Mechanically induced silyl ester cleavage under acidic conditions investigated by AFM-based single-molecule force spectroscopy in the force-ramp mode

AFM-based dynamic single-molecule force spectroscopy was used to stretch carboxymethylated amylose (CMA) polymers, which have been covalently tethered between a silanized glass substrate and a silanized AFM tip via acid-catalyzed ester condensation at pH 2.0. Rupture forces were measured as a function of temperature and force loading rate in the force-ramp mode. The data exhibit significant statistical scattering, which is fitted with a maximum likelihood estimation (MLE) algorithm. Bond rupture is described with a Morse potential based Arrhenius kinetics model. The fit yields a bond dissociation energy De = 35 kJ mol−1 and an Arrhenius pre-factor A = 6.6 × 104 s−1. The bond dissociation energy is consistent with previous experiments under identical conditions, where the force-clamp mode was employed. However, the bi-exponential decay kinetics, which the force-clamp results unambiguously revealed, are not evident in the force-ramp data. While it is possible to fit the force-ramp data with a bi-exponential model, the fit parameters differ from the force-clamp experiments. Overall, single-molecule force spectroscopy in the force-ramp mode yields data whose information content is more limited than force-clamp data. It may, however, still be necessary and advantageous to perform force-ramp experiments. The number of successful events is often higher in the force-ramp mode, and competing reaction pathways may make force-clamp experiments impossible

Mechanically activated rupture of single covalent bonds: evidence of force induced bond hydrolysis.

We have used temperature-dependent single molecule force spectroscopy to stretch covalently anchored carboxymethylated amylose (CMA) polymers attached to an amino-functionalized AFM cantilever. Using an Arrhenius kinetics model based on a Morse potential as a one-dimensional representation of covalent bonds, we have extracted kinetic and structural parameters of the bond rupture process. With 35.5 kJ mol−1, we found a significantly smaller dissociation energy and with 9.0 × 102 s−1 to 3.6 × 103 s−1 also smaller Arrhenius pre-factors than expected for homolytic bond scission. One possible explanation for the severely reduced dissociation energy and Arrhenius pre-factors is the mechanically activated hydrolysis of covalent bonds. Both the carboxylic acid amide and the siloxane bond in the amino-silane surface linker are in principle prone to bond hydrolysis. Scattering, slope and curvature of the scattered data plots indicate that in fact two competing rupture mechanisms are observed

Unzipping Kinetics of Double-Stranded DNA in a Nanopore

We studied the unzipping kinetics of single molecules of double-stranded DNA by pulling one of their two strands through a narrow protein pore. PCR analysis yielded the first direct proof of DNA unzipping in such a system. The time to unzip each molecule was inferred from the ionic current signature of DNA traversal. The distribution of times to unzip under various experimental conditions fit a simple kinetic model. Using this model, we estimated the enthalpy barriers to unzipping and the effective charge of a nucleotide in the pore, which was considerably smaller than previously assumed.Comment: 10 pages, 5 figures, Accepted: Physics Review Letter

Global Optimization by Energy Landscape Paving

We introduce a novel heuristic global optimization method, energy landscape paving (ELP), which combines core ideas from energy surface deformation and tabu search. In appropriate limits, ELP reduces to existing techniques. The approach is very general and flexible and is illustrated here on two protein folding problems. For these examples, the technique gives faster convergence to the global minimum than previous approaches.Comment: to appear in Phys. Rev. Lett. (2002

Dragging a polymer chain into a nanotube and subsequent release

We present a scaling theory and Monte Carlo (MC) simulation results for a flexible polymer chain slowly dragged by one end into a nanotube. We also describe the situation when the completely confined chain is released and gradually leaves the tube. MC simulations were performed for a self-avoiding lattice model with a biased chain growth algorithm, the pruned-enriched Rosenbluth method. The nanotube is a long channel opened at one end and its diameter $D$ is much smaller than the size of the polymer coil in solution. We analyze the following characteristics as functions of the chain end position $x$ inside the tube: the free energy of confinement, the average end-to-end distance, the average number of imprisoned monomers, and the average stretching of the confined part of the chain for various values of $D$ and for the number of monomers in the chain, $N$. We show that when the chain end is dragged by a certain critical distance $x^*$ into the tube, the polymer undergoes a first-order phase transition whereby the remaining free tail is abruptly sucked into the tube. This is accompanied by jumps in the average size, the number of imprisoned segments, and in the average stretching parameter. The critical distance scales as $x^*\sim ND^{1-1/\nu}$. The transition takes place when approximately 3/4 of the chain units are dragged into the tube. The theory presented is based on constructing the Landau free energy as a function of an order parameter that provides a complete description of equilibrium and metastable states. We argue that if the trapped chain is released with all monomers allowed to fluctuate, the reverse process in which the chain leaves the confinement occurs smoothly without any jumps. Finally, we apply the theory to estimate the lifetime of confined DNA in metastable states in nanotubes.Comment: 13pages, 14figure

Fate and effects of silver nanoparticles at the aquatic-terrestrial interface: A floodplain mesocosm experiment

The production volume of engineered inorganic nanoparticles (EINP) successively increased over the last years. Once released into the natural environment, these particles may change their size and surface properties in interaction with other substances. This is expected to control their mobility and their impact on biochemical processes. However, the underlying processes are not fully understood yet. Transformation processes and long-term fate of citrate-coated silver nanoparticles (Ag NP) were investigated in an innovative floodplain mesocosm, which was run with river Rhine water and natural soil from an adjacent floodplain for 33 weeks. Flooding events were simulated every three weeks. The Ag NP with a concentration of 5 mg L-1 were continuously introduced into the water for three weeks followed by a three-week period without spiking. Every third week the ecotoxicological impact of Ag NP was determined by means of Gammarus mortality and feeding assays. At the end of the experiment, the total Ag concentrations were measured in profiles of the floodplain soil and the sediment as well as in algae that developed in the mesocosm. The total Ag concentration in the aquatic phase in the main zone as well as in the floodplain fluctuated according to the periodic Ag NP pulse. Further, significant amounts of Ag accumulated in algae (up to 4.7 mg g-1) and exposed leaves (up to 170 μg g-1). However, for the applied experimental conditions we did neither observed mortality nor sublethal effects on Gammarus feeding activity. More than 40 % of the Ag remained in the sediment of the main zone and 7 % were transported during flooding into the floodplain soil. Furthermore, 0.5 % of the Ag was still in the water phase. Most of the particles were immobilized in the top layer of the sediments and soil. Only very little transport in deeper soil layers was observed in the soil columns and sediment. Accumulation in algae, sediment, and soil is alarming for long-term environmental impact assessments and the long lifetime in the aqueous phase suggests long-range transport of Ag NP in rivers

Investigations of the LHC Emittance Blow-Up During the 2012 Proton Run

About 30 % of the potential luminosity performance is lost through the different phases of the LHC cycle, mainly due to transverse emittance blow-up. Measuring the emittance growth is a difficult task with high intensity beams and changing energies. Improvements of the LHC transverse profile instrumentation helped to study various effects. A breakdown of the growth through the different phases of the LHC cycle is given as well as a comparison with the data from the LHC experiments for transverse beam size. In 2012 a number of possible sources and remedies have been studied. Among these are intra beam scattering, 50 Hz noise and the effect of the transverse damper gain. The results of the investigations are summarized in this paper. Requirements for transverse profile instrumentation for post LHC long shutdown operation to finally tackle the emittance growth are given as well