Supersymmetry and cohomology of graph complexes

Letters in Mathematical Physics - I describe a combinatorial construction of the cohomology classes in compactified moduli spaces of curves $$widehat{Z}_{I}in H^{*}left( bar{mathcal...     

Localization for a Random Walk in Slowly Decreasing Random Potential

We consider a continuous time random walk X in a random environment on ?⁺ such that its potential can be approximated by the function V:?⁺→? given by $V(x)=\sigma W(x) -\frac {b}{1-\alpha}x^{1-\alpha}$ where σW a Brownian motion with diffusion coefficient σ>0 and parameters b, α are such that b>0 and 0<α<1/2. We show that P-a.s. (where P is the averaged law) $\lim_{t\to\infty} \frac{X_{t}}{(C^{*}(\ln\ln t)^{-1}\ln t)^{\frac{1}{\alpha}}}=1$ with $C^{*}=\frac{2\alpha b}{\sigma^{2}(1-2\alpha)}$ . In fact, we prove that by showing that there is a trap located around $(C^{*}(\ln\ln t)^{-1}\ln t)^{\frac{1}{\alpha}}$ (with corrections of smaller order) where the particle typically stays up to time t. This is in sharp contrast to what happens in the “pure” Sinai’s regime, where the location of this trap is random on the scale ln² t.     

New insights into the transition pathway from nonspecific to specific complex of DNA with Escherichia coli integration host factor

To elucidate the nature of the transition-state ensemble along the reaction pathway from a nonspecific protein-DNA complex to the specific complex, we have carried out measurements of DNA bending/unbending dynamics on a cognate DNA substrate in complex with integration host factor (IHF), an architectural protein from E. coli that bends its cognate site by approximately 180 degrees . We use a laser temperature jump to perturb the IHF-DNA complex and monitor the relaxation kinetics with time-resolved FRET measurements on DNA substrates end-labeled with a FRET pair. Previously, we showed that spontaneous bending/kinking of DNA, from thermal disruption of base-pairing/-stacking interactions, may be the rate-limiting step in the formation of the specific complex (Kuznetsov, S. V.; Sugimura, S.; Vivas, P.; Crothers, D. M.; Ansari, A. Proc. Natl. Acad. Sci. USA 2006, 103, 18515). Here, we probe the effect of varying [KCl], which affects the stability of the complex, on this rate-limiting step. We find that below approximately 250 mM KCl, the observed relaxation kinetics are from the unimolecular bending/unbending of DNA, and the relaxation rate kr is independent of [KCl]. Above approximately 300 mM KCl, dissociation of the IHF-DNA complex becomes significant, and the observed relaxation process includes contributions from the association/dissociation step, with kr decreasing with increasing [KCl]. The DNA bending step occurs with a positive activation enthalpy, despite the large negative enthalpy change reported for the specific IHF-DNA complex (Holbrook, J. A.; Tsodikov, O. V.; Saecker, R. M.; Record, M. T., Jr. J. Mol. Biol. 2001, 310, 379). Our conclusion from these studies is that in the uphill climb to the transition state, the DNA is kinked, but with no release of ions, as indicated by the salt-independent behavior of k(r) at low [KCl]. Any release of ions in the unimolecular process, together with conformational changes in the protein-DNA complex that facilitate favorable interactions and that contribute to the negative enthalpy change, must occur as the system leaves the transition state, downhill to the final complex.     

An Improved Measurement of Isotopic Ratios by High Resolution Mass Spectrometry

The study of protein kinetics requires an accurate measurement of isotopic ratios of peptides. Although Fourier transform-ion cyclotron resonance (FT-ICR) mass spectrometers yield accurate mass measurements of analytes, the isotopologue ratios are consistently lower than predicted. Recently, we demonstrated that the magnitude of the spectral error in the FT-ICR mass spectrometer is proportional to the scan duration of ions. Here, we present a novel isotopic ratio extrapolation (IRE) method for obtaining accurate isotopic ratio measurements. Accuracy is achieved by performing scans with different duration and extrapolation of the data to the initial moment of the ion rotation; IRE minimizes the absolute isotopic ratio error to ≤1 %. We demonstrate the application of IRE in protein turnover studies using ²H₂O-metabolic labeling. Overall, this technique allows accurate measurements of the isotopic ratios of proteolytic peptides, a critical step for enabling routine studies of proteome dynamics.      

Survival of Branching Random Walks in Random Environment

We study survival of nearest-neighbor branching random walks in random environment (BRWRE) on ℤ. A priori there are three different regimes of survival: global survival, local survival, and strong local survival. We show that local and strong local survival regimes coincide for BRWRE and that they can be characterized with the spectral radius of the first moment matrix of the process. These results are generalizations of the classification of BRWRE in recurrent and transient regimes. Our main result is a characterization of global survival that is given in terms of Lyapunov exponents of an infinite product of i.i.d. 2×2 random matrices.     

Circular consecutive choosability of k‐choosable graphs

Let S(r) denote a circle of circumference r. The circular consecutive choosability ch_cc(G) of a graph G is the least real number t such that for any r≥χ_c(G), if each vertex v is assigned a closed interval L(v) of length t on S(r), then there is a circular r‐coloring f of G such that f(v)∈L(v). We investigate, for a graph, the relations between its circular consecutive choosability and choosability. It is proved that for any positive integer k, if a graph G is k‐choosable, then ch_cc(G)?k + 1 ? 1/k; moreover, the bound is sharp for k≥3. For k = 2, it is proved that if G is 2‐choosable then ch_cc(G)?2, while the equality holds if and only if G contains a cycle. In addition, we prove that there exist circular consecutive 2‐choosable graphs which are not 2‐choosable. In particular, it is shown that ch_cc(G) = 2 holds for all cycles and for K_{2, n} with n≥2. On the other hand, we prove that ch_cc(G)>2 holds for many generalized theta graphs. © 2011 Wiley Periodicals, Inc. J Graph Theory 67: 178‐197, 2011     

Adaptive efficient estimation for generalized semi-Markov big data models

Annals of the Institute of Statistical Mathematics - In this paper we study generalized semi-Markov high dimension regression models in continuous time, observed at fixed discrete time moments. The...     

A one-dimensional version of the random interlacements

We base ourselves on the construction of the two-dimensional random interlacements (Comets et al., 2016) to define the one-dimensional version of the process. For this, we consider simple random walks conditioned on never hitting the origin. We compare this process to the conditional random walk on the ring graph. Our results are the convergence of the vacant set on the ring graph to the vacant set of one-dimensional random interlacements, a central limit theorem for the interlacements’ local time and the convergence in law of the local times of the conditional walk on the ring graph to the interlacements’ local times.     

On uniform closeness of local times of Markov chains and i.i.d. sequences

In this paper we consider the field of local times of a discrete-time Markov chain on a general state space, and obtain uniform (in time) upper bounds on the total variation distance between this field and the one of a sequence of $n$ i.i.d. random variables with law given by the invariant measure of that Markov chain. The proof of this result uses a refinement of the soft local time method of Popov and Teixeira (2015).     

Caractéristique directionnelle calculée et mesurée d'une sonde électrochimiqueCalculated and measured directional characteristic of an electrochemical probe

The present paper demonstrates how the directional characteristics of an actual three-segment electrodiffusional sensor can be calculated from the probe image. It was shown that utilization of ‘ideal’ directional characteristics lead to an important (up to 15^°) error in flow angle determination. The directional characteristics calculated from the probe image improve significantly (up to 50%) the accuracy of the flow angle measurements. To cite this article: F. Barbeu et al., C. R. Mecanique 330 (2002) 433–436.