CiteULike: dchen's people

Solvent-Induced DNA Conformational Transition

B Gu — 2008-05-07T23:28:21-00:00

Physical Review Letters, Vol. 100, No. 8. (2008)

Modified water models with scaled charges are used to investigate solvent polarity effects on DNA structure. Several intensive molecular dynamics simulations of the DNA EcoRI dodecamer d(CGCGAATTCGCG) in different model solvents are performed. When the polarity of the solvent molecule decreases, from overpolarized to less polarized, DNA experiences the conformational transitions of constrainedB form(A-B)mixA form. We demonstrate that one important cause of these structure changes is the competition between hydration and direct cation coupling to the free oxygen atoms in the phosphate groups on DNA backbones.

Heating Mechanism Affects Equipartition in a Binary Granular System

Hong Wang — 2008-05-06T14:42:31-00:00

Physical Review Letters, Vol. 100, No. 15. (2008)

Two species of particles in a binary granular system typically do not have the same mean kinetic energy, in contrast to the equipartition of energy required in equilibrium. We investigate the role of the heating mechanism in determining the extent of nonequipartition of kinetic energy. In most experiments, different species are unequally heated at the boundaries. We show by event-driven simulations that differential boundary heating affects nonequipartition even in the bulk of the system. This conclusion is fortified by studying numerical and solvable stochastic models without spatial degrees of freedom. In both cases, even in the limit where heating events are rare compared to collisions, the effect of the heating mechanism persists.

Time-Resolved Shadowgraphs of Material Ejection in Intense Femtosecond Laser Ablation of Aluminum

Nan Zhang — 2008-05-03T23:46:49-00:00

Physical Review Letters, Vol. 99, No. 16. (2007)

The dynamic process of intense 50 fs laser ablation of aluminum is investigated by ultrafast time-resolved microscopy. A stripe pattern preceding phase explosion is clearly seen in the shadowgraph of 1 ns time delay. Intermittent material ejections are observed within the ejected plume after 2.5 and 7 ns time delay, respectively, which may be attributed to the material response to the generation of an extremely strong thermoelastic wave. Similar processes are also recorded in the ablation of silicon and glass samples, except for the glass samples, the intermittent material ejections are not found.

Spontaneous Formation of Complex Micelles from a Homogeneous Solution

Xuehao He — 2008-05-03T17:52:28-00:00

Physical Review Letters, Vol. 100, No. 13. (2008)

We present an extensive computer simulation study of structure formation in amphiphilic block copolymer solutions after a quench from a homogeneous state. By using a mesoscopic field-based simulation method, we are able to access time scales in the range of a second. A “phase diagram” of final structures is mapped out as a function of the concentration and solvent philicity of the copolymers. A rich spectrum of structures is observed, ranging from spherical and rodlike micelles and vesicles to toroidal and net-cage micelles. The dynamical pathways leading to these structures are analyzed in detail, and possible ways to control the structures are discussed briefly.

Controllable Monodisperse Multiple Emulsions

Liang-Yin Chu — 2008-04-17T18:59:41-00:00

Angewandte Chemie International Edition, Vol. 46, No. 47. (2007), pp. 8970-8974.

No Abstract

Molecular Theory of Physical Aging in Polymer Glasses

Kang Chen — 2008-03-18T23:12:48-00:00

Physical Review Letters, Vol. 98, No. 16. (2007)

A molecular level theory for the physical aging of polymer glasses is proposed. The nonequilibrium time evolution of the amplitude of long wavelength density fluctuations, and its influence on activated barrier hopping, plays an essential role. The theory predicts temperature-dependent apparent power-law aging of the segmental relaxation time and logarithmic aging of thermodynamiclike properties, in good accord with experiments. A physical origin for the quantitative nonuniversal aspects based on the amplitude of quenched density fluctuations is suggested.

Surface Diffusion Dynamics of a Single Polymer Chain in Dilute Solution

Hu Qian — 2008-03-18T21:08:38-00:00

Physical Review Letters, Vol. 99, No. 6. (2007)

Comprehensive three-dimensional dissipative particle dynamics simulations are carried out to elucidate the diffusion mechanism of a strongly adsorbed polymer chain on a solid surface in dilute solutions. We find Rouse and reptation dynamics for polymer chain diffusing on smooth and rough surfaces (with obstacles or sticking points), respectively. Combining with scaling analysis, we find that the interactions between the surface and the fluid screen the hydrodynamic interaction. The different scaling as found for a polymer chain diffusing on a fluid membrane [Phys. Rev. Lett. 82, 1911 (1999)] and on a solid surface [Nature (London) 406, 146 (2000)] may be explained by the solid surface inhomogeneity that induces reptation.

Temperature Oscillations in a Compartmentalized Bidisperse Granular Gas

Meiying Hou — 2008-03-18T00:51:22-00:00

Physical Review Letters, Vol. 100, No. 6. (2008)

A granular clock is observed in a vertically vibrated compartmentalized granular gas composed of two types of grains with the same size. The dynamics of the clock is studied in terms of an unstable evaporation or condensation model for the granular gas. In this model, the temperatures of the two types of grains are considered to be different, and they are functions of the composition of the gas. Oscillations in the system are driven by the asymmetric collisions properties between the two types of grains. Both our experiments and model show that the transition of the system from a homogeneous state to an oscillatory state is via a Hopf bifurcation.

Molecular Dynamics Simulation of Cage Effect in the Glass Transition of Argon

Sun Yong-Li — 2008-03-01T20:40:20-00:00

Chinese Physics Letters, Vol. 23, No. 10. (2006), pp. 2830-2833.

The glass transition process of argon is studied by molecular dynamics simulations with Lennard-Jones potential. The cage effect appears at about 24 K. The Lindemann length of argon is found to be 0.55 Å. Two relaxation processes are clearly observed near the glass transition temperature, which is in agreement with the mode-coupling theory.

Spatially Heterogeneous Dynamics and Dynamic Facilitation in a Model of Viscous Silica

Michael Vogel — 2006-08-01T23:05:33-00:00

Physical Review Letters, Vol. 92, No. 25. (2004)

We perform molecular dynamics simulations to study the structural relaxation dynamics of a model of viscous silica, the prototype of a strong glass former. We find that the melt dynamics are spatially heterogeneous regardless of whether the bulk relaxation is non-Arrhenius or Arrhenius, and cannot be understood as a statistical bondbreaking process. Further, we show that stringlike motion is suppressed by the covalent bondings, yet high particle mobility propagates continuously, supporting the concept of dynamic facilitation emphasized in recent theoretical work.