Force-extension behavior of folding polymers

The elastic response of flexible polymers made of elements which can be either folded or unfolded, having different lengths in these two states, is discussed. These situations are common for biopolymers as a result of folding interactions intrinsic to the monomers, or as a result of binding of other smaller molecules along the polymer length. Using simple flexible-chain models, we show that even when the energy ε associated with maintaining the folded state is comparable to k _B T, the elastic response of such a chain can mimic usual polymer linear elasticity, but with a force scale enhanced above that expected from the flexibility of the chain backbone. We discuss recent experiments on single-stranded DNA, chromatin fiber and double-stranded DNA with proteins weakly absorbed along its length which show this effect. Effects of polymer semiflexiblity and torsional stiffness relevant to experiments on proteins binding to dsDNA are analyzed. We finally discuss the competition between electrostatic self-repulsion and folding interactions responsible for the complex elastic response of single-stranded DNA. Received 7 August 2002 and Received in final form 7 March 2003 / Published online: 15 April 2003 RID="a" ID="a"e-mail: jmarko@uic.edu     

Force-extension curves of bacterial flagella

Bacterial flagella assume different helical shapes during the tumbling phase of a bacterium but also in response to varying environmental conditions. Force-extension measurements by Darnton and Berg explicitly demonstrate a transformation from the coiled to the normal helical state (N.C. Darnton, H.C. Berg, Biophys. J. 92, 2230 (2007)). We here develop an elastic model for the flagellum based on Kirchhoff's theory of an elastic rod that describes such a polymorphic transformation and use resistive force theory to couple the flagellum to the aqueous environment. We present Brownian-dynamics simulations that quantitatively reproduce the force-extension curves and study how the ratio G \Gamma of torsional to bending rigidity and the extensional rate influence the response of the flagellum. An upper bound for G \Gamma is given. Using clamped flagella, we show in an adiabatic approximation that the mean extension, where a local coiled-to-normal transition occurs first, depends on the logarithm of the extensional rate.     

Force-extension curves of dimerized polyglutamic acid

Measurement of the force-extension curve for the mechanical unfolding process of a single protein molecule is expected to provide a value for the force necessary to deform the molecule. Integration of the observed curves can then yield an accurate estimate of the intra-molecular cohesive energy of the protein. To understand the details of such force-extension curves, it is necessary to begin by understanding the mechanical properties of simple structural elements such as the !-helix and #-sheet. In a series of experiments designed to obtain force-extension curves of helical and randomly coiled polyglutamic acid, we found an interesting phenomenon in linearly cross-linked dimer samples of the polymer. The remarkable observation indicated the possibility of a lateral interaction of helical rods within molecules. Mechanical distinction of such interactions will be useful for application of atomic force microscopy in studying the nanomechanics of tertiary interactions among peptide segments in protein molecules.     

Force-extension curve of a polymer in a high-frequency electric field

We study theoretically the conformation and force-extension curve of a semiflexible polymer in a spatially uniform ac electric field. The polymer backbone minimizes its energy by aligning along one of two orientations parallel to the field. In a strong ac field, hairpin kinks develop between regions of opposite alignment. These kinks are mathematically described as sine-Gordon solitons. We calculate the equation of state of the one-dimensional kink gas, which yields the force-extension curve of the polymer. A sufficiently strong ac field causes the polymer to extend spontaneously to almost its full contour length. The theory is applied to recent experiments on dielectrophoretic stretching of DNA.     

Force-extension curves for a single polymer chain under varying solvent conditions

We show that Langevin dynamics can be used to obtain force-extension curves for a single polymer chain under varying solvent conditions. We find that the chains obey Hooke-type and Pincus regime behavior for Theta and good solvents. However, in poor solvents a coil-strand coexistence is observed in the equilibrium state and this leads to a quite different type of deformation behavior.     

