Brownian Molecules Formed by Delayed Harmonic Interactions

A time-delayed response of individual living organisms to information exchanged within flocks or swarms leads to the emergence of complex collective behaviors. A recent experimental setup by (Khadka et al 2018 Nat. Commun. 9 3864), employing synthetic microswimmers, allows to emulate and study such behavior in a controlled way, in the lab. Motivated by these experiments, we study a system of N Brownian particles interacting via a retarded harmonic interaction. For $N \leq 3$ , we characterize its collective behavior analytically, by solving the pertinent stochastic delay-differential equations, and for $N>3$ by Brownian dynamics simulations. The particles form molecule-like non-equilibrium structures which become unstable with increasing number of particles, delay time, and interaction strength. We evaluate the entropy and information fluxes maintaining these structures and, to quantitatively characterize their stability, develop an approximate time-dependent transition-state theory to characterize transitions between different isomers of the molecules. For completeness, we include a comprehensive discussion of the analytical solution procedure for systems of linear stochastic delay differential equations in finite dimension, and new results for covariance and time-correlation matrices.Comment: 36 pages, 26 figures, current version: further improvements and one correctio

Resummed Kinetic Field Theory: Using Mesoscopic Particle Hydrodynamics to Describe Baryonic Matter in a Cosmological Framework

Recently, Bartelmann et al. presented a 'Kinetic Field Theory' (KFT) formalism to tackle the difficulties of large scale structure formation. In this approach, the dynamics of a non-equilibrium ensemble of classical particles are examined based on methods of statistical field theory. So far, only contributions coming from dark matter were considered, which is assumed to pose an accurate description of our universe on very large scales. Nevertheless, going to smaller scales, also baryonic contributions have to be taken into account. Building on the ideas of Viermann et al. we present an effective particle model of hydrodynamics to describe baryonic matter in a cosmological framework. Using this model, the baryonic density contrast power spectrum is computed to lowest perturbative order within the resummed KFT framework of Lilow et al. We discuss the qualitative differences to the dark matter case and perform a quantitative comparison to the baryonic spectrum obtained from Eulerian perturbation theory. A subsequent paper will resolve the problem of coupling both theories describing dark and baryonic matter, respectively, to gain a full model of cosmic matter. Even though our focus is on cosmological systems only, we want to emphasize that all methods presented here are of a quite general fashion, making it applicable also to other fields.Comment: 24 pages, 2 figures, current version: added more explanatory material (especially on the underlying RKFT-formalism), added references to literature on non-linear structure formation, make difference to pure dark matter model clearer, further minor changes; content matches published versio

Brownian Thermometry Beyond Equilibrium

Since Albert Einstein's seminal 1905-paper on Brownian motion, the temperature of fluids and gases of known viscosity can be deduced from observations of the fluctuations of small suspended probe particles. We summarize recent generalizations of this standard technique of Brownian thermometry to situations involving spatially heterogeneous temperature fields and other non-equilibrium conditions in the solvent medium. The notion of effective temperatures is reviewed and its scope critically assessed. Our emphasis is on practically relevant real-world applications, for which effective temperatures have been explicitly computed and experimentally confirmed. We also elucidate the relation to the more general concept of (effective) temperature spectra and their measurement by Brownian thermospectrometry. Finally, we highlight the conceptual importance of non-equilibrium thermometry for active and biological matter, such as microswimmer suspensions or biological cells, which often play the role of non-thermal ('active') heat baths for embedded Brownian degrees of freedom.Comment: 19 pages, 4 figures, minireview, current version: added new reference

Brownian molecules formed by delayed harmonic interactions

A time-delayed response of individual living organisms to information exchanged within flocks or swarms leads to the emergence of complex collective behaviors. A recent experimental setup by (Khadka et al 2018 Nat. Commun. 9 3864), employing synthetic microswimmers, allows to emulate and study such behavior in a controlled way, in the lab. Motivated by these experiments, we study a system of N Brownian particles interacting via a retarded harmonic interaction. For N 3 , we characterize its collective behavior analytically, by solving the pertinent stochastic delay-differential equations, and for N>3 by Brownian dynamics simulations. The particles form molecule-like non-equilibrium structures which become unstable with increasing number of particles, delay time, and interaction strength. We evaluate the entropy and information fluxes maintaining these structures and, to quantitatively characterize their stability, develop an approximate time-dependent transition-state theory to characterize transitions between different isomers of the molecules. For completeness, we include a comprehensive discussion of the analytical solution procedure for systems of linear stochastic delay differential equations in finite dimension, and new results for covariance and time-correlation matrice

