Two-phase stretching of molecular chains

While stretching of most polymer chains leads to rather featureless force-extension diagrams, some, notably DNA, exhibit non-trivial behavior with a distinct plateau region. Here we propose a unified theory that connects force-extension characteristics of the polymer chain with the convexity properties of the extension energy profile of its individual monomer subunits. Namely, if the effective monomer deformation energy as a function of its extension has a non-convex (concave up) region, the stretched polymer chain separates into two phases: the weakly and strongly stretched monomers. Simplified planar and 3D polymer models are used to illustrate the basic principles of the proposed model. Specifically, we show rigorously that when the secondary structure of a polymer is mostly due to weak non-covalent interactions, the stretching is two-phase, and the force-stretching diagram has the characteristic plateau. We then use realistic coarse-grained models to confirm the main findings and make direct connection to the microscopic structure of the monomers. We demostrate in detail how the two-phase scenario is realized in the \alpha-helix, and in DNA double helix. The predicted plateau parameters are consistent with single molecules experiments. Detailed analysis of DNA stretching demonstrates that breaking of Watson-Crick bonds is not necessary for the existence of the plateau, although some of the bonds do break as the double-helix extends at room temperature. The main strengths of the proposed theory are its generality and direct microscopic connection.Comment: 16 pges, 22 figure

Modeling DNA Structure, Elasticity and Deformations at the Base-pair Level

We present a generic model for DNA at the base-pair level. We use a variant of the Gay-Berne potential to represent the stacking energy between neighboring base-pairs. The sugar-phosphate backbones are taken into account by semi-rigid harmonic springs with a non-zero spring length. The competition of these two interactions and the introduction of a simple geometrical constraint leads to a stacked right-handed B-DNA-like conformation. The mapping of the presented model to the Marko-Siggia and the Stack-of-Plates model enables us to optimize the free model parameters so as to reproduce the experimentally known observables such as persistence lengths, mean and mean squared base-pair step parameters. For the optimized model parameters we measured the critical force where the transition from B- to S-DNA occurs to be approximately $140{pN}$. We observe an overstretched S-DNA conformation with highly inclined bases that partially preserves the stacking of successive base-pairs.Comment: 15 pages, 25 figures. submitted to PR

A DMRG Study of Low-Energy Excitations and Low-Temperature Properties of Alternating Spin Systems

We use the density matrix renormalization group (DMRG) method to study the ground and low-lying excited states of three kinds of uniform and dimerized alternating spin chains. The DMRG procedure is also employed to obtain low-temperature thermodynamic properties of these systems. We consider a 2N site system with spins $s_1$ and $s_2$ alternating from site to site and interacting via a Heisenberg antiferromagnetic exchange. The three systems studied correspond to $(s_1 ,s_2 )$ being equal to $(1,1/2),(3/2,1/2)$ and $(3/2,1)$; all of them have very similar properties. The ground state is found to be ferrimagnetic with total spin $s_G =N(s_1 - s_2)$. We find that there is a gapless excitation to a state with spin $s_G -1$, and a gapped excitation to a state with spin $s_G +1$. Surprisingly, the correlation length in the ground state is found to be very small for this gapless system. The DMRG analysis shows that the chain is susceptible to a conditional spin-Peierls instability. Furthermore, our studies of the magnetization, magnetic susceptibility $\chi$ and specific heat show strong magnetic-field dependences. The product $\chi T$ shows a minimum as a function of temperature T at low magnetic fields; the minimum vanishes at high magnetic fields. This low-field behavior is in agreement with earlier experimental observations. The specific heat shows a maximum as a function of temperature, and the height of the maximum increases sharply at high magnetic fields. Although all the three systems show qualitatively similar behavior, there are some notable quantitative differences between the systems in which the site spin difference, $|s_1 - s_2|$, is large and small respectively.Comment: 16 LaTeX pages, 13 postscript figure

Superconductivity in Fullerides

Experimental studies of superconductivity properties of fullerides are briefly reviewed. Theoretical calculations of the electron-phonon coupling, in particular for the intramolecular phonons, are discussed extensively. The calculations are compared with coupling constants deduced from a number of different experimental techniques. It is discussed why the A_3 C_60 are not Mott-Hubbard insulators, in spite of the large Coulomb interaction. Estimates of the Coulomb pseudopotential $\mu^*$, describing the effect of the Coulomb repulsion on the superconductivity, as well as possible electronic mechanisms for the superconductivity are reviewed. The calculation of various properties within the Migdal-Eliashberg theory and attempts to go beyond this theory are described.Comment: 33 pages, latex2e, revtex using rmp style, 15 figures, submitted to Review of Modern Physics, more information at http://radix2.mpi-stuttgart.mpg.de/fullerene/fullerene.htm

Early-stage rifting of the northern Tyrrhenian Sea Basin: Results from a combined wide-angle and multichannel seismic study