Database of amino acid-nucleotide contacts in contacts in DNA-homeodomain protein

The analysis of amino acid-nucleotide contacts in interfaces of the protein-DNA complexes, intended to find consistencies in the protein-DNA recognition, is a complex problem that requires an analysis of the physicochemical characteristics of these contacts and the positions of the participating amino acids and nucleotides in the chains of the protein and the DNA, respectively, as well as conservatism of these contacts. Thus, those heterogeneous data should be systematized. For this purpose we have developed a database of amino acid-nucleotide contacts ANTPC (Amino acid Nucleotide Type Position Conservation) following the archetypal example of the proteins in the homeodomain family. We show that it can be used to compare and classify the interfaces of the protein-DNA complexes.     

On the supramolecular mechanism of cell-cell commutation

Processes of cell commutation via anisometric supramolecular structures (strings) are considered in vitro and using physicochemical models of lipids and trifluoroacetylated amino alcohols. The biological effectiveness of commutation via strings is demonstrated to be higher compared to the diffusion mechanism of transfer of biologically active molecules over distances between objects typical of populations of microorganisms. A kinetic model of strings is developed, and the rate of signal transmission in such systems is estimated. It is shown that the condition of the chirality of lipids forming the biomembranes of cells follows from the experimentally observed cell commutation by means of supramolecular anisometric structures.     

Enzymatic quantification of cell-matrix and cell-cell adhesion

Adhesion assays are powerful tools to investigate the adhesive properties of cells. The quantification of cell adhesion enables determination of the capacity of cells to stick to a target, screening for novel adhesion involved binding molecules, exploration of structure-function relationships of adhesion molecules, evaluation of adhesion targets, and examination of compounds interfering with cell adhesion. Thus, quantification of cell adhesion needs simple and reliable methods that might be applied for both research and diagnostic purposes. This review presents methodological principles of enzymatic approaches for quantification of cell adhesion. In particular, the advantages of exogenous cell labelling with horseradish peroxidase are described.     

Theory of superconducting contacts

Metallic contacts between superconducting and normal films are known to have a pair-breaking effect on the electron pairs. By limiting our considerations to the gapless regime and to contacts between superconducting and paramagnetic metals the features of this pair-breaking mechanism are investigated. We compute the normalization of the order parameter and with it such quantities as the tunneling conductance, electrical and thermal conductivity and the critical current parallel to the contact. Furthermore we investigate the influence of a magnetic field. By calculating the? ₂(t)-parameter we demonstrate the interplay between the different pair-breaking mechanisms in perpendicular and parallel fields. In the latter case we discuss the influence of the contact on the superconducting sheath proposed bySaint-James andde Gennes. Experiments to test the present theory are suggested.     

Properties of metal-zinc oxide contacts

The known methods of forming surface barrier structures on zinc oxide are analyzed. The dependence of surface and contact properties of zinc oxide on thermal processing temperature in air and vacuum is studied. It is established that the contact may become rectifying or ohmic depending on the character of surface processing. It is shown that the major factor determining the properties of zinc-oxide contacts is the state of the semiconductor surface. The effect of moisture on the properties of such contact is studied.Translated from Izvestiya Vysshikh Uchebnykh Zavedenii, Fizika, No. 6, pp. 72–75, June, 1981.     

Thermodynamical properties of superconducting contacts

We investigate the thermodynamical properties of superconducting contacts, and concentrate on the calculation of the specific heat in the vicinity of the superconducting transition point. By considering the thick film limit, it is found that the reduction in the specific heat is a much more delicate measure of the proximity effect than is the change in transition temperature, for example. For the case that the normal film consists of a paramagnetic metal, it can be shown that for superconducting films even as thick as 100-times the coherence distance the reduction in the specific heat is still approximately 15%. Our computations apply to arbitrary mean free path. Finally we discuss experiments byShiffman et al. on eutectic Pb-Sn alloys and show that reasonable good agreement between theory and experiment can be obtained.     

Superconducting quantum point contacts

We review our experiments on the electronic transport properties of atomic contacts between metallic electrodes, in particular superconducting ones. Despite ignorance of the exact atomic configuration, these ultimate quantum point contacts can be manipulated and well characterized in-situ. They allow performing fundamental tests of the scattering theory of quantum transport. In particular, we discuss the case of the Josephson effect.     

