Stretching DNA: Role of electrostatic interactions

The effect of electrostatic interactions on the stretching of DNA is investigated using a simple worm like chain model. In the limit of small force there are large conformational fluctuations which are treated using a self-consistent variational approach. For small values of the external force f, we find the extension scales as where is the Debye screening length. In the limit of large force the electrostatic effects can be accounted for within the semiflexible chain model of DNA by assuming that only small excursions from rod-like conformations are possible. In this regime the extension approaches the contour length as where f is the magnitude of the external force. The theory is used to analyze experiments that have measured the extension of double-stranded DNA subject to tension at various salt concentrations. The theory reproduces nearly quantitatively the elastic response of DNA at small and large values of f and for all concentration of the monovalent counterions. The limitations of the theory are also pointed out. Received 13 October 1998 and Received in final form 9 June 1999     

Growth of attached actin filaments

In several studies of actin-based cellular motility, the barbed ends of actin filaments have been observed to be attached to moving obstacles. Filament growth in the presence of such filament-obstacle interactions is studied via Brownian dynamics simulations of a three-dimensional energy-based model. We find that with a binding energy greater than 24k _B T and a highly directional force field, a single actin filament is able to push a small obstacle for over a second at a speed of half of the free filament elongation rate. These results are consistent with experimental observations of plastic beads in cell extracts. Calculations of an external force acting on a single-filament-pushed obstacle show that for typical in vitro free-actin concentrations, a 3pN pulling force maximizes the obstacle speed, while a 4pN pushing force almost stops the obstacle. Extension of the model to treat beads propelled by many filaments suggests that most of the propulsive force could be generated by attached filaments.     

Statistical theory of force-induced unzipping of DNA

The unzipping transition under the influence of external force of a dsDNA molecule has been studied using the Peyrard-Bishop Hamiltonian. The critical force F_c(T) for unzipping calculated in the constant force ensemble is found to depend on the potential parameter k which measures the stiffness associated with a single strand of DNA and on D, the well depth of the on-site potential representing the strength of hydrogen bonds in a base pair. The dependence on temperature of F_c(T) is found to be (T_D - T)^1/2 (T_D being the thermal denaturation temperature) with F_c(T_D) = 0 and F_c(0) = . We used the constant extension ensemble to calculate the average force F(y) required to stretch a base pair a y distance apart. The value of F(y) needed to stretch a base pair located far away from the ends of a dsDNA molecule is found twice the value of the force needed to stretch a base pair located at one of the ends to the same distance for y 1.0 . The force F(y) in both cases is found to have a very large value for y 0.2 compared to the critical force found from the constant force ensemble to which F(y) approaches for large values of y. It is shown that the value of F(y) at the peak depends on the value of k which measures the energy barrier associated with the reduction in DNA strand rigidity as one passes from dsDNA to ssDNA and on the value of the depth of the on-site potential. The effect of defects on the position and height of the peak in the F(y) curve is investigated by replacing some of the base pairs including the one being stretched by defect base pairs. The formation and behaviour of a loop of Y shape when one of the ends base pair is stretched and a bubble of ssDNA with the shape of an eye when a base pair far from ends is stretched are investigated.     

Force distributions and force chains in random stiff fiber networks

We study the elasticity of random stiff fiber networks. The elastic response of the fibers is characterized by a central force stretching stiffness as well as a bending stiffness that acts transverse to the fiber contour. Previous studies have shown that this model displays an anomalous elastic regime where the stretching mode is fully frozen out and the elastic energy is completely dominated by the bending mode. We demonstrate by simulations and scaling arguments that, in contrast to the bending dominated elastic energy, the equally important elastic forces are to a large extent stretching dominated. By characterizing these forces on microscopic, mesoscopic and macroscopic scales we find two mechanisms of how forces are transmitted in the network. While forces smaller than a threshold F_c are effectively balanced by a homogeneous background medium, forces larger than F_c are found to be heterogeneously distributed throughout the sample, giving rise to highly localized force chains known from granular media.     

