89 research outputs found
Viruses and civilizations. The new impact of biocataclysms on the evolution of sociocultural models and civilization projects
No full textThe article considers the situation associated with the coronavirus pandemic in Russia and in the world as a whole and its possible consequences for the economy, politics, and sociocultural processes. The author analyzes the publications that have appeared recently and focused on questions about what the world expects after the end of the pandemic. In the reviews of the topic “The World after the Pandemiс” some optical defects typical of technocratic positivism were revealed. The reduction of levels of psychohistory and psychoideology leads to an underestimation of the scale of the disaster and the breakdown of communication between the regulator and the population. The “historical size” of events of this kind is set by the great plague epidemics in their influence on the way out of the Middle Ages into the Modern civilization. Such comparability confirms the appeal to images of emptiness in art and philosophy. The symbolism of “life on pause” speaks about the scale and possible irreversibility of changes, at least in local civilizations. Thus, the coronacrisis undermines the foundations of the resource society and the “civilization of oil” – the basis of the Russian political ethnonarcissism. A closed circuit with positive feedback is formed, its swing is fraught with landslide changes and risks with unacceptable damage. Tough clashes with reality strike at the regimes of simulation, political postmodernism in general. Ideas about “political eschatology” and plurality of interpretations of the concept of civilization allow us to discuss the prospects of transformation of the civilizational project in Russia
Two stage decoherence of optical phonons in long oligomers
No full textIntramolecular energy transport is generally responsible for chemical energy
balance in molecular systems. The transport is fast and efficient if energy is
transferred by optical phonons in periodic oligomers, but its efficiently is
limited by decoherence emerging due to anharmonic interactions with acoustic
phonons. We show that in the most common case of the optical phonon band being
narrower than the acoustic bands decoherence takes place in two stages. The
faster stage involves optical phonon multiple forward scattering due to
absorption and emission of transverse acoustic phonons, i. e. collective
bending modes with a quadratic spectrum; the transport remains ballistic and
the speed can be altered. The subsequent slower stage involves phonon
backscattering in multiphonon processes involving two or more acostic phonons
resulting is a switch to diffusive transport. If the initially excited optical
phonon possesses a relatively small group velocity, then its equilibration in
the first stage is accompanied by its acceleration due to its transitions to
states propagating faster. This theoretical expectation is consistent with the
recent measurements of optical phonon transport in alkane chains, accelerating
with increasing the chain length.Comment: 21 page, 10 figure
High heterogeneity in genomic differentiation between phenotypically divergent songbirds: A test of mitonuclear co-introgression
No full textAbstractComparisons of genomic variation among closely related species often show more differentiation in mitochondrial DNA (mtDNA) and sex chromosomes than in autosomes, a pattern expected due to the differing effective population sizes and evolutionary dynamics of these genomic components. Yet, introgression can cause species pairs to deviate dramatically from general differentiation trends. The yellowhammer (Emberiza citrinella) and pine bunting (E. leucocephalos) are hybridizing avian sister species that differ greatly in appearance and moderately in nuclear DNA, but that show no mtDNA differentiation. This discordance is best explained by adaptive mtDNA introgression—a process that can select for co-introgression at nuclear genes with mitochondrial functions (mitonuclear genes). To better understand these discordant differentiation patterns and characterize nuclear differentiation in this system, we investigated genome-wide differentiation between allopatric yellowhammers and pine buntings and compared it to what was seen previously in mtDNA. We found significant nuclear differentiation that was highly heterogeneous across the genome, with a particularly wide differentiation peak on the sex chromosome Z. We further investigated mitonuclear gene co-introgression between yellowhammers and pine buntings and found support for this process in the direction of pine buntings into yellowhammers. Genomic signals indicative of co-introgression were common in mitonuclear genes coding for subunits of the mitoribosome and electron transport chain complexes. Such introgression of mitochondrial DNA and mitonuclear genes provides a possible explanation for the patterns of high genomic heterogeneity in genomic differentiation seen among some species groups.MethodsFull methods can be found in the linked 2023 Heredity paper with additional details provided in the attached scripts and text files. Briefly, DNA was extracted from blood and tissue samples taken from avian individuals and then sequenced using a Genotyping-By-Sequencing approach. DNA reads were processed using the scripts provided in the "GBS_Reads_processing_to_VCF.txt" file and then analyzed using the scripts provided in both the "Heredity_Pub_PopulationGenetic_Analysis_Code.R" and "Heredity_Pub_Mitonuclear_Analysis_Code.R" files. The former of these two R files contains general genetic analyses while the latter contains mitonuclear analyses.Usage notesGBS_Reads_processing_to_VCF.txt
This text file contains the scripts used to convert raw Illumina GBS sequence reads into a genome-wide variant site file (in "012NA" format) and into chromosome-specific "all sites" files which include both variant and invariant sites (in "012NA" format). The resulting files were input into R and investigated with genetic and mitonuclear analyses. These scripts were adapted from those applied in Irwin et al. (2018; citation below). The scripts employed by Irwin et al. (2018) are available on Dryad at: https://doi.org/10.5061/dryad.4j2662g
GBS_Plate#_Barcods.txt
These four text files contain the nucleotide barcodes associated with DNA samples that were sequenced on four GBS plates. This information is necessary when running the GBS read processing scripts contained within "GBS_Reads_processing_to_VCF.txt".
Genome_wide_variant_site_files.zip
This zip file contains the files produced (.indv, .pos, .012NA) when using the scripts available in "GBS_Reads_processing_to_VCF.txt" to create a genome-wide variant site dataset (in "012NA" format). The produced files were loaded into R and analyzed using the scripts contained in "Heredity_Pub_Mitonuclear_Analysis_Code.R" and "Heredity_Pub_PopulationGenetic_Analysis_Code.R".