Extension of the continental lithosphere leads to the formation of rift basins and ultimately may create passive continental margins. The mechanisms that operate during the early stage of crustal extension are still intensely debated. We present the results from coincident multichannel seismic and wide-angle seismic profiles that transect across the northern Tyrrhenian Sea Basin. The profiles cross the Corsica Basin (France) to the Latium Margin (Italy) where the early-rift stage of the basin is well preserved. We found two domains, each with a distinct tectonic style, heat flow and crustal thickness. One domain is the Corsica Basin in the west that formed before the main rift phase of the northern Tyrrhenian Sea opening (∼8–4 Ma). The second domain is rifted continental crust characterized by tilted blocks and half-graben structures in the central region and at the Latium Margin. These two domains are separated by a deep (∼10 km) sedimentary complex of the eastern portion of the Corsica Basin. Travel-time tomography of wide-angle seismic data reveals the crustal architecture and a subhorizontal 15–17 ± 1 km deep Moho discontinuity under the basin. To estimate the amount of horizontal extension we have identified the pre-, syn-, and post-tectonic sedimentary units and calculated the relative displacement of faults. We found that major faults initiated at angles of 45°–50° and that the rifted domain is horizontally stretched by a factor of β ∼ 1.3 (∼8–10 mm/a). The crust has been thinned from ∼24 to ∼17 km indicating a similar amount of extension (∼30%). The transect represents one of the best imaged early rifts and implies that the formation of crustal-scale detachments, or long-lived low-angle normal faults, is not a general feature that controls the rift initiation of continental crust. Other young rift basins, like the Gulf of Corinth, the Suez Rift or Lake Baikal, display features resembling the northern Tyrrhenian Basin, suggesting that half-graben formations and distributed homogeneous crustal thinning are a common feature during rift initiation

Single-molecule experiments in biological physics: methods and applications

I review single-molecule experiments (SME) in biological physics. Recent technological developments have provided the tools to design and build scientific instruments of high enough sensitivity and precision to manipulate and visualize individual molecules and measure microscopic forces. Using SME it is possible to: manipulate molecules one at a time and measure distributions describing molecular properties; characterize the kinetics of biomolecular reactions and; detect molecular intermediates. SME provide the additional information about thermodynamics and kinetics of biomolecular processes. This complements information obtained in traditional bulk assays. In SME it is also possible to measure small energies and detect large Brownian deviations in biomolecular reactions, thereby offering new methods and systems to scrutinize the basic foundations of statistical mechanics. This review is written at a very introductory level emphasizing the importance of SME to scientists interested in knowing the common playground of ideas and the interdisciplinary topics accessible by these techniques. The review discusses SME from an experimental perspective, first exposing the most common experimental methodologies and later presenting various molecular systems where such techniques have been applied. I briefly discuss experimental techniques such as atomic-force microscopy (AFM), laser optical tweezers (LOT), magnetic tweezers (MT), biomembrane force probe (BFP) and single-molecule fluorescence (SMF). I then present several applications of SME to the study of nucleic acids (DNA, RNA and DNA condensation), proteins (protein-protein interactions, protein folding and molecular motors). Finally, I discuss applications of SME to the study of the nonequilibrium thermodynamics of small systems and the experimental verification of fluctuation theorems. I conclude with a discussion of open questions and future perspectives.Comment: Latex, 60 pages, 12 figures, Topical Review for J. Phys. C (Cond. Matt

Modeling of droplet generation in a top blowing steelmaking process

Quantification of metal droplets ejected due to impinging gas jet on the surface of liquid metal is an important parameter for the understanding and for the modeling of the refining kinetics of reactions in slag-metal emulsion zone. In the present work, a numerical study has been carried out to critically examine the applicability of droplet generation rate correlation previously proposed by Subagyo et al. on the basis of dimensionless blowing number (N B). The blowing number was re-evaluated at the impingement point of jet with taking into account the temperature effect of change in density and velocity of the gas jet. The result obtained from the work shows that the modified blowing number N B,T at the furnace temperature of 1873 K (1600 °C) is approximately double in magnitude compared to N B calculated by Subagyo and co-workers. When N B,T has been employed to the Subagyo’s empirical correlation for droplet generation, a wide mismatch is observed between the experimental data obtained from cold model and hot model experiments. The reason for this large deviation has been investigated in the current study, and a theoretical approach to estimate the droplet generation rate has been proposed. The suitability of the proposed model has been tested by numerically calculating the amount of metals in slag. The study shows that the weight of metals in emulsion falls in the range of 0 to 21 wt pct of hot metal weight when droplet generation rate has been calculated at ambient furnace temperature of 1873 K (1600 °C)

Spatially distributed calibration of a hydrological model with variational optimization constrained by physiographic maps for flash flood forecasting in France

This contribution presents a regionalization approach to estimate spatially distributed hydrologic parameters based on: (i) the SMASH (Spatially distributed Modelling and ASsimilation for Hydrology) hydrological modeling and assimilation platform (Jay-Allemand, 2020; Jay-Allemand et al., 2020) underlying the French national flash flood forecasting system Vigicrues Flash (Javelle et al., 2019); (ii) the variational assimilation algorithm from (Jay-Allemand et al., 2020), adapted to high dimensional inverse problems; (iii) spatial constraints added to the optimization problem, based on masks derived from physiographic maps (e.g., land cover, terrain slope); (iv) multi-site global optimization, which targets multiple independent watersheds. This method gives a regional estimation of the spatially distributed parameters over the whole modeled area. This study uses a distributed rainfall-runoff model with 4 parameters to calibrate, with a spatial resolution of 1×1 km2 and a 15 min time step. Performances of the calibrated hydrological model and the parameters robustness are evaluated on two French study areas with 20 catchments in each, in spatio-temporal extrapolation based on cross-validation experiments over a 12-year period. Several spatial regularization strategies are tested to better constrain the high dimensional optimization problem. The model parameters are calibrated based on the Nash-Sutcliffe Efficiency (NSE) computed for multiple calibration basins in the study area. Results are discussed based on the Nash-Sutcliffe Efficiency and the Kling-Gupta Efficiency criteria obtained on calibration and validation catchments for two subperiods of 6 years. Further work aims to improve the global search of prior parameter sets and to better balance the adjoint sensitivity with respect to the spatial constraints resolution and catchment characteristics. This will ensure a better consistency of simulated fluxes variabilities and enhance the applicability of the regionalization method at higher spatial scales and over larger domains.</p