Helix coil mixing in twist-storing polymers

Twist-storing polymers respond with elastic energy penalty to coherent or random twisting along the local chain axis away from its equilibrium, which can be straight (as in “ribbons”) or helical (as in DNA and other biopolymers). Here we study the equilibrium conformation of such polymers, focusing on the thermodynamic balance between twist and writhe, resulting from the competition between the random coil entropy and the potential energy stored in superhelical portions of the polymer chain. Two macroscopic variables characterise such a chain, the end-to-end distance R and the link number Lk, which is a topological invariant of a given polymer with clamped ends. We find that with increasing link number Lk, the chain accommodates its excess twist in growing plectonemes, unless forced out of this state by stretching its end-to-end distance R. We calculate the force-extension relation, which exhibits crossovers between different deformation regimes. Received 16 November 2000 and Received in final form 6 February 2001     

Spatial variations of the mean and statistical quantities in the thermal boundary layers of turbulent convection

We have studied the dynamics of the contact line of a viscous liquid on a solid substrate with macroscopic random defects. We have first characterized the friction force f₀ at microscopic scale for a substrate without defects; f₀ is found to be a strongly nonlinear function of the velocity U of the contact line. In presence of macroscopic defects, we find that the applied force F(U) is simply shifted with respect to f₀(U) by a constant: we do not observe any critical behavior at the depinning transition. The only observable effect of the substrate disorder is to increase the hysteresis. We have also performed realistic numerical simulation of the motion of the contact line. Using the same values of the parameters as in the experiment, we find that the experimental data is qualitatively well reproduced. In light of experimental and numerical results, we discuss the possibility of measuring a true critical behavior.Received: 6 October 2003, Published online: 19 February 2004PACS: 46.65. + g Random phenomena and media - 64.60.Ht Dynamic critical phenomena - 68.08.Bc Wetting     

On the fluctuations of the force exerted by a lipid nanotubule

After deriving the projected stress tensor in cylindrical geometry for a fluid membrane described by the Helfrich Hamiltonian, we calculate the average force f exerted by a thermally fluctuating nanotubule of radius R , and its standard deviation f . We obtain f and f in terms of the internal membrane tension , the bending rigidity , the temperature k _B T and a molecular cutoff . We find for f a shift ∼ 1/ with respect to the mean field behavior ∼ . We obtain ( f )² ∼ R ln(R/b) where b is a molecular length, f being typically small compared to f . Taking into account the difference between the internal tension and the actual mechanical tension applied to the membrane from which the tubule is drawn, we discuss the amplitude of the fluctuation-induced corrections to the average force. Our results, obtained in the harmonic approximation, hold for tubules with aspect ratio not larger than 200 , of radius significantly smaller than 100nm, that are connected to a large membrane reservoir, e.g., a giant vesicle.     

Growth kinetics of polymer crystals in bulk

Temperature-dependent measurements of spherulite growth rates carried out for i-polystyrene, poly(ε -caprolactone) and linear polyethylene show that the controlling activation barrier diverges at a temperature which is 14K, 22K and 12K, respectively, below the equilibrium melting points. We discuss the existence of such a “zero growth temperature” T _zg in the framework of a recently introduced thermodynamic multiphase scheme and identify T _zg with the temperature of a (hidden) transition between the melt and a mesomorphic phase which mediates the crystal growth. The rate-determining step in our model of crystal growth is the attachment of chain sequences from the melt onto the lateral face of a mesomorphic layer at the growth front. The necessary straightening of the sequence prior to an attachment is the cause of the activation barrier. A theory based on this view describes correctly the observations. With a knowledge of T _zg it is possible to fully establish the nanophase diagram describing the stability ranges of crystalline and mesomorphic layers in a melt. An evaluation of data from small-angle X-ray scattering, calorimetry and optical growth rate measurements yields heats of transition and surface free energies of crystals and mesophase layers, as well as the activation barrier per monomer associated with the chain stretching. According to the theory, the temperature dependence of the crystallization rate is determined by both the activation energy per monomer and the surface free energy of the preceding mesomorphic layer. Data indicate that the easiness of crystallization in polyethylene is first of all due to a particularly low surface free energy of the mesomorphic layer.     

