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PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations
- Todd J. Dolinsky, Paul Czodrowski, +4 authors Nathan A. Baker
- Medicine, Computer Science
- Nucleic Acids Res.
- 8 May 2007
The significantly expanded PDB2PQR is reported that includes robust standalone command line support, improved pKa estimation via the PROPKA framework, ligand parameterization via PEOE_PB charge methodology, expanded set of force fields and easily incorporated user-defined parameters via XML input files, and improvement of atom addition and optimization code. Expand
Formation of hard power laws in the energetic particle spectra resulting from relativistic magnetic reconnection.
Using fully kinetic simulations, we demonstrate that magnetic reconnection in relativistic plasmas is highly efficient at accelerating particles through a first-order Fermi process resulting from the… Expand
Ringed Structures of the HD 163296 Protoplanetary Disk Revealed by ALMA.
From the measurements of the dust and gas densities, it is deduce that the gas-to-dust ratio varies across the disk and, in particular, it increases by at least a factor 5 within the inner dust gap compared to adjacent regions of the disk. Expand
Scaling of magnetic reconnection in relativistic collisionless pair plasmas.
- Yi-Hsin Liu, F. Guo, W. Daughton, Hui Li, M. Hesse
- Physics, Medicine
- Physical review letters
- 13 October 2014
The results demonstrate that the aspect ratio of the diffusion region, modified by the compression factor of proper density, remains ∼0.1 in both the nonrelativistic and relativistic limits. Expand
Solar wind magnetic fluctuation spectra: Dispersion versus damping
Solar wind magnetic fluctuation power spectra at frequencies ƒ < 1 Hz are commonly observed to have the approximate power law dependence ƒ−5/3. These observations may be described by Kolmogorov… Expand
Geometric Decay in a QBD Process with Countable Background States with Applications to a Join-the-Shortest-Queue Model
- Hui Li
A geometric tail decay of the stationary distribution has been recently studied for the GI/G/1 type Markov chain with both countable level and background states. This method is essentially the matrix… Expand
TURBULENCE AND DYNAMO IN GALAXY CLUSTER MEDIUM: IMPLICATIONS ON THE ORIGIN OF CLUSTER MAGNETIC FIELDS
We present self-consistent cosmological magnetohydrodynamic (MHD) simulations that simultaneously follow the formation of a galaxy cluster and the magnetic field ejection by an active galactic… Expand
On the dissipation of magnetic fluctuations in the solar wind
Magnetic fluctuations in the solar wind show an f−5/3 power-law spectrum below the Doppler-shifted proton cyclotron frequency but steepen to f−s with s ≥ 3 for higher frequencies. The origin of this… Expand
New constraints on turbulence and embedded planet mass in the HD 163296 disk from planet-disk hydrodynamic simulations
Recent Atacama Large Millimeter and Submillimeter Array (ALMA) observations of the protoplanetary disk around the Herbig Ae star HD 163296 revealed three depleted dust gaps at 60, 100 and 160 au in… Expand
Solar wind impacts on growth phase duration and substorm intensity: A statistical approach
A statistical survey of 379 interplanetary magnetic field (IMF) southward turning events during the time period from 1995 to 2011 is performed to study the impact of solar wind conditions on the… Expand