Topology by Design in Magnetic nano-Materials: Artificial Spin Ice

Artificial Spin Ices are two dimensional arrays of magnetic, interacting nano-structures whose geometry can be chosen at will, and whose elementary degrees of freedom can be characterized directly. They were introduced at first to study frustration in a controllable setting, to mimic the behavior of spin ice rare earth pyrochlores, but at more useful temperature and field ranges and with direct characterization, and to provide practical implementation to celebrated, exactly solvable models of statistical mechanics previously devised to gain an understanding of degenerate ensembles with residual entropy. With the evolution of nano--fabrication and of experimental protocols it is now possible to characterize the material in real-time, real-space, and to realize virtually any geometry, for direct control over the collective dynamics. This has recently opened a path toward the deliberate design of novel, exotic states, not found in natural materials, and often characterized by topological properties. Without any pretense of exhaustiveness, we will provide an introduction to the material, the early works, and then, by reporting on more recent results, we will proceed to describe the new direction, which includes the design of desired topological states and their implications to kinetics.Comment: 29 pages, 13 figures, 116 references, Book Chapte

Towards a matrix mechanics framework for dynamic protein network

Protein–protein interaction networks are currently visualized by software generated interaction webs based upon static experimental data. Current state is limited to static, mostly non-compartmental network and non time resolved protein interactions. A satisfactory mathematical foundation for particle interactions within a viscous liquid state (situation within the cytoplasm) does not exist nor do current computer programs enable building dynamic interaction networks for time resolved interactions. Building mathematical foundation for intracellular protein interactions can be achieved in two increments (a) trigger and capture the dynamic molecular changes for a select subset of proteins using several model systems and high throughput time resolved proteomics and, (b) use this information to build the mathematical foundation and computational algorithm for a compartmentalized and dynamic protein interaction network. Such a foundation is expected to provide benefit in at least two spheres: (a) understanding physiology enabling explanation of phenomenon such as incomplete penetrance in genetic disorders and (b) enabling several fold increase in biopharmaceutical production using impure starting materials

Properties of Graphene: A Theoretical Perspective

In this review, we provide an in-depth description of the physics of monolayer and bilayer graphene from a theorist's perspective. We discuss the physical properties of graphene in an external magnetic field, reflecting the chiral nature of the quasiparticles near the Dirac point with a Landau level at zero energy. We address the unique integer quantum Hall effects, the role of electron correlations, and the recent observation of the fractional quantum Hall effect in the monolayer graphene. The quantum Hall effect in bilayer graphene is fundamentally different from that of a monolayer, reflecting the unique band structure of this system. The theory of transport in the absence of an external magnetic field is discussed in detail, along with the role of disorder studied in various theoretical models. We highlight the differences and similarities between monolayer and bilayer graphene, and focus on thermodynamic properties such as the compressibility, the plasmon spectra, the weak localization correction, quantum Hall effect, and optical properties. Confinement of electrons in graphene is nontrivial due to Klein tunneling. We review various theoretical and experimental studies of quantum confined structures made from graphene. The band structure of graphene nanoribbons and the role of the sublattice symmetry, edge geometry and the size of the nanoribbon on the electronic and magnetic properties are very active areas of research, and a detailed review of these topics is presented. Also, the effects of substrate interactions, adsorbed atoms, lattice defects and doping on the band structure of finite-sized graphene systems are discussed. We also include a brief description of graphane -- gapped material obtained from graphene by attaching hydrogen atoms to each carbon atom in the lattice.Comment: 189 pages. submitted in Advances in Physic

Temperature Control of Fimbriation Circuit Switch in Uropathogenic Escherichia coli: Quantitative Analysis via Automated Model Abstraction

Uropathogenic Escherichia coli (UPEC) represent the predominant cause of urinary tract infections (UTIs). A key UPEC molecular virulence mechanism is type 1 fimbriae, whose expression is controlled by the orientation of an invertible chromosomal DNA element—the fim switch. Temperature has been shown to act as a major regulator of fim switching behavior and is overall an important indicator as well as functional feature of many urologic diseases, including UPEC host-pathogen interaction dynamics. Given this panoptic physiological role of temperature during UTI progression and notable empirical challenges to its direct in vivo studies, in silico modeling of corresponding biochemical and biophysical mechanisms essential to UPEC pathogenicity may significantly aid our understanding of the underlying disease processes. However, rigorous computational analysis of biological systems, such as fim switch temperature control circuit, has hereto presented a notoriously demanding problem due to both the substantial complexity of the gene regulatory networks involved as well as their often characteristically discrete and stochastic dynamics. To address these issues, we have developed an approach that enables automated multiscale abstraction of biological system descriptions based on reaction kinetics. Implemented as a computational tool, this method has allowed us to efficiently analyze the modular organization and behavior of the E. coli fimbriation switch circuit at different temperature settings, thus facilitating new insights into this mode of UPEC molecular virulence regulation. In particular, our results suggest that, with respect to its role in shutting down fimbriae expression, the primary function of FimB recombinase may be to effect a controlled down-regulation (rather than increase) of the ON-to-OFF fim switching rate via temperature-dependent suppression of competing dynamics mediated by recombinase FimE. Our computational analysis further implies that this down-regulation mechanism could be particularly significant inside the host environment, thus potentially contributing further understanding toward the development of novel therapeutic approaches to UPEC-caused UTIs

Single amino acid radiocarbon dating of Upper Paleolithic modern humans.