The secondary structure of RNA under tension

We study the force-induced unfolding of random disordered RNA or single-stranded DNA polymers. The system undergoes a second-order phase transition from a collapsed globular phase at low forces to an extensive necklace phase with a macroscopic end-to-end distance at high forces. At low temperatures, the sequence inhomogeneities modify the critical behaviour. We provide numerical evidence for the universality of the critical exponents which, by extrapolation of the scaling laws to zero force, contain useful information on the ground-state (f = 0) properties. This provides a good method for quantitative studies of scaling exponents characterizing the collapsed globule. In order to get rid of the blurring effect of thermal fluctuations, we restrict ourselves to the ground state at fixed external force. We analyze the statistics of rearrangements, in particular below the critical force, and point out its implications for force-extension experiments on single molecules. Received 18 June 2002 and Received in final form 23 September 2002 RID="a" ID="a"e-mail: muller@ipno.in2p3.fr     

Effect of spermine and DNase on DNA release from bacteriophage T5

Bacterial viruses (bacteriophages) consist of nucleic acid protected by a protein envelope called capsid. At the start of infection, the phage genome is translocated into the bacterial cytoplasm. In vitro (and also in vivo), this DNA release can be triggered by binding a specific receptor protein to the phage tail. The force responsible for the release arises from energy stored in the capsid due to strong confinement of the DNA. We show that this force can be modified by adding molecules like spermine that affect DNA conformation. The tetravalent cation spermine can reduce the pressure inside the capsid and induce condensation of the released DNA. We examine the effect of spermine on DNA ejection from phage T5 by using light scattering and gel electrophoresis to measure the amount of DNA remaining in the capsid at the end of ejection. We discuss the results in terms of free energy minimization and we demonstrate that the presence of a DNA condensate outside the phage generates an additional force pulling passively on the DNA remaining inside the capsid.     

Specific biomembrane adhesion --Indirect lateral interactions between bound receptor molecules

We studied biomembrane adhesion using the micropipet aspiration technique. Adhesion was caused by contact site A, a laterally mobile and highly specific cell adhesion molecule from Dictyostelium discoideum, reconstituted in lipid vesicles of DOPC (L-α-dioleoylphosphatidylcholine) with an addition of 5 mol % DOPE-PEG₂₀₀₀ (1,2-diacyl-sn-glycero-3-phosphatidylethanolamine-N-[poly(ethyleneglycol) 2000]). The “fuzzy” membrane mimics the cellular plasma membrane including the glycocalyx. We found adhesion and subsequent receptor migration into the contact zone. Using membrane tension jumps to probe the equation of state of the two-dimensional “gas” of bound receptor pairs within the contact zone, we found strong, attractive lateral interactions. Received 16 February 2001     

Comment on the paper “Comparison of the measured phase diagrams in the force-temperature plane for the unzipping of two different natural DNA sequences” by C.H. Lee, C. Danilowicz, V.W Coljee, and M. Prentiss

The paper by Lee et al. describes the experiments on the unzipping of λ DNA sequences as a function of force and temperature. This comment aims to stress that the unzipping takes place out of equilibrium due to high sequence-dependent free-energy barriers. The force at which a heterogeneous sequence is unzipped therefore depends on the experimental waiting time.     

