Information based clustering

In an age of increasingly large data sets, investigators in many different disciplines have turned to clustering as a tool for data analysis and exploration. Existing clustering methods, however, typically depend on several nontrivial assumptions about the structure of data. Here we reformulate the clustering problem from an information theoretic perspective which avoids many of these assumptions. In particular, our formulation obviates the need for defining a cluster "prototype", does not require an a priori similarity metric, is invariant to changes in the representation of the data, and naturally captures non-linear relations. We apply this approach to different domains and find that it consistently produces clusters that are more coherent than those extracted by existing algorithms. Finally, our approach provides a way of clustering based on collective notions of similarity rather than the traditional pairwise measures.Comment: To appear in Proceedings of the National Academy of Sciences USA, 11 pages, 9 figure

Characterizing upward lightning with and without a terrestrial gamma-ray flash

We compare two observations of gamma-rays before, during, and after lightning flashes initiated by upward leaders from a tower during low-altitude winter thunderstorms on the western coast of Honshu, Japan. While the two leaders appear similar, one produced a terrestrial gamma-ray flash (TGF) so bright that it paralyzed the gamma-ray detectors while it was occurring, and could be observed only via the weaker flux of neutrons created in its wake, while the other produced no detectable TGF gamma-rays at all. The ratio between the indirectly derived gamma-ray fluence for the TGF and the 95% confidence gamma-ray upper limit for the gamma-ray quiet flash is a factor of $1\times10^7$. With the only two observations of this type providing such dramatically different results -- a TGF probably as bright as those seen from space and a powerful upper limit -- we recognize that weak, sub-luminous TGFs in this situation are probably not common, and we quantify this conclusion. While the gamma-ray quiet flash appeared to have a faster leader and more powerful initial continuous current pulse than the flash that produced a TGF, the TGF-producing flash occurred during a weak gamma-ray "glow", while the gamma-ray quiet flash did not, implying a higher electric field aloft when the TGF was produced. We suggest that the field in the high-field region approached by a leader may be more important for whether a TGF is produced than the characteristics of the leader itself.Comment: 21 pages, 6 figures, accepted for publication by the Journal of Geophysical Research - Atmosphere

Photodissociation of Conformer-Selected Ubiquitin Ions Reveals Site-Specific Cis/Trans Isomerization of Proline Peptide Bonds

Ultraviolet photodissociation (UVPD) of gas-phase proteins has attracted increased attention in recent years. This growing interest is largely based on the fact that, in contrast to slow heating techniques such as collision induced dissociation (CID), the cleavage propensity after absorption of UV light is distributed over the entire protein sequence, which can lead to a very high sequence coverage as required in typical top-down proteomics applications. However, in the gas phase, proteins can adopt a multitude of distinct and sometimes coexisting conformations, and it is not clear how this three-dimensional structure affects the UVPD fragmentation behavior. Using ion mobility–UVPD–mass spectrometry in conjunction with molecular dynamics simulations, we provide the first experimental evidence that UVPD is sensitive to the higher order structure of gas-phase proteins. Distinct UVPD spectra were obtained for different extended conformations of 11+ ubiquitin ions. Assignment of the fragments showed that the majority of differences arise from cis/trans isomerization of one particular proline peptide bond. Seen from a broader perspective, these data highlight the potential of UVPD to be used for the structural analysis of proteins in the gas phas

The Lemaitre-Schwarzschild Problem Revisited

The Lemaitre and Schwarzschild analytical solutions for a relativistic spherical body of constant density are linked together through the use of the Weyl quadratic invariant. The critical radius for gravitational collapse of an incompressible fluid is shown to vary continuously from 9/8 of the Schwarzschild radius to the Schwarzschild radius itself while the internal pressures become locally anisotropic.Comment: Final version as accepted by GR&G (to appear in vol. 34, september 2002

Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS

GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest supercomputers in the world. Here, we describe some of the ways we have been able to realize this through the use of parallelization on all levels, combined with a constant focus on absolute performance. Release 4.6 of GROMACS uses SIMD acceleration on a wide range of architectures, GPU offloading acceleration, and both OpenMP and MPI parallelism within and between nodes, respectively. The recent work on acceleration made it necessary to revisit the fundamental algorithms of molecular simulation, including the concept of neighborsearching, and we discuss the present and future challenges we see for exascale simulation - in particular a very fine-grained task parallelism. We also discuss the software management, code peer review and continuous integration testing required for a project of this complexity.Comment: EASC 2014 conference proceedin

Two tricritical lines from a Ginzburg-Landau expansion: application to the LOFF phase

We study the behavior of the two plane waves configuration in the LOFF phase close to T=0. The study is performed by using a Landau-Ginzburg expansion up to the eighth order in the gap. The general study of the corresponding grand potential shows, under the assumption that the eighth term in the expansion is strictly positive, the existence of two tricritical lines. This allows to understand the existence of a second tricritical point for two antipodal plane waves in the LOFF phase and justifies why the transition becomes second order at zero temperature. The general analysis done in this paper can be applied to other cases.Comment: LaTex file, 15 pages, 6 figure

Near Infrared Spectra of Type Ia Supernovae

We report near infrared (NIR) spectroscopic observations of twelve ``Branch-normal'' Type Ia supernovae (SNe Ia) which cover the wavelength region from 0.8-2.5 microns. Our sample more than doubles the number of SNe Ia with published NIR spectra within three weeks of maximum light. The epochs of observation range from thirteen days before maximum light to eighteen days after maximum light. A detailed model for a Type Ia supernovae is used to identify spectral features. The Doppler shifts of lines are measured to obtain the velocity and, thus, the radial distribution of elements. The NIR is an extremely useful tool to probe the chemical structure in the layers of SNe Ia ejecta. This wavelength region is optimal for examining certain products of the SNe Ia explosion that may be blended or obscured in other spectral regions. We identify spectral features from MgII, CaII, SiII, FeII, CoII, NiII and possibly MnII. We find no indications for hydrogen, helium or carbon in the spectra. The spectral features reveal important clues about the physical characteristics of SNe Ia. We use the features to derive upper limits for the amount of unburned matter, to identify the transition regions from explosive carbon to oxygen burning and from partial to complete silicon burning, and to estimate the level of mixing during and after the explosion.Comment: 44 pages, 7 figures, 3 tables, accepted by Ap

Exploring alternative routes to realising the benefits of simulation in healthcare

Discrete event simulation should offer numerous benefits in designing healthcare systems but the reality is often problematic. Healthcare modelling faces particular challenges: genuine, fundamental variations in practice and an opposition to any suggestion of standardisation from some professional groups. This paper compares the experiences of developing a new simulation in an Accident and Emergency (A&E) Department, a subsequent adaptation for modelling an outpatient clinic and applications of a generic A&E simulation. These studies provide examples of three distinct approaches to realising the potential benefits of simulation: the bespoke, the reuse and the generic route. Reuse has many advantages: it is relatively efficient in exploiting previous modelling experience, delivering timely results while providing scope for adaptations to local practice. Explicitly demonstrating this willingness to adapt to local conditions and engaging with stakeholders is particularly important in healthcare simulation

Simulations of electromagnetic effects in high frequency capacitively coupled discharges using the Darwin approximation

The Darwin approximation is investigated for its possible use in simulation of electromagnetic effects in large size, high frequency capacitively coupled discharges. The approximation is utilized within the framework of two different fluid models which are applied to typical cases showing pronounced standing wave and skin effects. With the first model it is demonstrated that Darwin approximation is valid for treatment of such effects in the range of parameters under consideration. The second approach, a reduced nonlinear Darwin approximation-based model, shows that the electromagnetic phenomena persist in a more realistic setting. The Darwin approximation offers a simple and efficient way of carrying out electromagnetic simulations as it removes the Courant condition plaguing explicit electromagnetic algorithms and can be implemented as a straightforward modification of electrostatic algorithms. The algorithm described here avoids iterative schemes needed for the divergence cleaning and represents a fast and efficient solver, which can be used in fluid and kinetic models for self-consistent description of technical plasmas exhibiting certain electromagnetic activity