A tail-like assembly at the portal vertex in intact herpes simplex type-1 virions

Herpes viruses are prevalent and well characterized human pathogens. Despite extensive study, much remains to be learned about the structure of the genome packaging and release machinery in the capsids of these large and complex double-stranded DNA viruses. However, such machinery is well characterized in tailed bacteriophage, which share a common evolutionary origin with herpesvirus. In tailed bacteriophage, the genome exits from the virus particle through a portal and is transferred into the host cell by a complex apparatus (i.e. the tail) located at the portal vertex. Here we use electron cryo-tomography of human herpes simplex type-1 (HSV-1) virions to reveal a previously unsuspected feature at the portal vertex, which extends across the HSV-1 tegument layer to form a connection between the capsid and the viral membrane. The location of this assembly suggests that it plays a role in genome release into the nucleus and is also important for virion architecture

Chiral fermions on the lattice and index relations

Comparing recent lattice results on chiral fermions and old continuum results for the index puzzling questions arise. To clarify this issue we start with a critical reconsideration of the results on finite lattices. We then work out various aspects of the continuum limit. After determining bounds and norm convergences we obtain the limit of the anomaly term. Collecting our results the index relation of the quantized theory gets established. We then compare in detail with the Atiyah-Singer theorem. Finally we analyze conventional continuum approaches.Comment: 34 pages; a more detaild introduction and a subsection with remarks on literature adde

An Incremental and Optimized Learning Method for the Automatic Classification of Protein Crystal Images

Protein production has experienced great advances in recent years. In particular, high throughput protein production, coupled with the use of robotics, outputs thousands of mixtures in micro-array wells. To detect the presence of protein crystal formation, images of these wells are acquired regularly using robotic cameras. Traditionally, a crystallographer would manually process each image — identifying the wells that resulted in protein crystal formation. This manual inspection process is slow and given the high rate of mixture output, it has become near impossible for crystallographers keep up. Our aim is to create an automated method of detecting which wells have crystals and which ones do not. We make use of a neural network that is trained based on manually classified ground truth data. After it is trained, the automatic classifier would give a binary output — a value of one for the detection of crystals and precipitates in images and a value of zero otherwise. In our previous papers, the core methods of using multi-scale Laplacian image representation to extract image features and the implementation of the neural network classifier were discussed. Here we present a new, optimized approach to training the neural network and results from a large-scale test. We claim that the neural network can be better trained if the training image dataset is optimized in the sense that ambiguous images are removed during the initial training processes. Incremental training is implemented so that the network can be improved as more data becomes available. From initial results with training based on a 6,000 optimized image dataset, the accuracy of the improved classifier approaches 95% in identifying a wide array of images

Orbital Ferromagnetism and Quantum Collapse in Stellar Plasmas

The possibility of quantum collapse and characteristics of nonlinear localized excitations is examined in dense stars with Landau orbital ferromagnetism in the framework of conventional quantum magnetohydrodynamics (QMHD) model including Bohm force and spin-orbit polarization effects. Employing the concepts of effective potential and Sagdeev pseudopotential, it is confirmed that the quantum collapse and Landau orbital ferromagnetism concepts are consistent with the magnetic field and mass-density range present in some white dwarf stars. Furthermore, the value of ferromagnetic-field found in this work is about the same order of magnitude as the values calculated earlier. It is revealed that the magnetosonic nonlinear propagations can behave much differently in the two distinct non-relativistic and relativistic degeneracy regimes in a ferromagnetic dense astrophysical object. Current findings should help to understand the origin of the most important mechanisms such as gravitational collapse and the high magnetic field present in many compact stars.Comment: To appear in journal Physics of Plasma

Statistical Mechanics of Two-dimensional Foams

The methods of statistical mechanics are applied to two-dimensional foams under macroscopic agitation. A new variable -- the total cell curvature -- is introduced, which plays the role of energy in conventional statistical thermodynamics. The probability distribution of the number of sides for a cell of given area is derived. This expression allows to correlate the distribution of sides ("topological disorder") to the distribution of sizes ("geometrical disorder") in a foam. The model predictions agree well with available experimental data

Role of material properties and mesostructure on dynamic deformation and shear instability in Al-W granular composites

Dynamic experiments with Al-W granular/porous composites revealed qualitatively different behavior with respect to shear localization depending on bonding between Al particles. Two-dimensional numerical modeling was used to explore the mesomechanics of the large strain dynamic deformation in Al-W granular/porous composites and explain the experimentally observed differences in shear localization between composites with various mesostructures. Specifically, the bonding between the Al particles, the porosity, the roles of the relative particle sizes of Al and W, the arrangements of the W particles, and the material properties of Al were investigated using numerical calculations. It was demonstrated in simulations that the bonding between the "soft" Al particles facilitated shear localization as seen in the experiments. Numerical calculations and experiments revealed that the mechanism of the shear localization in granular composites is mainly due to the local high strain flow of "soft" Al around the "rigid" W particles causing localized damage accumulation and subsequent growth of the meso/macro shear bands/cracks. The "rigid" W particles were the major geometrical factor determining the initiation and propagation of "kinked" shear bands in the matrix of "soft" Al particles, leaving some areas free of extensive plastic deformation as observed in experiments and numerical calculations.Comment: 10 pages, 14 figures, submitted to Journal of Applied Physic

Link-space formalism for network analysis

We introduce the link-space formalism for analyzing network models with degree-degree correlations. The formalism is based on a statistical description of the fraction of links l_{i,j} connecting nodes of degrees i and j. To demonstrate its use, we apply the framework to some pedagogical network models, namely, random-attachment, Barabasi-Albert preferential attachment and the classical Erdos and Renyi random graph. For these three models the link-space matrix can be solved analytically. We apply the formalism to a simple one-parameter growing network model whose numerical solution exemplifies the effect of degree-degree correlations for the resulting degree distribution. We also employ the formalism to derive the degree distributions of two very simple network decay models, more specifically, that of random link deletion and random node deletion. The formalism allows detailed analysis of the correlations within networks and we also employ it to derive the form of a perfectly non-assortative network for arbitrary degree distribution.Comment: This updated version has been expanded to include a number of new results. 19 pages, 11 figures. Minor Typos correcte