WGD on vertebrates and can be freely accessed at http://ohnologs.curie.fr.

Sign in / Sign up

Export Citation Format

Share Document