Lattice Boltzmann Thermohydrodynamics

We introduce a lattice Boltzmann computational scheme capable of modeling thermohydrodynamic flows of monatomic gases. The parallel nature of this approach provides a numerically efficient alternative to traditional methods of computational fluid dynamics. The scheme uses a small number of discrete velocity states and a linear, single-time-relaxation collision operator. Numerical simulations in two dimensions agree well with exact solutions for adiabatic sound propagation and Couette flow with heat transfer.Comment: 11 pages, Physical Review E: Rapid Communications, in pres

Pauli Blocking of Collisions in a Quantum Degenerate Atomic Fermi Gas

We have produced an interacting quantum degenerate Fermi gas of atoms composed of two spin-states of magnetically trapped $^{40}$K. The relative Fermi energies are adjusted by controlling the population in each spin-state. Measurements of the thermodynamics reveal the resulting imbalance in the mean energy per particle between the two species, which is as large as a factor of 1.4 at our lowest temperature. This imbalance of energy comes from a suppression of collisions between atoms in the gas due to the Pauli exclusion principle. Through measurements of the thermal relaxation rate we have directly observed this Pauli blocking as a factor of two reduction in the effective collision cross-section in the quantum degenerate regime.Comment: 11 pages, 4 figure

On the microscopic foundation of dissipative particle dynamics

Mesoscopic particle based fluid models, such as dissipative particle dynamics, are usually assumed to be coarse-grained representations of an underlying microscopic fluid. A fundamental question is whether there exists a map from microscopic particles in these systems to the corresponding coarse-grained particles, such that the coarse-grained system has the same bulk and transport properties as the underlying system. In this letter, we investigate the coarse-graining of microscopic fluids using a Voronoi type projection that has been suggested in several studies. The simulations show that the projection fails in defining coarse-grained particles that have a physically meaningful connection to the microscopic fluid. In particular, the Voronoi projection produces identical coarse-grained equilibrium properties when applied to systems with different microscopic interactions and different bulk properties.Comment: First revisio

Observation of p-wave Threshold Law Using Evaporatively Cooled Fermionic Atoms

We have measured independently both s-wave and p-wave cross-dimensional thermalization rates for ultracold potassium-40 atoms held in a magnetic trap. These measurements reveal that this fermionic isotope has a large positive s-wave triplet scattering length in addition to a low temperature p-wave shape resonance. We have observed directly the p-wave threshold law which, combined with the Fermi statistics, dramatically suppresses elastic collision rates at low temperatures. In addition, we present initial evaporative cooling results that make possible these collision measurements and are a precursor to achieving quantum degeneracy in this neutral, low-density Fermi system.Comment: 5 pages, 3 figures, 1 tabl

A Dissipative-Particle-Dynamics Model for Simulating Dynamics of Charged Colloid

A mesoscopic colloid model is developed in which a spherical colloid is represented by many interacting sites on its surface. The hydrodynamic interactions with thermal fluctuations are taken accounts in full using Dissipative Particle Dynamics, and the electrostatic interactions are simulated using Particle-Particle-Particle Mesh method. This new model is applied to investigate the electrophoretic mobility of a charged colloid under an external electric field, and the influence of salt concentration and colloid charge are systematically studied. The simulation results show good agreement with predictions from the electrokinetic theory.Comment: 17 pages, 8 figures, submitted to the proceedings of High Performance Computing in Science & Engineering '1

1S-2S Spectrum of a Hydrogen Bose-Einstein Condensate

We calculate the two-photon 1S-2S spectrum of an atomic hydrogen Bose-Einstein condensate in the regime where the cold collision frequency shift dominates the lineshape. WKB and static phase approximations are made to find the intensities for transitions from the condensate to motional eigenstates for 2S atoms. The excited state wave functions are found using a mean field potential which includes the effects of collisions with condensate atoms. Results agree well with experimental data. This formalism can be used to find condensate spectra for a wide range of excitation schemes.Comment: 13 pages, 4 figure

Simultaneous Magneto-Optical Trapping of Two Lithium Isotopes

We confine 4 10^8 fermionic 6Li atoms simultaneously with 9 10^9 bosonic 7Li atoms in a magneto-optical trap based on an all-semiconductor laser system. We optimize the two-isotope sample for sympathetic evaporative cooling. This is an essential step towards the production of a quantum-degenerate gas of fermionic lithium atoms.Comment: 4 pages, 3 figure

Comparative analysis of morabine grasshopper genomes reveals highly abundant transposable elements and rapidly proliferating satellite DNA repeats