Transverse fluctuation analysis of single extended DNA molecules

We observed fluctuations of elongated DNA molecules by fluorescence microscopy. The molecules are fixed at both ends and undulate. Mode analysis of the thermally excited undulations of the labeled DNA molecules gives access to the spectral density of the amplitude fluctuations. From these measurements we estimate the tension acting on the DNA molecules. We found the forces to be within the entropic elasticity range of a typical DNA molecule (measured on the single-molecule level). Received: 11 November 2002 / Accepted: 12 May 2002 / Published online: 4 June 2003 RID="a" ID="a"Present address: Center for Studies in Physics and Biology, Rockefeller University, 1230 York Avenue, New York, NY 10021, USA. e-mail: zoherg@rockefeller.edu     

Small-angle neutron scattering studies of aqueous solutions of short-chain amphiphiles

We present small angle neutron scattering measurements on binary aqueous solutions of some short-chain amphiphiles (diols, triols, glycols and diglycols) at room temperature. The spectra were analysed in terms of the Teubner-Strey phenomenological formula which allows to obtain a measure for the amphiphilicity strength of each system (amphiphilicity factor f _a). In some systems, however, other models, valid for micellar solutions, give also a good representation of the spectra. As a result, we find that, independently of the type of hydrophilic group side (oxydrilic or oxirane), these systems cover the entire accessible amphiphilicity scale ( -1 < f _a < 1). Some disordered systems ( f _a > 1) presumably are able to form micelle-like aggregates. Received 12 June 2002 Published online: 16 April 2003 RID="a" ID="a"e-mail: giovanni.darrigo@uniroma1.it     

Elasticity theory of a twisted stack of plates

We present an elastic model of B-form DNA as a stack of thin, rigid plates or base pairs that are not permitted to deform. The symmetry of DNA and the constraint of plate rigidity limit the number of bulk elastic constants contributing to a macroscopic elasticity theory of DNA to four. We derive an effective twist-stretch energy in terms of the macroscopic stretch along and relative excess twist about the DNA molecular axis. In addition to the bulk stretch and twist moduli found previously, we obtain a twist-stretch modulus with the following remarkable properties: 1) it vanishes when the radius of the helical curve following the geometric center of each plate is zero, 2) it vanishes with the elastic constant K₂₃ that couples compression normal to the plates to a shear strain, if the plates are perpendicular to the molecular axis, and 3) it is nonzero if the plates are tilted relative to the molecular axis. This implies that a laminated helical structure carved out of an isotropic elastic medium will not twist in response to a stretching force, but an isotropic material will twist if it is bent into the shape of a helix. Received: 4 July 1997 / Received in final form: 16 October 1997 / Accepted: 21 October 1997     

Comparison of the measured phase diagrams in the force-temperature plane for the unzipping of two different natural DNA sequences

In this work, we consider the critical force required to unzip two different naturally occurring sequences of double-stranded DNA (dsDNA) at temperatures ranging from 20 ^°C to 50 ^°C, where one of the sequences has a 53% average guanine-cytosine (GC) content and the other has a 40% GC content. We demonstrate that the force required to separate the dsDNA of the 53% GC sequence into single-stranded DNA (ssDNA) is approximately 0.5 pN, or approximately 5% greater than the critical force required to unzip the 40% GC sequence at the same temperature. In the temperature range between 20 and 40 ^°C the measured critical forces correspond reasonably well to predictions based on a simple theoretical homopolymeric model, but at temperatures above 40 ^°C the measured critical forces are much smaller than the predicted forces. The correspondence between theory and experiment is not improved by using Monte Carlo simulations that consider the heteropolymeric nature of the sequences.     

