arXiv subjects

Zhou Haijun

Publications and source records attributed to Zhou Haijun.

9 recordsLinked to original sources

arXiv1999

Monte Carlo implementation of supercoiled double-stranded DNA

Metropolis Monte Carlo simulation is used to investigate the elasticity of torsionally stressed double-stranded DNA, in which twist and supercoiling are incorporated as a natural result of base-stacking interaction and backbone bending constrained by hydrogen bonds formed between DNA complementary nucleotide bases. Three evident regimes are found in extension versus torsion and/or force versus extension plots: a low-force regime in which over- and underwound molecules behave similarly under stretching; an intermediate-force regime in which chirality appears for negatively and positively supercoiled DNA and extension of underwound molecule is insensitive to the supercoiling degree of the polymer; and a large-force regime in which plectonemic DNA is fully converted to extended DNA and supercoiled DNA behaves quite like a torsionless molecule. The striking coincidence between theoretic calculations and recent experimental measurement of torsionally stretched DNA [Strick et al., Science {\bf 271}, 1835 (1996), Biophys. J. {\bf 74}, 2016 (1998)] strongly suggests that the interplay between base-stacking interaction and permanent hydrogen-bond constraint takes an important role in understanding the novel properties of elasticity of supercoiled DNA polymer.

physics.bio-ph↗

arXiv1999

Can pulling cause right- to left-handed structural transitions in negatively supercoiled DNA double-helix?

The folding angle distribution of stretched and negatively supercoiled DNA double-helix is investigated based on a theoretical model we proposed earlier [H. Zhou et al., Phys. Rev. Lett. 82, 4560 (1999)]. It is shown that pulling can transit a negatively supercoiled DNA double-helix from the right-handed B-form to a left-handed configuration which resembles DNA Z-form in some important respects. The energetics of this possible transition is calculated and the comparison with recent experimental observations are qualitatively discussed.

cond-mat.soft↗

arXiv1999

Spheres and Prolate and Oblate Ellipsoids from an Analytical Solution of Spontaneous Curvature Fluid Membrane Model

An analytic solution for Helfrich spontaneous curvature membrane model (H. Naito, M.Okuda and Ou-Yang Zhong-Can, Phys. Rev. E {\bf 48}, 2304 (1993); {\bf 54}, 2816 (1996)), which has a conspicuous feature of representing the circular biconcave shape, is studied. Results show that the solution in fact describes a family of shapes, which can be classified as: i) the flat plane (trivial case), ii) the sphere, iii) the prolate ellipsoid, iv) the capped cylinder, v) the oblate ellipsoid, vi) the circular biconcave shape, vii) the self-intersecting inverted circular biconcave shape, and viii) the self-intersecting nodoidlike cylinder. Among the closed shapes (ii)-(vii), a circular biconcave shape is the one with the minimum of local curvature energy.

cond-mat.soft↗

arXiv1999

Entropic Elasticity, Cooperative Extensibility and Supercoiling Property of DNA: A Unified Viewpoint

A unified model is constructed to study the recently observed DNA entropic elasticity, cooperative extensibility, and supercoiling property. With the introduction of a new structural parameter (the folding angle $ϕ$), bending deformations of sugar-phosphate backbones, steric effects of nucleotide basepairs, and short-range basestacking interactions are considered. The comprehensive agreement of theoretical results with experimental observations on both torsionally relaxed and negatively supercoiled DNAs strongly indicates that, basestacking interactions, although short-ranged in nature, dominate the elasticity of DNA and hence are of vital biological significance.

cond-mat.soft↗

arXiv1998

Bending and Base-Stacking Interactions in Double-Stranded Semiflexible Polymer

Simple expressions for the bending and the base-stacking energy of double-stranded semiflexible biopolymers (such as DNA and actin) are derived. The distribution of the folding angle between the two strands is obtained by solving a Schrödinger equation variationally. Theoretical results based on this model on the extension versus force and extension versus degree of supercoiling relations of DNA chain are in good agreement with the experimental observations of Cluzel {\it et al.} [Science {\bf 271}, 792 (1996)], Smith {\it et al.} [{\it ibid.} {\bf 271}, 795 (1996)], and Strick {\it et al.} [{\it ibid.} {\bf 271}, 1835 (1996)].

cond-mat.soft↗

arXiv1998

Spontaneous curvature-induced dynamical instability of Kirchhoff filaments: Application to DNA kink deformations

The Kirchhoff elastic theory of thin filaments with spontaneous curvature is employed in the understanding of the onset of the kink transitions observed in short DNA rings. Dynamical analysis shows that when its actual curvature is less than some threshold value determined by the spontaneous curvature, a circular DNA will begin to buckle to other shapes. The observable and the dominant deformation modes are also determined by dynamical instability analysis, and the different effects of Zn$^{2+}$ and Mg$^{2+}$ ions on DNA configurational properties are qualitatively discussed.

physics.bio-ph↗

arXiv1998

Theory on quench-induced pattern formation: Application to the isotropic to smectic-A phase transitions

During catastrophic processes of environmental variations of a thermodynamic system, such as rapid temperature decreasing, many novel and complex patterns often form. To understand such phenomena, a general mechanism is proposed based on the competition between heat transfer and conversion of heat to other energy forms. We apply it to the smectic-A filament growth process during quench-induced isotropic to smectic-A phase transition. Analytical forms for the buckling patterns are derived and we find good agreement with experimental observation [Phys. Rev. {\bf E55} (1997) 1655]. The present work strongly indicates that rapid cooling will lead to structural transitions in the smectic-A filament at the molecular level to optimize heat conversion. The force associated with this pattern formation process is estimated to be in the order of $10^{-1}$ piconewton.

cond-mat.soft↗

arXiv1998

Bending and Twisting Elasticity: a Revised Marko-Siggia Model on DNA Chirality

A revised Marko-Siggia elastic model for DNA double helix [Macromolecules 27, 981 (1994)] is proposed, which includes the WLC bending energy and a new chiral twisting energy term. It is predicted that the mean helical repeat length (HRL) for short DNA rings increases with the decreasing of chain length; while for very long chains, their mean HRL is the same, independent of both the chain length and whether the ends are closed, it is longer than the value for rectilinear DNAs. Our results are in good agreement with experiments.

cond-mat.soft↗

arXiv1998

Instability and Periodic Deformation in Bilayer Membranes Induced by Freezing

The instability and periodic deformation of bilayer membranes during freezing processes are studied as a function of the difference of the shape energy between the high and the low temperature membrane states. It is shown that there exists a threshold stability condition, bellow which a planar configuration will be deformed. Among the deformed shapes, the periodic curved square textures are shown being one kind of the solutions of the associated shape equation. In consistency with recent expe rimental observations, the optimal ratio of period and amplitude for such a texture is found to be approximately equal to (2)^{1/2}π.

cond-mat.soft↗