Background Repetitive DNA sequences, including transposable elements (TEs) and tandemly repeated satellite DNA (satDNAs), collectively called the “repeatome”, are found in high proportion in organisms across the Tree of Life. Grasshoppers have large genomes, averaging 9 Gb, that contain a high proportion of repetitive DNA, which has hampered progress in assembling reference genomes. Here we combined linked-read genomics with transcriptomics to assemble, characterize, and compare the structure of repetitive DNA sequences in four chromosomal races of the morabine grasshopper Vandiemenella viatica species complex and determine their contribution to genome evolution. Results We obtained linked-read genome assemblies of 2.73–3.27 Gb from estimated genome sizes of 4.26–5.07 Gb DNA per haploid genome of the four chromosomal races of V. viatica. These constitute the third largest insect genomes assembled so far. Combining complementary annotation tools and manual curation, we found a large diversity of TEs and satDNAs, constituting 66 to 75% per genome assembly. A comparison of sequence divergence within the TE classes revealed massive accumulation of recent TEs in all four races (314–463 Mb per assembly), indicating that their large genome sizes are likely due to similar rates of TE accumulation. Transcriptome sequencing showed more biased TE expression in reproductive tissues than somatic tissues, implying permissive transcription in gametogenesis. Out of 129 satDNA families, 102 satDNA families were shared among the four chromosomal races, which likely represent a diversity of satDNA families in the ancestor of the V. viatica chromosomal races. Notably, 50 of these shared satDNA families underwent differential proliferation since the recent diversification of the V. viatica species complex. Conclusion This in-depth annotation of the repeatome in morabine grasshoppers provided new insights into the genome evolution of Orthoptera. Our TEs analysis revealed a massive recent accumulation of TEs equivalent to the size of entire Drosophila genomes, which likely explains the large genome sizes in grasshoppers. Despite an overall high similarity of the TE and satDNA diversity between races, the patterns of TE expression and satDNA proliferation suggest rapid evolution of grasshopper genomes on recent timescales

Lattice Boltzmann simulations of soft matter systems

This article concerns numerical simulations of the dynamics of particles immersed in a continuum solvent. As prototypical systems, we consider colloidal dispersions of spherical particles and solutions of uncharged polymers. After a brief explanation of the concept of hydrodynamic interactions, we give a general overview over the various simulation methods that have been developed to cope with the resulting computational problems. We then focus on the approach we have developed, which couples a system of particles to a lattice Boltzmann model representing the solvent degrees of freedom. The standard D3Q19 lattice Boltzmann model is derived and explained in depth, followed by a detailed discussion of complementary methods for the coupling of solvent and solute. Colloidal dispersions are best described in terms of extended particles with appropriate boundary conditions at the surfaces, while particles with internal degrees of freedom are easier to simulate as an arrangement of mass points with frictional coupling to the solvent. In both cases, particular care has been taken to simulate thermal fluctuations in a consistent way. The usefulness of this methodology is illustrated by studies from our own research, where the dynamics of colloidal and polymeric systems has been investigated in both equilibrium and nonequilibrium situations.Comment: Review article, submitted to Advances in Polymer Science. 16 figures, 76 page

Transmission in Heteronymous Spinal Pathways Is Modified after Stroke and Related to Motor Incoordination

Changes in reflex spinal pathways after stroke have been shown to affect motor activity in agonist and antagonist muscles acting at the same joint. However, only a few studies have evaluated the heteronymous reflex pathways modulating motoneuronal activity at different joints. This study investigates whether there are changes in the spinal facilitatory and inhibitory pathways linking knee to ankle extensors and if such changes may be related to motor deficits after stroke. The early facilitation and later inhibition of soleus H reflex evoked by the stimulation of femoral nerve at 2 times the motor threshold of the quadriceps were assessed in 15 healthy participants and on the paretic and the non-paretic sides of 15 stroke participants. The relationships between this reflex modulation and the levels of motor recovery, coordination and spasticity were then studied. Results show a significant (Mann-Whitney U; P<0.05) increase in both the peak amplitude (mean±SEM: 80±22% enhancement of the control H reflex) and duration (4.2±0.5 ms) of the facilitation on the paretic side of the stroke individuals compared to their non-paretic side (36±6% and 2.9±0.4 ms) and to the values of the control subjects (33±4% and 2.8±0.4 ms, respectively). Moreover, the later strong inhibition observed in all control subjects was decreased in the stroke subjects. Both the peak amplitude and the duration of the increased facilitation were inversely correlated (Spearman r = −0.65; P = 0.009 and r = −0.67; P = 0.007, respectively) with the level of coordination (LEMOCOT) of the paretic leg. Duration of this facilitation was also correlated (r = −0.58, P = 0.024) with the level of motor recovery (CMSA). These results confirm changes in transmission in heteronymous spinal pathways that are related to motor deficits after stroke