A New Approach based on Langevin type Equation for Driven Granular Gas under Gravity

We propose a novel approach based on a Langevin equation for fluctuating motion of the center of mass of granular media fluidized by energy injection from a bottom plate. In this framework, the analytical solution of the Langevin equation is used to derive analytic expressions for several macroscopic quantities and the power spectrum for the center of mass. In order to test our theory, we performed event-driven molecular dynamics simulations for one- and two-dimensional systems. Energy is injected from a vibrating bottom plate in the one-dimensional case and from a thermal wall at the bottom in the two-dimensional case. We found that the theoretical predictions are in good agreement with the results of those simulations under the assumption that the fluctuation-dissipation relation holds in the case of nearly elastic collisions between particles. However, as the inelasticity of the interparticle collisions increases, the power spectrum for the center of mass obtained by the simulations gradually deviates from the prediction of theoretical curve. Connection between this deviation and violation of the fluctuation-dissipation relation is discussed.Comment: 13 pages, 11 figures; corrected typos, to be published in the AIP Conference Proceedings of the IUTAM-ISIMM Symposium "Mathematical and Physical Instances of Granular Flows" held in Reggio Calabria, September 14-18, 200

Target-selective homologous recombination cloning for high-throughput generation of monoclonal antibodies from single plasma cells

<p>Abstract</p> <p>Background</p> <p>Molecular cloning of functional immunoglobulin genes from single plasma cells is one of the most promising technologies for the rapid development of monoclonal antibody drugs. However, the proper insertion of PCR-amplified immunoglobulin genes into expression vectors remains an obstacle to the high-throughput production of recombinant monoclonal antibodies.</p> <p>Results</p> <p>We developed a single-step cloning method, target-selective homologous recombination (TS-HR), in which PCR-amplified immunoglobulin variable genes were selectively inserted into vectors, even in the presence of nonspecifically amplified DNA. TS-HR utilizes Red/ET-mediated homologous recombination with a target-selective vector (TS-vector) with unique homology arms on its termini. Using TS-HR, immunoglobulin variable genes were cloned directly into expression vectors by co-transforming unpurified PCR products and the TS-vector into <it>E. coli</it>. Furthermore, the high cloning specificity of TS-HR allowed plasmids to be extracted from pools of transformed bacteria without screening single colonies for correct clones. We present a one-week protocol for the production of recombinant mouse monoclonal antibodies from large numbers of single plasma cells.</p> <p>Conclusion</p> <p>The time requirements and limitations of traditional cloning procedures for the production of recombinant immunoglobulins have been significantly reduced with the development of the TS-HR cloning technique.</p

Hard-disk equation of state: First-order liquid-hexatic transition in two dimensions with three simulation methods

We report large-scale computer simulations of the hard-disk system at high densities in the region of the melting transition. Our simulations reproduce the equation of state, previously obtained using the event-chain Monte Carlo algorithm, with a massively parallel implementation of the local Monte Carlo method and with event-driven molecular dynamics. We analyze the relative performance of these simulation methods to sample configuration space and approach equilibrium. Our results confirm the first-order nature of the melting phase transition in hard disks. Phase coexistence is visualized for individual configurations via the orientational order parameter field. The analysis of positional order confirms the existence of the hexatic phase.Comment: 9 pages, 8 figures, 2 table

Long Time Tail of the Velocity Autocorrelation Function in a Two-Dimensional Moderately Dense Hard Disk Fluid

Alder and Wainwright discovered the slow power decay $\sim t^{-d/2}$ ($d$:dimension) of the velocity autocorrelation function in moderately dense hard sphere fluids using the event-driven molecular dynamics simulations. In the two-dimensional case, the diffusion coefficient derived using the time correlation expression in linear response theory shows logarithmic divergence, which is called the ``2D long-time-tail problem''. We revisited this problem to perform a large-scale, long-time simulation with one million hard disks using a modern efficient algorithm and found that the decay of the long tail in moderately dense fluids is slightly faster than the power decay ($\sim 1/t$). We also compared our numerical data with the prediction of the self-consistent mode-coupling theory in the long time limit ($\sim 1/(t\sqrt{\ln{t}})$).Comment: 5 pages, 5 figures, to appear in Phys. Rev.

Applicability of dynamic facilitation theory to binary hard disk systems

We numerically investigate the applicability of dynamic facilitation (DF) theory for glass-forming binary hard disk systems where supercompression is controlled by pressure. By using novel efficient algorithms for hard disks, we are able to generate equilibrium supercompressed states in an additive nonequimolar binary mixture, where microcrystallization and size segregation do not emerge at high average packing fractions. Above an onset pressure where collective heterogeneous relaxation sets in, we find that relaxation times are well described by a “parabolic law” with pressure. We identify excitations, or soft spots, that give rise to structural relaxation and find that they are spatially localized, their average concentration decays exponentially with pressure, and their associated energy scale is logarithmic in the excitation size. These observations are consistent with the predictions of DF generalized to systems controlled by pressure rather than temperature