Novel metal-encapsulated caged clusters of silicon and germanium

We report the recent findings of metal (M) encapsulated clusters of silicon from computer experiments based on ab initio total energy calculations and a cage shrinkage and atom removal approach. Our results show that using a guest atom, it is possible to wrap silicon in fullerenelike (f) structures, as sp² bonding is not favorable to produce empty cages unlike for carbon. Transition M atoms have a strong bonding with the silicon cage that are responsible for the compact structures. The size and structure of the cage change from 14 to 20 Si atoms depending upon the size and valence of the M atom. Fewer Si atoms lead to relatively open structures. We find cubic, f, Frank-Kasper (FK) polyheral type, decahedral, icosahedral and hexagonal structures for M@Si_n with n = 12-16 and several different M atoms. The magic behavior of 15 and 16 atom Si cages is in agreement with experiments. The FK polyhedral cluster, M@Si₁₆ has an exceptionally large density functional gap of about 2.35 eV calculated within the generalized gradient approximation. It is likely to give rise to visible luminescence in these clusters. The cluster-cluster interaction is weak that makes such clusters attractive for cluster assembled materials. Further studies to stabilize Si₂₀ cage with M = Zr, Ba, Sr, and Pb show that in all cases there is a distortion of the f cage. Similar studies on M encapsulated germanium clusters show FK polyhedral and decahedral isomers to be more favorable. Also perfect icosahedral M@Ge₁₂ and M@Sn₁₂ clusters have been obtained with large gaps by doping with divalent M atoms. Recent results of the H interaction with these clusters, hydrogenated silicon fullerenes as well as assemblies of clusters such as nanowires and nanotubes are briefly presented.     

Impact of gel balls beyond the Hertzian regime

We study experimentally the impact of spherical gel balls on a rigid substrate, where the balls largely deform like a pancake at high impact velocities. In our previous study (Y. Tanaka, Y. Yamazaki, K. Okumura, Europhys. Lett. 63, 149 (2003)), we measured the contact time τ_f and maximally deformed size versus impact velocity and explained the behaviors at the scaling level. In this study, we further measure τ_m, the time required to reach the maximum deformation (from the initial contact), and the restitution coefficient e. We also make a static experiment where we obtain the force-deformation curve of the gel balls up to fairly large deformations to explain the data on the impact. We propose two phenomenological treatments going beyond the scaling argument, one for intermediate impact velocities and the other for large velocities; the former is based on the static experiment while the latter on a Lagrangian constructed from appropriate constraints. Results from these treatments reproduce the experimental behavior of τ_m.     

Mössbauer study of the vibrational anisotropy and of the light-induced population of metastable states in single-crystalline guanidinium nitroprusside

M?ssbauer studies were performed on single crystals of guanidinium nitroprusside with different orientations of their principal crystallographic axes (a, b, c) with respect to the incident radiation. The markedly anisotropic Lamb-M?ssbauer factor f _LM , i.e. f _LM ^(a) = 0.118(8), f _LM ^(b) = 0.174(8), f _LM ^(c) = 0.202(8) is in contrast to that of nitroprussides with inorganic anions. The observed anisotropy is ascribed to the anisotropic vibrational mean-square displacement of the nitroprusside anions as a whole which is due to the specific packing of both, anions and cations, as well as the very weak chemical bonding between the ions, typical only for guanidinium nitroprusside. The vibrational anisotropy of iron atoms in barium nitroprusside that has been observed by X-ray structural investigations has a different origin and therefore does not result in an anisotropic Lamb-M?ssbauer factor. We have also investigated metastable states in guanidinium nitroprusside that have been populated by means of incoherent irradiation from light-emitting diodes. With a specific orientation of the guanidinium nitroprusside single crystal a population of the metastable states up to 26% could be achieved. Populations of comparable size on lithium, sodium and potassium nitroprussides have only been reached using coherent laser irradiation. Received 15 December 1998 and Received in final form 3 March 1999     

Active membranes studied by X-ray scattering

In view of recent theories of “active” membranes, we have studied multilamellar phospholipid membrane stacks with reconstituted transmembrane protein bacteriorhodopsin (BR) under different illumination conditions by X-ray scattering. The light-active protein is considered as an active constituent which drives the system out of equilibrium and is predicted to change the collective fluctuation properties of the membranes. Using X-ray reflectivity, X-ray non-specular (diffuse) scattering, and grazing incidence scattering, we find no detectable change in the scattering curves when changing the illumination condition. In particular the intermembrane spacing d remains constant, after eliminating hydration-related artifacts by design of a suitable sample environment. The absence of any observable non-equilibrium effects in the experimental window is discussed in view of the relevant parameters and recent theories.