Archaeological bones are usually dated by radiocarbon measurement of extracted collagen. However, low collagen content, contamination from the burial environment, or museum conservation work, such as addition of glues, preservatives, and fumigants to "protect" archaeological materials, have previously led to inaccurate dates. These inaccuracies in turn frustrate the development of archaeological chronologies and, in the Paleolithic, blur the dating of such key events as the dispersal of anatomically modern humans. Here we describe a method to date hydroxyproline found in collagen (~10% of collagen carbon) as a bone-specific biomarker that removes impurities, thereby improving dating accuracy and confidence. This method is applied to two important sites in Russia and allows us to report the earliest direct ages for the presence of anatomically modern humans on the Russian Plain. These dates contribute considerably to our understanding of the emergence of the Mid-Upper Paleolithic and the complex suite of burial behaviors that begin to appear during this period

The age of the ‘Anosovka-Tel’manskaya Culture’ and the issue of a late Streletskian at Kostёnki 11, SW Russia

Triangular, concave-base ‘Streletskian points’ are documented in several assemblages from the Kostёnki complex of Upper Palaeolithic sites in south-western Russia. Some of these assemblages have been argued to evidence very early modern human occupation of Eastern Europe. However, Streletskian points are also recorded from younger contexts, notably at Kostёnki 11, where examples are attributed both to Layer V and the stratigraphically higher Layer III. The apparent relatively young age of Layer III has led some to view it as the latest manifestation of the Streletskian, although its assemblage has also been compared to the non-Streletskian Layer I of Kostёnki 8, with the two described together as the Anosovka-Tel’manskaya Culture. Radiocarbon dates of 24–23,000 bp (c. 28,500–27,000 cal bp) for a wolf burial associated with Layer III of Kostёnki 11 confirm the layer as younger than other Streletskian assemblages at Kostёnki. New radiocarbon dates for Kostёnki 8 Layer I show that the two layers are broadly contemporary, and that both are close in age to assemblages of Kostёnki’s (Late Gravettian) Kostёnki-Avdeevo Culture. In the light of these new radiocarbon dates the context of the Streletskian point from Kostёnki 11 Layer III is considered. Although firm conclusions are not possible, unresolved stratigraphic problems and the lack of technological context for this single artefact at the very least leave a question mark over its association with other material from the layer

The age of the ‘Anosovka-Tel’manskaya Culture’ and the issue of a late Streletskian at Kostёnki 11, SW Russia

Triangular, concave-base ‘Streletskian points’ are documented in several assemblages from the Kostёnki complex of Upper Palaeolithic sites in south-western Russia. Some of these assemblages have been argued to evidence very early modern human occupation of Eastern Europe. However, Streletskian points are also recorded from younger contexts, notably at Kostёnki 11, where examples are attributed both to Layer V and the stratigraphically higher Layer III. The apparent relatively young age of Layer III has led some to view it as the latest manifestation of the Streletskian, although its assemblage has also been compared to the non-Streletskian Layer I of Kostёnki 8, with the two described together as the Anosovka-Tel’manskaya Culture. Radiocarbon dates of 24–23,000 bp (c. 28,500–27,000 cal bp) for a wolf burial associated with Layer III of Kostёnki 11 confirm the layer as younger than other Streletskian assemblages at Kostёnki. New radiocarbon dates for Kostёnki 8 Layer I show that the two layers are broadly contemporary, and that both are close in age to assemblages of Kostёnki’s (Late Gravettian) Kostёnki-Avdeevo Culture. In the light of these new radiocarbon dates the context of the Streletskian point from Kostёnki 11 Layer III is considered. Although firm conclusions are not possible, unresolved stratigraphic problems and the lack of technological context for this single artefact at the very least leave a question mark over its association with other material from the layer

Wide dispersal and deposition of distal tephra during the Pleistocene 'Campanian Ignimbrite/Y5' eruption, Italy

A trachytic volcanic ash layer is widely distributed across south-western Russia, where it is found both in well-characterised archaeological contexts close to the Don River (the Paleolithic sites of Kostenki-Borschevo (51.4°N, 39.0°E), and in undisturbed geological contexts. This ash layer has all of the characteristics of a distal tephra fall deposit: it is fine grained and unimodal with a grain size of 60-170 μm, dominated by strongly elongate glass shard fragments. Chemical analysis confirms that this ash layer is a distal equivalent of the deposits of the ca 39.3 ka Campanian Ignimbrite eruption of the Phlegrean Fields, Italy, and correlates with the widely recognised Y5 ash layer in marine cores in the south-eastern Mediterranean. This work shows that ash particles can be dispersed over considerable distances (>2500 km) and areas (>1.5-3×106 km2) during large-magnitude explosive eruptions. The volume of the products associated with this event (31-50 km3 of magma erupted as fallout tephra, and a total volume of 105-210 km3 of magma, or 2.5-5×1014 kg) confirms the Campanian Ignimbrite/Y5 eruption as the most significant known volcanic eruption in Europe of the past 100 ka. This correlation places tight constraints on the absolute ages of a number of important archaeological horizons in southern Russia. © 2006 Elsevier Ltd. All rights reserved