How dsDNA breathing enhances its flexibility and instability on short length scales

We study the unexpected high flexibility of short dsDNA which recently has been reported by a number of experiments. Via the Langevin dynamics simulation of our Breathing DNA model, first we observe the formation of bubbles within the duplex and also forks at the ends, with the size distributions independent of the contour length. We find that these local denaturations at a physiological temperature, despite their rare and transient presence, can lower the persistence length drastically for a short DNA segment in agreement with experiment

INCORPORATION OF QUANTUM STATISTICAL FEATURES IN MOLECULAR DYNAMICS

We formulate a method for incorporating quantum fluctuations into molecular- dynamics simulations of many-body systems, such as those employed for energetic nuclear collision processes. Based on Fermi's Golden Rule, we allow spontaneous transitions to occur between the wave packets which are not energy eigenstates. The ensuing diffusive evolution in the space of the wave packet parameters exhibits appealing physical properties, including relaxation towards quantum- statistical equilibrium.Comment: 8 latex pages + 1 uuencoded ps figur

Surface Polymer Network Model and Effective Membrane Curvature Elasticity

A microscopic model of a surface polymer network - membrane system is introduced, with contact polymer surface interactions that can be either repulsive or attractive and sliplinks of functionality four randomly distributed over the supporting membrane surface anchoring the polymers to it. For the supporting surface perturbed from a planar configuration and a small relative number of surface sliplinks, we investigate an expansion of the free energy in terms of the local curvatures of the surface and the surface density of sliplinks, obtained through the application of the Balian - Bloch - Duplantier multiple surface scattering method. As a result, the dependence of the curvature elastic modulus, the Gaussian modulus as well as of the spontaneous curvature of the "dressed" membrane, ~{\sl i.e.} polymer network plus membrane matrix, is obtained on the mean polymer bulk end to end separation and the surface density of sliplinks.Comment: 15 pages with one included compressed uuencoded figure

Effect of symmetry energy on two-nucleon correlation functions in heavy-ion collisions induced by neutron-rich nuclei

Using an isospin-dependent transport model, we study the effects of nuclear symmetry energy on two-nucleon correlation functions in heavy ion collisions induced by neutron-rich nuclei. We find that the density dependence of the nuclear symmetry energy affects significantly the nucleon emission times in these collisions, leading to larger values of two-nucleon correlation functions for a symmetry energy that has a stronger density dependence. Two-nucleon correlation functions are thus useful tools for extracting information about the nuclear symmetry energy from heavy ion collisions.Comment: Revised version, to appear in Phys. Rev. Let

Intermittency and Exotic Channels

It is pointed out that accurate measurements of short-range two-particle correlations in like-charge $K\pi$ and in $\pi^ 0\pi^ 0$ channels should be very helpful in determining the origin of the \lq\lq intermittency\rq\rq\ phenomenon observed recently for the like-charge pion pairs.Comment: 5 p., plain tex, preprint T94/078(Saclay), LPTHE 94/58(Orsay

Molecular Model of the Contractile Ring

We present a model for the actin contractile ring of adherent animal cells. The model suggests that the actin concentration within the ring and consequently the power that the ring exerts both increase during contraction. We demonstrate the crucial role of actin polymerization and depolymerization throughout cytokinesis, and the dominance of viscous dissipation in the dynamics. The physical origin of two phases in cytokinesis dynamics ("biphasic cytokinesis") follows from a limitation on the actin density. The model is consistent with a wide range of measurements of the midzone of dividing animal cells.Comment: PACS numbers: 87.16.Ka, 87.16.Ac http://www.ncbi.nlm.nih.gov/pubmed/16197254 http://www.weizmann.ac.il/complex/tlusty/papers/PhysRevLett2005.pd

