Transition event statistics in genetics and disordered kinetics. Theoretical approaches for extracting rate distributions from experimental data

We study the analogies between the theory of rate processes in disordered systems and the overdispersed molecular clocks in evolutionary biology. A biological "molecular clock" expresses the statistics of the number of amino acid or nucleotide substitutions during evolution. Random variations of the evolution rates lead to statistical (overdispersed) molecular clocks which are described by random point processes with random substitution rates. We find that the models for overdispersed molecular clocks are equivalent to those of the random-rate or random channel models used in disordered kinetics. The number of transport (reaction) events in disordered kinetics plays the same role as the number of substitution events in molecular biology. We study the connections between the (observed) statistics of the transition events and the statistics of random rate coefficients and random channels; a unified approach is developed which is valid both in molecular biology and in disordered kinetics. We develop methods for extracting statistical information about the variations of rate coefficients from experimental or observed data regarding the fluctuations of the numbers of substitution, reaction, or transport events. For systems with static disorder, the observed statistics of the number of reaction events, expressed in terms of probabilities at a given time or by the cumulants of the number of transition events at a given time, contains the information necessary for evaluating the cumulants or the probability density of the rate coefficients or the density of states for random channel kinetics. For dynamic disorder this is not possible; further information about multitime probability distributions of the reaction events is needed.     

Phthalocyanine-based field-effect transistors as gas sensors

In this review molecular field-effect transistors are described and compared with their gate-modified inorganic counterparts. The different processes involved in gas sensing are summarized. The advantages of transistors on resistors are demonstrated. The sensitivity of molecular field-effect transistors to strong oxidizing species, for example ozone, is detailed and compared with their sensitivity to humidity and volatile organic compounds. Application to ozone monitoring in urban atmospheres is also described.     

Has the world economy reached its globalization limit?

The economy globalization measure problem is discussed. Four macroeconomic indices of twenty among the “richest” countries are examined. Four types of “distances” are calculated. Two types of networks are next constructed for each distance measure definition. It is shown that the globalization process can be best characterised by an entropy measure, based on entropy Manhattan distance. It is observed that a globalization maximum was reached during the interval 1970-2000. More recently a deglobalization process has been observed.     

Axiomatisability and hardness for universal Horn classes of hypergraphs

We consider hypergraphs as symmetric relational structures. In this setting, we characterise finite axiomatisability for finitely generated universal Horn classes of loop-free hypergraphs. An Ehrenfeucht–Fraïssé game argument is employed to show that the results continue to hold when restricted to first order definability amongst finite structures. We are also able to show that every interval in the homomorphism order on hypergraphs contains a continuum of universal Horn classes and conclude the article by characterising the intractability of deciding membership in universal Horn classes generated by finite loop-free hypergraphs.     

A note on the surjectivity of operators on vector bundles over discrete spaces

In this note we give a short and self-contained proof for a criterion of Eidelheit on the solvability of linear equations in infinitely many variables. We use this criterion to study the surjectivity of magnetic Schrödinger operators on bundles over graphs.     

Inverse temperature transition of a biomimetic elastin model: reactive flux analysis of folding/unfolding and its coupling to solvent dielectric relaxation

The inverse temperature transition (ITT) of a biomimetic model for elastin, capped GVG(VPGVG) in liquid water, is investigated by a comprehensive classical molecular dynamics study. The temperature dependence of the solvation structure and dynamics of the octapeptide are compared using three common force fields, CHARMM, GROMOS, and OPLS. While these force fields differ in quantitative detail, they all predict this octapeptide to undergo a "folding transition" to closed conformations upon heating and a subsequent "unfolding transition" to open conformations at still higher temperatures, thus reproducing the ITT scenario. The peptide kinetics is analyzed within the reactive flux formalism applied to the largest-amplitude mode extracted from principal component analysis, and the solvent's dielectric fluctuations are obtained from the total water dipole autocorrelations. Most importantly, preliminary evidence for an intimate coupling of peptide folding/unfolding dynamics, and thus the ITT, and dielectric relaxation of bulk water is given, possibly being consistent with a "slave mode" picture.     

The Division Relation: Congruence Conditions and Axiomatisability

We examine a universal algebraic abstraction of the semigroup theoretic concept of “divides:” a divides b in an algebra A if for some n ∈ ω, there is a term t(x, y ₁,…, y _n ) involving all of the listed variables, and elements c ₁,…, c _n such that t ^A (a, c ₁,…, c _n ) = b. The first order definability of this relation is shown to be a very broad generalisation of some familiar congruence properties, such as definability of principal congruences. The algorithmic problem of deciding when a finitely generated variety has this relation definable is shown to be equivalent to an open problem concerning flat algebras. We also use the relation as a framework for establishing some results concerning the finite axiomatisability of finitely generated varieties.     

Understanding the mechanism of direct visible-light-activated [2 + 2] cycloadditions mediated by Rh and Ir photocatalysts: combined computational and spectroscopic studies

The mechanism of [2 + 2] cycloadditions activated by visible light and catalyzed by bis-cyclometalated Rh(iii) and Ir(iii) photocatalysts was investigated, combining density functional theory calculations and spectroscopic techniques. Experimental observations show that the Rh-based photocatalyst produces excellent yield and enantioselectivity whereas the Ir-photocatalyst yields racemates. Two different mechanistic features were found to compete with each other, namely the direct photoactivation of the catalyst–substrate complex and outer-sphere triplet energy transfer. Our integrated analysis suggests that the direct photocatalysis is the inner working of the Rh-catalyzed reaction, whereas the Ir catalyst serves as a triplet sensitizer that activates cycloaddition via an outer-sphere triplet excited state energy transfer mechanism.

The mechanism of [2 + 2] cycloadditions activated by visible light and catalyzed by bis-cyclometalated Rh(iii) and Ir(iii) photocatalysts was investigated, combining density functional theory calculations and spectroscopic techniques.     

Approximate analysis of single-server tandem queues with finite buffers

In this paper, we study single-server tandem queues with general service times and finite buffers. Jobs are served according to the Blocking-After-Service protocol. To approximately determine the throughput and mean sojourn time, we decompose the tandem queue into single-buffer subsystems, the service times of which include starvation and blocking, and then we iteratively estimate the unknown parameters of the service times of each subsystem. The crucial feature of this approach is that in each subsystem successive service times are no longer assumed to be independent, but a successful attempt is made to include dependencies due to blocking by employing the concept of Markovian Arrival Processes. An extensive numerical study shows that this approach produces very accurate estimates for the throughput and mean sojourn time, outperforming existing methods, especially for longer tandem queues and for tandem queues with service times with a high variability.