Conditions for duality between fluxes and concentrations in biochemical networks

Mathematical and computational modelling of biochemical networks is often done in terms of either the concentrations of molecular species or the fluxes of biochemical reactions. When is mathematical modelling from either perspective equivalent to the other? Mathematical duality translates concepts, theorems or mathematical structures into other concepts, theorems or structures, in a one-to-one manner. We present a novel stoichiometric condition that is necessary and sufficient for duality between unidirectional fluxes and concentrations. Our numerical experiments, with computational models derived from a range of genome-scale biochemical networks, suggest that this flux-concentration duality is a pervasive property of biochemical networks. We also provide a combinatorial characterisation that is sufficient to ensure flux-concentration duality. That is, for every two disjoint sets of molecular species, there is at least one reaction complex that involves species from only one of the two sets. When unidirectional fluxes and molecular species concentrations are dual vectors, this implies that the behaviour of the corresponding biochemical network can be described entirely in terms of either concentrations or unidirectional fluxes

Conformations of dendrimers in dilute solution

Conformations of isolated homo- dendrimers of G=1-7 generations with D=1-6 spacers have been studied in the good and poor solvents, as well as across the coil-to-globule transition, by means of a version of the Gaussian self-consistent (GSC) method and Monte Carlo (MC) simulation in continuous space based on the same coarse-grained model. The latter includes harmonic springs between connected monomers and the pair-wise Lennard-Jones potential with a hard core repulsion. The scaling law for the dendrimer size, the degrees of bond stretching and steric congestion, as well as the radial density, static structure factor, and asphericity have been analysed. It is also confirmed that while smaller dendrimers have a dense core, larger ones develop a hollow domain at some separation from the centre.Comment: RevTeX, 14 pages, 19 PS figures, Accepted for publication in J. Chem. Phy

Poland\u27s Rule of Law Snowball: The Increasing Severity of the Rift Between Poland and the European Union

This Comment will analyze one of the most recent bouts between the EC and Poland in their ongoing struggle over the image of European democracy, rule of law, and national sovereignty: the European Court of Justice’s June 2021 decision in Commission v. Poland. The EU’s conceptions of western democracy and rule of law, including strict adherence to the impartiality of a judicial branch, created the EC’s legal theory for taking a stand against Poland’s autocratic government. However, Poland’s ultimate sovereignty, brought to heightened attention thanks to its far-right leadership, stands in stark opposition to the perceived overreach of the EU’s regulatory authority. Part II starts by addressing the building tension between the European Commission and Poland over the last decade and how their legal relationship has been bogged in extensive litigation over disputes regarding Poland’s attempted judicial system overhaul. This sets the stage for Part III’s discussion of the case’s facts and the ultimate ruling by the European Court of Justice in favor of the EC. Part IV will analyze the reaction in Poland to the ECJ’s decision and why the EC’s actions might serve an antithetical purpose in the ongoing rule of law struggle

Intra-chain correlation functions and shapes of homopolymers with different architectures in dilute solution

We present results of Monte Carlo study of the monomer-monomer correlation functions, static structure factor and asphericity characteristics of a single homopolymer in the coil and globular states for three distinct architectures of the chain: ring, open and star. To rationalise the results we introduce the dimensionless correlation functions rescaled via the corresponding mean-squared distances between monomers. For flexible chains with some architectures these functions exhibit a large degree of universality by falling onto a single or several distinct master curves. In the repulsive regime, where a stretched exponential times a power law form (de Cloizeaux scaling) can be applied, the corresponding exponents $\delta$ and $\theta$ have been obtained. The exponent $\delta=1/\nu$ is found to be universal for flexible strongly repulsive coils and in agreement with the theoretical prediction from improved higher-order Borel-resummed renormalisation group calculations. The short-distance exponents $\theta_{\upsilon}$ of an open flexible chain are in a good agreement with the theoretical predictions in the strongly repulsive regime also. However, increasing the Kuhn length in relation to the monomer size leads to their fast cross-over towards the Gaussian behaviour. Likewise, a strong sensitivity of various exponents $\theta_{ij}$ on the stiffness of the chain, or on the number of arms in star polymers, is observed. The correlation functions in the globular state are found to have a more complicated oscillating behaviour and their degree of universality has been reviewed. Average shapes of the polymers in terms of the asphericity characteristics, as well as the universal behaviour in the static structure factors, have been also investigated.Comment: RevTeX 12 pages, 10 PS figures. Accepted by J. Chem. Phy

