Stochastic Hard-Sphere Dynamics for Hydrodynamics of Non-Ideal Fluids

A novel stochastic fluid model is proposed with non-ideal structure factor consistent with compressibility, and adjustable transport coefficients. This Stochastic Hard Sphere Dynamics (SHSD) algorithm is a modification of the Direct Simulation Monte Carlo (DSMC) algorithm and has several computational advantages over event-driven hard-sphere molecular dynamics. Surprisingly, SHSD results in an equation of state and pair correlation function identical to that of a deterministic Hamiltonian system of penetrable spheres interacting with linear core pair potentials. The fluctuating hydrodynamic behavior of the SHSD fluid is verified for the Brownian motion of a nano-particle suspended in a compressible solvent.Comment: This work performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344 (LLNL-JRNL-401745). To appear in Phys. Rev. Lett. 200

Epigenetic regulation of key developmental genes during early mouse development

In undifferentiated ES cells, many Polycomb Repressive Complex 2 (PRC2) target genes carry not only repressive H3K27me3 but are also enriched for conventional indicators of active chromatin including methylated H3K4. This so-called bivalent domain structure is thought to silence key developmental regulators while keeping them poised for future activation (or repression). Consistent with this hypothesis, bivalent genes assemble RNAP II preferentially phosphorylated on Serine 5 residues (poised RNAP II) and are transcribed at low levels. Productive expression is, however, prevented by the action of PRC1. Here, I have focused on the pre-implantation stage of mouse development to evaluate whether bivalent or poised chromatin signatures are indeed specific attributes of emerging pluripotent cells and investigate how the fate of key developmental genes is specified while the first lineage decision event (extra-embryonic lineage formation) occurs. Using blastocyst-derived stem cells and chromatin immunoprecipitation (ChIP), I have shown that lineage-inappropriate genes retain bivalent histone marking in extra-embryonic trophoblast stem (TS). However, and in contrast to ES cells, PRC1 (Ring1B) and poised RNAP II are not recruited to these loci in TS cells, indicating that gene priming is a unique hallmark of pluripotent cells in the early embryo. To investigate the intricate relationship between lineage identity and dynamic chromatin changes, I exploited the potential to convert ES cells into trophoblast-like stem (TSL) cells using a previously established artificial system dependent on doxycycline (Dox) induced repression of an Oct4 transgene. I demonstrated that Suv39h1-mediated H3K9me3 alongside DNA methylation is targeted to PRC2-bound bivalent, lineage-inappropriate genes upon trophectoderm lineage commitment. A change in chromatin conformation was observed upon differentiation of ES cells to TSL cells comparable to that seen in TS cells derived in the traditional manner from the trophectoderm (TE) of blastocyst stage embryos. Most importantly, I have begun to explore when epigenetic differences are specified, at the locus level, from 8-cell stage embryos onwards using newly designed Carrier ChIP technology. This data validated the occurrence of bivalent chromatin domains in vivo and further support the view that alternative strategies operate in the TE to silence key developmental regulators upon blastocyst lineage segregation

Study of Transient Nuclei near Freezing

The molasses tail in dense hard core fluids is investigated by extensive event-driven molecular dynamics simulation through the orientational autocorrelation functions. Near the fluid-solid phase transition, there exist three regimes in the relaxation of the pair orientational autocorrelation function, namely the kinetic, molasses (stretched exponential), and diffusional power decay. The density dependence of both the molasses and diffusional power regimes are evaluated and the latter compares with theoretical predictions in three dimensions. The largest cluster at the freezing density of only a few sphere diameter in size persist for only about 30 picoseconds (~ 2.8 x 10^{-11}[s]). The most striking observation through the bond orientatinal order parameter is the dramatic increase of the cluster size as the freezing density is approached.Comment: 12 pages, 8 figures, 3 tables, To appear in the Proceedings of YKIS2009 Frontiers in Nonequilibrium Physics, Progress of Theoretical Physics Supplement (2010)

Development and Validation of a Partitioned Fluid-Structure Solver for Transonic Panel Flutter with Focus on Boundary Layer Effects

A partitioned fluid-structure coupling code for transonic panel flutter has been developed and validated. The Reynolds-averaged Navier-Stokes equations are solved numerically by means of an implicit finite volume method to account for nonlinear aerodynamics, as there are shock waves and a viscous boundary layer at the panel surface. An implicit finite element formulation of the structural equations as well as a Galerkin solution of the von-Kármán plate equation are employed to solve elastic panel deformations with respect to geometric nonlinearities. A detailed validation process is presented in this paper for high subsonic and low supersonic Mach numbers. This comprises a discussion of available results from literature with the objective to propose a guideline for validation purposes of partitioned panel flutter solvers. Thereupon the code is used for studies on the impact of turbulent boundary layer characteristics on aeroelastic stability boundaries and post-flutter. An evaluation of flutter modes and frequencies in the post-flutter domain as well as a discussion of the corresponding flow phenomena is presented

Phase transition in inelastic disks

This letter investigates the molecular dynamics of inelastic disks without external forcing. By introducing a new observation frame with a rescaled time, we observe the virtual steady states converted from asymptotic energy dissipation processes. System behavior in the thermodynamic limit is carefully investigated. It is found that a phase transition with symmetry breaking occurs when the magnitude of dissipation is greater than a critical value.Comment: 9 pages, 6 figure

Influence on performance of feeding egg-strain laying hens increasing levels of phosphorus with increasing levels of calcium

Call number: LD2668 .T4 1969 A64Master of Scienc