Phase Transitions in Warm, Asymmetric Nuclear Matter

A relativistic mean-field model of nuclear matter with arbitrary proton fraction is studied at finite temperature. An analysis is performed of the liquid-gas phase transition in a system with two conserved charges (baryon number and isospin) using the stability conditions on the free energy, the conservation laws, and Gibbs' criteria for phase equilibrium. For a binary system with two phases, the coexistence surface (binodal) is two-dimensional. The Maxwell construction through the phase-separation region is discussed, and it is shown that the stable configuration can be determined uniquely at every density. Moreover, because of the greater dimensionality of the binodal surface, the liquid-gas phase transition is continuous (second order by Ehrenfest's definition), rather than discontinuous (first order), as in familiar one-component systems. Using a mean-field equation of state calibrated to the properties of nuclear matter and finite nuclei, various phase-separation scenarios are considered. The model is then applied to the liquid-gas phase transition that may occur in the warm, dilute matter produced in energetic heavy-ion collisions. In asymmetric matter, instabilities that produce a liquid-gas phase separation arise from fluctuations in the proton concentration (chemical instability), rather than from fluctuations in the baryon density (mechanical instability).Comment: Postscript file, 50 pages including 23 figure

The Interplay of Nonlinearity and Architecture in Equilibrium Cytoskeletal Mechanics

The interplay between cytoskeletal architecture and the nonlinearity of the interactions due to bucklable filaments plays a key role in modulating the cell's mechanical stability and affecting its structural rearrangements. We study a model of cytoskeletal structure treating it as an amorphous network of hard centers rigidly cross-linked by nonlinear elastic strings, neglecting the effects of motorization. Using simulations along with a self-consistent phonon method, we show that this minimal model exhibits diverse thermodynamically stable mechanical phases that depend on excluded volume, crosslink concentration, filament length and stiffness. Within the framework set by the free energy functional formulation and making use of the random first order transition theory of structural glasses, we further estimate the characteristic densities for a kinetic glass transition to occur in this model system. Network connectivity strongly modulates the transition boundaries between various equilibrium phases, as well as the kinetic glass transition density.Comment: 17 pages, 18 figure

An Improved Quantum Molecular Dynamics Model and its Applications to Fusion Reaction near Barrier

An improved Quantum Molecular Dynamics model is proposed. By using this model, the properties of ground state of nuclei from $^{6}$Li to $^{208}$Pb can be described very well with one set of parameters. The fusion reactions for $^{40}$Ca+$^{90}$Zr, $^{40}$Ca+$^{96}$Zr and $^{48}$Ca+$^{90}$Zr at energy near barrier are studied by this model. The experimental data of the fusion cross sections for $^{40}$Ca+$^{90,96}$Zr at the energy near barrier can be reproduced remarkably well without introducing any new parameters. The mechanism for the enhancement of fusion probability for fusion reactions with neutron-rich projectile or target is analyzed.Comment: 20 pages, 12 figures, 3 table

Bose-Einstein Correlations of Pion Wavepackets

A wavepacket model for a system of free pions, which takes into account the full permutation symmetry of the wavefunction and which is suitable for any phase space parametrization is developed. The properties of the resulting mixed ensembles and the two-particle correlation function are discussed. A physical interpretation of the chaoticity lambda as localizat of the pions in the source is presented. Two techniques to generate test-particles, which satisfy the probability densities of the wavepacket state, are studied: 1. A Monte Carlo procedure in momentum space based on the standard Metropolis technique. 2. A molecular dynamic procedure using Bohm's quantum theory of motion. In order to reduce the numerical complexity, the separation of the wavefunction into momentum space clusters is discussed. In this context th influence of an unauthorized factorization of the state, i. e. the omissio of interference terms, is investigated. It is shown that the correlation radius remains almost uneffected, but the chaoticity parameter decreases substantially. A similar effect is observed in systems with high multiplic where the omission of higher order corrections in the analysis of two-part correlations causes a reduction of the chaoticity and the radius. The approximative treatment of the Coulomb interaction between pions and source is investigated. The results suggest that Coulomb effects on the co radii are not symmetric for pion pairs of different charges. For negative the radius, integrated over the whole momentum spectrum, increases substan while for positive pions the radius remains almost unchanged.Comment: 15 pages, 8 figures, 0.8 Mb, uses ljour2-macro, Submitted to Z. Phys. A (1997