Metal contacts to n-GaN

Al, Au, Ti/Al and Ti/Au contacts were prepared on n-GaN and annealed up to 900 °C. The structure, phase and morphology were studied by cross-sectional transmission and scanning electron microscopy as well as by X-ray diffraction (XRD), the electrical behaviour by current-voltage measurements. It was obtained that annealing resulted in interdiffusion, lateral diffusion along the surface, alloying and bowling up of the metal layers. The current-voltage characteristics of as-deposited Al and Ti/Al contacts were linear, while the Au and Ti/Au contacts exhibited rectifying behaviour. Except the Ti/Au contact which became linear, the contacts degraded during heat treatment at 900 °C. The surface of Au and Ti/Au contacts annealed at 900 °C have shown fractal-like structures revealed by scanning electron microscopy. Transmission electron microscopy and XRD investigations of the Ti/Au contact revealed that Au diffused into the n-GaN layer at 900 °C. X-ray diffraction examinations showed, that new Ti₂N, Au₂Ga and Ga₃Ti₂ interface phases formed in Ti/Au contact at 900 °C, new Ti₂N phase formed in Ti/Al contact at 700 and 900 °C, as well as new AlN interface phase developed in Ti/Al contact at 900 °C.     

Stiffness of contacts between rough surfaces

The effect of self-affine roughness on solid contact is examined with molecular dynamics and continuum calculations. The contact area and normal stiffness rise linearly with the applied load, and the load rises exponentially with decreasing separation between surfaces. Results for a wide range of roughness, system size, and Poisson ratio can be collapsed using Persson's contact theory for continuous elastic media. The compliance due to atomic-scale motion at the interface between solids has little effect on the area and normal stiffness, but can reduce the total transverse stiffness by orders of magnitude. The scaling of this effect with system size is discussed.     

Graphene-based superconducting quantum point contacts

We investigate the Josephson effect in the graphene nanoribbons of length L smaller than the superconducting coherence length and an arbitrary width W. We find that in contrast to an ordinary superconducting quantum point contact (SQPC), the critical supercurrent I_c is not quantized for the nanoribbons with smooth and armchair edges. For a low concentration of the carriers, I_c decreases monotonically with lowering W/L and tends to a constant minimum for a narrow nanoribbon with . The minimum I_c is zero for the smooth edges but for the armchair edges. At higher concentrations of the carriers this monotonic variation acquires a series of peaks. Further analysis of the current-phase relation and the Josephson coupling strength I_cR_N in terms of W/L and the concentration of carriers revels significant differences with those of an ordinary SQPC. On the other hand for a zigzag nanoribbon, we find that, similar to an ordinary SQPC, I_c is quantized but to the half-integer values . PACS 74.45.+c; 74.50.+r; 73.63.-b; 74.78.Na     

Peculiar scaling of self-avoiding walk contacts

The nearest neighbor contacts between the two halves of an N-site lattice self-avoiding walk offer an unusual example of scaling random geometry: for N-->infinity they are strictly finite in number but their radius of gyration R(c) is power law distributed proportional to R(-tau)(c), where tau>1 is a novel exponent characterizing universal behavior. A continuum of diverging length scales is associated with the R(c) distribution. A possibly superuniversal tau = 2 is also expected for the contacts of a self-avoiding or random walk with a confining wall.     

Thermal conductance of ballistic point contacts

We study the thermal conductance of ballistic point contacts. These contacts are realized as few nanometer long pillars in so-called air-gap heterostructures (AGHs). The pillar length is orders of magnitude smaller than the mean free path of the phonons up to room temperature. Because of the small dimension and the low density of the pillars, the thermal conductance of the AGHs is several orders of magnitude reduced in comparison to bulk structures. The measurement results are in quantitative agreement with a simple model that is based on the Boltzmann transport equation.