Resummed Kinetic Field Theory: a model of coupled baryonic and dark matter

We present a new analytical description of cosmic structure formation in a mixture of dark and baryonic matter, using the framework of Kinetic Field Theory (KFT) -- a statistical field theory for classical particle dynamics. So far, KFT has only been able to describe a single type of particles, sufficient to consider structure growth due to the gravitational interactions between dark matter. However, the influence of baryonic gas dynamics becomes increasingly relevant when describing smaller scales. In this paper, we thus demonstrate how to extend the KFT formalism as well as a previously presented resummation scheme towards describing such mixtures of two particle species. Thereby, the gas dynamics of baryons are accounted for using the recently developed model of Mesoscopic Particle Hydrodynamics. Assuming a flat $\Lambda$CDM Universe and a simplified model for the thermal gas evolution, we demonstrate the validity of this approach by computing the linear evolution of the individual and total matter power spectra between the epoch of recombination and today. Our results correctly reproduce the expected behaviour, showing a suppression of both baryonic and dark matter structure growth on scales smaller than the baryonic Jeans length, in good agreement with results from the numerical Boltzmann solver CLASS. Nonlinear corrections within this approach will be investigated in upcoming works.Comment: 23 pages, 9 figures, current version: added more explanatory material, content matches published versio

Grasping the Links in the Chain: Understanding the Unintended Consequences of International Counter-Narcotics Measures for the EU

No abstract available

SUMOylation of DRIL1 Directs Its Transcriptional Activity Towards Leukocyte Lineage-Specific Genes

DRIL1 is an ARID family transcription factor that can immortalize primary mouse fibroblasts, bypass RASV12-induced cellular senescence and collaborate with RASV12 or MYC in mediating oncogenic transformation. It also activates immunoglobulin heavy chain transcription and engages in heterodimer formation with E2F to stimulate E2F-dependent transcription. Little, however, is known about the regulation of DRIL1 activity. Recently, DRIL1 was found to interact with the SUMO-conjugating enzyme Ubc9, but the functional relevance of this association has not been assessed. Here, we show that DRIL1 is sumoylated both in vitro and in vivo at lysine 398. Moreover, we provide evidence that PIASy functions as a specific SUMO E3-ligase for DRIL1 and promotes its sumoylation both in vitro and in vivo. Furthermore, consistent with the subnuclear localization of PIASy in the Matrix-Associated Region (MAR), SUMO-modified DRIL1 species are found exclusively in the MAR fraction. This post-translational modification interferes neither with the subcellular localization nor the DNA-binding activity of the protein. In contrast, DRIL1 sumoylation impairs its interaction with E2F1 in vitro and modifies its transcriptional activity in vivo, driving transcription of subset of genes regulating leukocyte fate. Taken together, these results identify sumoylation as a novel post-translational modification of DRIL1 that represents an important mechanism for targeting and modulating DRIL1 transcriptional activity

MassCode Liquid Arrays as a Tool for Multiplexed High-Throughput Genetic Profiling

Multiplexed detection assays that analyze a modest number of nucleic acid targets over large sample sets are emerging as the preferred testing approach in such applications as routine pathogen typing, outbreak monitoring, and diagnostics. However, very few DNA testing platforms have proven to offer a solution for mid-plexed analysis that is high-throughput, sensitive, and with a low cost per test. In this work, an enhanced genotyping method based on MassCode technology was devised and integrated as part of a high-throughput mid-plexing analytical system that facilitates robust qualitative differential detection of DNA targets. Samples are first analyzed using MassCode PCR (MC-PCR) performed with an array of primer sets encoded with unique mass tags. Lambda exonuclease and an array of MassCode probes are then contacted with MC-PCR products for further interrogation and target sequences are specifically identified. Primer and probe hybridizations occur in homogeneous solution, a clear advantage over micro- or nanoparticle suspension arrays. The two cognate tags coupled to resultant MassCode hybrids are detected in an automated process using a benchtop single quadrupole mass spectrometer. The prospective value of using MassCode probe arrays for multiplexed bioanalysis was demonstrated after developing a 14plex proof of concept assay designed to subtype a select panel of Salmonella enterica serogroups and serovars. This MassCode system is very flexible and test panels can be customized to include more, less, or different markers

DAF-12 Regulates a Connected Network of Genes to Ensure Robust Developmental Decisions

The nuclear receptor DAF-12 has roles in normal development, the decision to pursue dauer development in unfavorable conditions, and the modulation of adult aging. Despite the biologic importance of DAF-12, target genes for this receptor are largely unknown. To identify DAF-12 targets, we performed chromatin immunoprecipitation followed by hybridization to whole-genome tiling arrays. We identified 1,175 genomic regions to be bound in vivo by DAF-12, and these regions are enriched in known DAF-12 binding motifs and act as DAF-12 response elements in transfected cells and in transgenic worms. The DAF-12 target genes near these binding sites include an extensive network of interconnected heterochronic and microRNA genes. We also identify the genes encoding components of the miRISC, which is required for the control of target genes by microRNA, as a target of DAF-12 regulation. During reproductive development, many of these target genes are misregulated in daf-12(0) mutants, but this only infrequently results in developmental phenotypes. In contrast, we and others have found that null daf-12 mutations enhance the phenotypes of many miRISC and heterochronic target genes. We also find that environmental fluctuations significantly strengthen the weak heterochronic phenotypes of null daf-12 alleles. During diapause, DAF-12 represses the expression of many heterochronic and miRISC target genes, and prior work has demonstrated that dauer formation can suppress the heterochronic phenotypes of many of these target genes in post-dauer development. Together these data are consistent with daf-12 acting to ensure developmental robustness by committing the animal to adult or dauer developmental programs despite variable internal or external conditions