High Temperature Degradation Mechanisms in Polymer Matrix Composites

Polymer matrix composites are increasingly used in demanding structural applications in which they may be exposed to harsh environments. The durability of such materials is a major concern, potentially limiting both the integrity of the structures and their useful lifetimes. The goal of the current investigation is to develop a mechanism-based model of the chemical degradation which occurs, such that given the external chemical environment and temperatures throughout the laminate, laminate geometry, and ply and/or constituent material properties, we can calculate the concentration of diffusing substances and extent of chemical degradation as functions of time and position throughout the laminate. This objective is met through the development and use of analytical models, coupled to an analysis-driven experimental program which offers both quantitative and qualitative information on the degradation mechanism. Preliminary analyses using a coupled diffusion/reaction model are used to gain insight into the physics of the degradation mechanisms and to identify crucial material parameters. An experimental program is defined based on the results of the preliminary analysis which allows the determination of the necessary material coefficients. Thermogravimetric analyses are carried out in nitrogen, air, and oxygen to provide quantitative information on thermal and oxidative reactions. Powdered samples are used to eliminate diffusion effects. Tests in both inert and oxidative environments allow the separation of thermal and oxidative contributions to specimen mass loss. The concentration dependency of the oxidative reactions is determined from the tests in pure oxygen. Short term isothermal tests at different temperatures are carried out on neat resin and unidirectional macroscopic specimens to identify diffusion effects. Mass loss, specimen shrinkage, the formation of degraded surface layers and surface cracking are recorded as functions of exposure time. Geometry effects in the neat resin, and anisotropic diffusion effects in the composites, are identified through the use of specimens with different aspect ratios. The data is used with the model to determine reaction coefficients and effective diffusion coefficients. The empirical and analytical correlations confirm the preliminary model results which suggest that mass loss at lower temperatures is dominated by oxidative reactions and that these reaction are limited by diffusion of oxygen from the surface. The mechanism-based model is able to successfully capture the basic physics of the degradation phenomena under a wide range of test conditions. The analysis-based test design is successful in separating out oxidative, thermal, and diffusion effects to allow the determination of material coefficients. This success confirms the basic picture of the process; however, a more complete understanding of some aspects of the physics are required before truly predictive capability can be achieved

Monte Carlo simulations of infinitely dilute solutions of amphiphilic diblock star copolymers

Single-chain Monte Carlo simulations of amphiphilic diblock star copolymers were carried out in continuous space using implicit solvents. Two distinct architectures were studied: stars with the hydrophobic blocks attached to the core, and stars with the polar blocks attached to the core, with all arms being of equal length. The ratio of the lengths of the hydrophobic block to the length of the polar block was varied from 0 to 1. Stars with 3, 6, 9 or 12 arms, each of length 10, 15, 25, 50, 75 and 100 Kuhn segments were analysed. Four distinct types of conformations were observed for these systems. These, apart from studying the snapshots from the simulations, have been quantitatively characterised in terms of the mean-squared radii of gyration, mean-squared distances of monomers from the centre-of-mass, asphericity indices, static scattering form factors in the Kratky representation as well as the intra-chain monomer-monomer radial distribution functions.Comment: 12 pages, 11 ps figures. Accepted for publication in J. Chem. Phy

Distinction of representations via Bruhat-Tits buildings of p-adic groups

Introductory and pedagogical treatmeant of the article : P. Broussous "Distinction of the Steinberg representation", with an appendix by Fran\c{c}ois Court\`es, IMRN 2014, no 11, 3140-3157. To appear in Proceedings of Chaire Jean Morlet, Dipendra Prasad, Volker Heiermann Ed. 2017. Contains modified and simplified proofs of loc. cit. This article is written in memory of Fran\c{c}ois Court\`es who passed away in september 2016.Comment: 33 pages, 4 figure