Slow nucleic acid unzipping kinetics from sequence-defined barriers

Recent experiments on unzipping of RNA helix-loop structures by force have shown that ≈40-base molecules can undergo kinetic transitions between two well-defined “open” and “closed” states, on a timescale ≈1 sec [Liphardt et al., Science 297, 733-737 (2001)]. Using a simple dynamical model, we show that these phenomena result from the slow kinetics of crossing large free energy barriers which separate the open and closed conformations. The dependence of barriers on sequence along the helix, and on the size of the loop(s) is analyzed. Some DNA and RNA sequences that could show dynamics on different time scales, or three(or more)-state unzipping, are proposed. Our dynamical model is also applied to the unzipping of long (kilo-basepair) DNA molecules at constant force. Received 29 July 2002 / Received in final form 5 February 2003 Published online: 16 April 2003 RID="a" ID="a"e-mail: cocco@ldfc.u-strasbg.fr RID="b" ID="b"e-mail: jmarko@uic.edu RID="c" ID="c"e-mail: monasson@lpt.ens.fr     

Probing chromosome structure with dynamic force relaxation

We report measurements of the dynamics of force relaxation in single mitotic chromosomes, following step strains applied with micropipettes of force constant approximately 1 nN/microm. The force relaxes exponentially after an elongation (l/l(0)) to less than 3x native length, with a relaxation time approximately 2 sec. This relaxation time corresponds to an effective viscosity approximately 10(5) times that of water. We experimentally rule out solvent flow into the chromosome as the mechanism for the relaxation time. Instead, the relaxation can be explained in terms of the disentanglement dynamics of approximately 80 kb chromatin loop domains.     

High-power pulsed diode-pumped Er:ZBLAN fiber laser

We report on the operation and performance of a gain-switched Er:ZBLAN fiber laser based on an active pulsed diode pump system. The produced laser pulses offer high peak powers while retaining the high average powers and efficiency of the cw regime. The measured pulse duration was about 300 ns and nearly independent of the pump repetition frequency. The maximum obtained 68 W of peak power is the highest reported, to our knowledge, for diode-pumped Er:ZBLAN fiber lasers, and the 2 W of average power at the repetition frequency of 100 kHz is 2 orders of magnitude higher than previously reported average power in a pulsed regime. The obtained slope efficiency was 34%.     

The influence of ethylene glycol chains on the thermodynamics of hydrogen-bonded supramolecular assemblies in apolar solvents

Substitution of hydrogen bond directed supramolecular assemblies with ethylene glycol chains leads to a reduction in the association constant in apolar solvents, where the reduction of the association constant is dependent on the length of the aliphatic spacer connecting the hydrogen bonds and the ethylene glycol chain.     

Synthesis of novel 4-(2-amino-5-thiazolyl)-pyrimidine-2-amines as potential protein kinase inhibitors

Abstract  A short and efficient sequence for the synthesis of a series of 4-(2-amino-5-thiazolyl)-pyrimidine-2-amines was developed. 1-Phenyl-2-(6-pyrimidinyl)-ethanones, obtained via Weinreb’s methodology, were used in a Hantzsch thiazole cyclization reaction, followed by introduction of the aniline moieties via nucleophilic substitution. Graphical abstract        

Rebalancing Multiple Assets with Mutual Price Impact

We find asymptotically optimal trading policies for long-term investors with constant relative risk aversion, in a multiple-assets market, where expected returns and covariances are constant, and the execution price of each asset is linear in the trading intensities of all assets. Trading toward the frictionless target is optimal, when the current portfolio differs from the target by a principal portfolio—an eigenvector of the inverse impact matrix times the covariance matrix. Optimal policies approach the frictionless target along nonlinear, power-shaped paths, trading faster in more liquid directions, while tolerating wider oscillations along less liquid directions.     

Free energy and entropy production in planar Couette flow far from equilibrium

The macroscopic thermodynamic stability of a system of 108 diatomic molecules undergoing planar Couette flow far from equilibrium is reported. The system is perturbed from the steady state using a nondissipative variable colour field which induces a polarization in the system. It is found that the steady state for the system corresponds to an extremum in the generalized free energy and entropy production. However, while the free energy is always a minimum, the entropy production may be either a minimum or a maximum depending upon the direction of the colour field. These results, for a molecular system, are fundamentally different from those for an equivalent atomic system.     

Determination of heavy metal concentrations in plants exposed to different degrees of pollution using ICP-AES

Plant samples (Plantago lanceolata - narrow leaf plantain and Cichorium endiviae - endive) were collected in the surroundings of heavy metal emission sources and in other less contaminated areas. After digestion in a closed microwave system using HNO(3), the concentrations of Cd, Co, Cr, Cu, Fe, Mn, Mo, Ni, Pb, and Zn were determined using ICP-AES. Detection limits for all the elements of interest are given. Differences in heavy metal uptake rate between both plant species were observed. The uptake is more intensive for endive than for narrow leaf plantain. High concentrations of some heavy metals were determined in the unwashed plant samples as a result of exposure to aerosols. Tukey's statistical test was used to confirm the discrepancy of Cr concentration in plant samples from various areas. Washing the leaves with water was found to remove a large amount of water-soluble aerosols.     

Estimation of surfactant activity of polluted seawater by kalousek commutator technique

The polarographic method of discontinuously changing potential, known as the Kalousek commutator technique, was applied to the estimation of surfactant activity of seawater samples from polluted area of a harbour. Adsorption isotherms of different detergents, lecithin and lauric acid at the HMDE have been used as calibration curves. The method is recommended for direct and rapid determination of the degree of seawater pollution by organic surface active substances.