Chromosome_Info_site_files.zip
This zip file contains the files produced (.indv, .pos, .012NA) when using the scripts available in "GBS_Reads_processing_to_VCF.txt" to create chromosome-specific "all sites" datasets that contain both variant and invariant sites (in "012NA" format). There is a trio of files associated with each of the chromosomes analyzed in this research. The "all sites" files were loaded into R and analyzed using the scripts contained in "Heredity_Pub_Mitonuclear_Analysis_Code.R" and "Heredity_Pub_PopulationGenetic_Analysis_Code.R".
Heredity_Pub_PopulationGenetic_Analysis_Code.R
This R file contains the R scripts used to both conduct the genetic analyses and produce the figures found in the associated paper. Author comments accompany major lines of code to explain their purpose. The input files for these analyses can be found within "Genome-wide_variant_site_files.zip" and "Chromosome_Info_site_files.zip". To run these analyses, the "Genomics_R_functions_TajD.Ellen.Fixes.R" file must also be loaded in R. This file contains necessary functions that are applied in the analysis scripts. Also, two additional CSV files ("All_Plates_Fst_Allo_Sym.csv" and "Allopatric_Map_Info.csv") are needed to run certain parts of the analysis.
Heredity_Pub_Mitonuclear_Analysis_Code.R
This R file contains the R scripts used to conduct the mitonuclear analyses described in the associated paper. Author comments accompany major lines of code to explain their purpose. The input files for these analyses can be found within "Genome-wide_variant_site_files.zip" and "Chromosome_Info_site_files.zip". To run these analyses, the "Genomics_R_functions_TajD.Ellen.Fixes.R" file must also be loaded into R. This file contains necessary functions that are applied in the analysis scripts. Also, one additional CSV file ("All_Plates_Fst_Allo_Sym.csv") is needed to run certain parts of the analysis.
Genomics_R_functions_TajD.Ellen.Fixes.R
This R file contains the R functions that were used to conduct the genetic and mitonuclear analyses contained within the "Heredity_Pub_PopulationGenetic_Analysis_Code.R" and "Heredity_Pub_Mitonuclear_Analysis_Code.R" files. This file was adapted from the functions file employed by Irwin et al. (2018) but contains some modifications and additional functions that can be used to calculate Tajima's D for the populations being analyzed. The scripts employed by Irwin et al. (2018) are available on Dryad at: https://doi.org/10.5061/dryad.4j2662g
All_Plates_Fst_Allo_Sym.csv
This CSV file contains the descriptive metadata for the samples analyzed in this study. This file contains information on the sex, phenotype, species, distribution and location of collection for each sample. This file was used to sort samples into discrete groups that were then compared in the genetic and mitonuclear analyses contained within the "Heredity_Pub_PopulationGenetic_Analysis_Code.R" and "Heredity_Pub_Mitonuclear_Analysis_Code.R" files.
Allopatric_Map_Info.csv
This CSV file contains the information necessary to create the map included in Figure 1 of the associated paper using scripts contained within the "Heredity_Pub_PopulationGenetic_Analysis_Code.R" file. This CSV file describes the number and the identities of individuals collected at specific sampling locations as well as the latitude and longitude of each sampling location. Some sampling locations were combined on the map because they were too close together to be shown accurately. Information on how sampling locations were combined can be found in the associated paper.
References:
Irwin, D. E., Milá, B., Toews, D. P. L., Brelsford, A., Kenyon, H. L., Porter, A. N., Grossen, C., Delmore, K. E., Alcaide, M., & Irwin, J. H. (2018). A comparison of genomic islands of differentiation across three young avian species pairs. Molecular Ecology, 27(23), 4839-4855. https://doi.org/10.1111/mec.14858</p
Maximum propagation speed and Cherenkov effect in optical phonon transport through periodic molecular chains
No full textOptical phonons serve as the fast and efficient carriers of energy across
periodic polymers due to their delocalization, large group velocity because of
covalent bonding and large energy quantum compared to that for acoustic
phonons, as it was observed in a number of recent measurements in different
oligomers. However, this transport is dramatically sensitive to anharmonic
interactions, including the unavoidable interaction with acoustic phonons
responsible for the transport decoherence, suppressing ballistic transport at
long distances. Here we show that this decoherence is substantially suppressed
if the group velocity of optical phonons is less than the sound velocity of
acoustic phonons; otherwise ballistic transport is substantially suppressed by
a Cherenkov's like emission of acoustic phonons. This conclusion is justified
considering energy and momentum conservation during phonon absorption or
emission and supported by the numerical evaluation of lifetimes of the optical
phonons. It is also consistent with the recent experimental investigations of
ballistic optical phonon transport in oligomers with minor exception of
relatively short oligophenylenes.Comment: 35 pages, 16 figures, to appear in Journal of Chemical Physic
Double Poisson brackets on free associative algebras
No full textAMS Special Session on Noncommutative Birational Geometry, Representations and Cluster Algebras, January 6–7, 2012 Boston, MA. We discuss double Poisson structures in sense of M. Van den Berghon free associative algebras focusing on the case of quadratic Poisson brackets.We establish their relations with an associative version of Yang-Baxter equa-tions, we study a bi-hamiltonian property of the linear-quadratic pencil of thedouble Poisson structure and propose a classification of the quadratic doublePoisson brackets in the case of the algebra with two free generators. Manynew examples of quadratic double Poisson brackets are proposed
Structure Dependent Energy Transport: Relaxation-Assisted 2DIR Measurements and Theoretical Studies
No full textSemiclassical Model for Vibrational Dynamics in Polyatomic Molecules: Investigation of Internal Vibrational Relaxation
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