A variable time step self-consistent mean field DSMC model for three-dimensional environments

A self-consistent mean field direct simulation Monte Carlo (SCMFD) algorithm was recently proposed for simulating collision environments for a range of one-dimensional model systems. This work extends the one-dimensional SCMFD approach to three dimensions and introduces a variable time step (3D-vt-SCMFD), enabling the modeling of a considerably wider range of different collision environments. We demonstrate the performance of the augmented method by modeling a varied set of test systems: ideal gas mixtures, Poiseuille flow of argon, and expansion of gas into high vacuum. For the gas mixtures, the 3D-vt-SCMFD method reproduces the properties (mean free path, mean free time, collision frequency, and temperature) in excellent agreement with theoretical predictions. From the Poiseuille flow simulations, we extract flow profiles that agree with the solution to the Navier–Stokes equations in the high-density limit and resemble free molecular flow at low densities, as expected. The measured viscosity from 3D-vt-SCMF is ∼15% lower than the theoretical prediction from Chapman–Enskog theory. The expansion of gas into vacuum is examined in the effusive regime and at the hydrodynamic limit. In both cases, 3D-vt-SCMDF simulations produce gas beam density, velocity, and temperature profiles in excellent agreement with analytical models. In summary, our tests show that 3D-vt-SCMFD is robust and computationally efficient, while also illustrating the diversity of systems the SCMFD model can be successfully applied to

Using Open Data to Rapidly Benchmark Biomolecular Simulations : Phospholipid Conformational Dynamics

Molecular dynamics (MD) simulations are widely used to monitor time-resolved motions of biomacromolecules, although it often remains unknown how closely the conformational dynamics correspond to those occurring in real life. Here, we used a large set of open-access MD trajectories of phosphatidylcholine (PC) lipid bilayers to benchmark the conformational dynamics in several contemporary MD models (force fields) against nuclear magnetic resonance (NMR) data available in the literature: effective correlation times and spin-lattice relaxation rates. We found none of the tested MD models to fully reproduce the conformational dynamics. That said, the dynamics in CHARMM36 and Slipids are more realistic than in the Amber Lipid14, OPLS-based MacRog, and GROMOS-based Berger force fields, whose sampling of the glycerol backbone conformations is too slow. The performance of CHARMM36 persists when cholesterol is added to the bilayer, and when the hydration level is reduced. However, for conformational dynamics of the PC headgroup, both with and without cholesterol, Slipids provides the most realistic description because CHARMM36 overestimates the relative weight of similar to 1 ns processes in the headgroup dynamics. We stress that not a single new simulation was run for the present work. This demonstrates the worth of open-access MD trajectory databanks for the indispensable step of any serious MD study: benchmarking the available force fields. We believe this proof of principle will inspire other novel applications of MD trajectory databanks and thus aid in developing biomolecular MD simulations into a true computational microscope-not only for lipid membranes but for all biomacromolecular systems.Peer reviewe

Isomeric states close to doubly magic 132^{132}Sn studied with JYFLTRAP

The double Penning trap mass spectrometer JYFLTRAP has been employed to measure masses and excitation energies for $11/2^-$ isomers in $^{121}$Cd, $^{123}$Cd, $^{125}$Cd and $^{133}$Te, for $1/2^-$ isomers in $^{129}$In and $^{131}$In, and for $7^-$ isomers in $^{130}$Sn and $^{134}$Sb. These first direct mass measurements of the Cd and In isomers reveal deviations to the excitation energies based on results from beta-decay experiments and yield new information on neutron- and proton-hole states close to $^{132}$Sn. A new excitation energy of 144(4) keV has been determined for $^{123}$Cd$^m$. A good agreement with the precisely known excitation energies of $^{121}$Cd$^m$, $^{130}$Sn$^m$, and $^{134}$Sb$^m$ has been found.Comment: 10 pages, 6 figures, submitted to Phys. Rev.

Precision mass measurements of radioactive nuclei at JYFLTRAP

The Penning trap mass spectrometer JYFLTRAP was used to measure the atomic masses of radioactive nuclei with an uncertainty better than 10 keV. The atomic masses of the neutron-deficient nuclei around the N = Z line were measured to improve the understanding of the rp-process path and the SbSnTe cycle. Furthermore, the masses of the neutron-rich gallium (Z = 31) to palladium (Z = 46) nuclei have been measured. The physics impacts on the nuclear structure and the r-process paths are reviewed. A better understanding of the nuclear deformation is presented by studying the pairing energy around A = 100.Comment: 4 pages and 4 figures, RNB7 conf. pro

Stimulation and Inhibition of Lymphangiogenesis Via Adeno-Associated Viral Gene Delivery

The lymphatic vessels can be selectively stimulated to grow in adult mice, rats and pigs by application of viral vectors expressing the lymphangiogenic factors VEGF-C or VEGF-D. Vice versa, lymphangiogenesis in various pathological settings can be inhibited by the blocking of the VEGF-C/VEGFR3 interaction using a ligand-binding soluble form of VEGFR3. Furthermore, the recently discovered plasticity of meningeal and lacteal lymphatic vessels provides novel opportunities for their manipulation in disease. Adenoviral and adeno-associated viral vectors (AAVs) provide suitable tools for establishing short- and long-term gene expression, respectively and adenoviral vectors have already been used in clinical trials. As an example, we describe here ways to manipulate the meningeal lymphatic vasculature in the adult mice via AAV-mediated gene delivery. The possibility of stimulation and inhibition of lymphangiogenesis in adult mice has enabled the analysis of the role and function of lymphatic vessels in mouse models of disease.Peer reviewe

Characterization of a Be(p,xn) neutron source for fission yields measurements

We report on measurements performed at The Svedberg Laboratory (TSL) to characterize a proton-neutron converter for independent fission yield studies at the IGISOL-JYFLTRAP facility (Jyv\"askyl\"a, Finland). A 30 MeV proton beam impinged on a 5 mm water-cooled Beryllium target. Two independent experimental techniques have been used to measure the neutron spectrum: a Time of Flight (TOF) system used to estimate the high-energy contribution, and a Bonner Sphere Spectrometer able to provide precise results from thermal energies up to 20 MeV. An overlap between the energy regions covered by the two systems will permit a cross-check of the results from the different techniques. In this paper, the measurement and analysis techniques will be presented together with some preliminary results.Comment: 3 pages, 3 figures, also submitted as proceedings of the International Conference on Nuclear Data for Science and Technology 201

Q-value of the superallowed beta decay of Ga-62

Masses of the radioactive isotopes 62Ga, 62Zn and 62Cu have been measured at the JYFLTRAP facility with a relative precision of better than 18 ppb. A Q_EC value of (9181.07 +- 0.54) keV for the superallowed decay of 62Ga is obtained from the measured cyclotron frequency ratios of 62Ga-62Zn, 62Ga-62Ni and 62Zn-62Ni ions. The resulting Ft-value supports the validity of the conserved vector current hypothesis (CVC). The mass excess values measured were (-51986.5 +-1.0) keV for 62Ga, (-61167.9 +- 0.9) keV for 62Zn and (-62787.2 +- 0.9) keV for 62Cu.Comment: 12 pages, 3 figures, 2 tables, submitted to Phys. Lett. B. v2: added acknowledgement