Diverse corrugation pattern in radially shrinking carbon nanotubes

Stable cross-sections of multi-walled carbon nanotubes subjected to electron-beam irradiation are investigated in the realm of the continuum mechanics approximation. The self-healing nature of sp$^2$ graphitic sheets implies that selective irradiation of the outermost walls causes their radial shrinkage with the remaining inner walls undamaged. The shrinking walls exert high pressure on the interior part of nanotubes, yielding a wide variety of radial corrugation patterns ({\it i.e.,} circumferentially wrinkling structures) in the cross section. All corrugation patterns can be classified into two deformation phases for which the corrugation amplitudes of the innermost wall differ significantly.Comment: 8 pages, 4 figure

On the nonequilibrium entropy of large and small systems

Thermodynamics makes definite predictions about the thermal behavior of macroscopic systems in and out of equilibrium. Statistical mechanics aims to derive this behavior from the dynamics and statistics of the atoms and molecules making up these systems. A key element in this derivation is the large number of microscopic degrees of freedom of macroscopic systems. Therefore, the extension of thermodynamic concepts, such as entropy, to small (nano) systems raises many questions. Here we shall reexamine various definitions of entropy for nonequilibrium systems, large and small. These include thermodynamic (hydrodynamic), Boltzmann, and Gibbs-Shannon entropies. We shall argue that, despite its common use, the last is not an appropriate physical entropy for such systems, either isolated or in contact with thermal reservoirs: physical entropies should depend on the microstate of the system, not on a subjective probability distribution. To square this point of view with experimental results of Bechhoefer we shall argue that the Gibbs-Shannon entropy of a nano particle in a thermal fluid should be interpreted as the Boltzmann entropy of a dilute gas of Brownian particles in the fluid

Adaptive cluster expansion for the inverse Ising problem: convergence, algorithm and tests

We present a procedure to solve the inverse Ising problem, that is to find the interactions between a set of binary variables from the measure of their equilibrium correlations. The method consists in constructing and selecting specific clusters of variables, based on their contributions to the cross-entropy of the Ising model. Small contributions are discarded to avoid overfitting and to make the computation tractable. The properties of the cluster expansion and its performances on synthetic data are studied. To make the implementation easier we give the pseudo-code of the algorithm.Comment: Paper submitted to Journal of Statistical Physic

The arrow of time: from universe time-asymmetry to local irreversible processes

In several previous papers we have argued for a global and non-entropic approach to the problem of the arrow of time, according to which the ''arrow'' is only a metaphorical way of expressing the geometrical time-asymmetry of the universe. We have also shown that, under definite conditions, this global time-asymmetry can be transferred to local contexts as an energy flow that points to the same temporal direction all over the spacetime. The aim of this paper is to complete the global and non-entropic program by showing that our approach is able to account for irreversible local phenomena, which have been traditionally considered as the physical origin of the arrow of time.Comment: 48 pages, 8 figures, revtex4. Accepted for publication in Foundations of Physic

DNA-PK-Dependent RPA2 Hyperphosphorylation Facilitates DNA Repair and Suppresses Sister Chromatid Exchange

Hyperphosphorylation of RPA2 at serine 4 and serine 8 (S4, S8) has been used as a marker for activation of the DNA damage response. What types of DNA lesions cause RPA2 hyperphosphorylation, which kinase(s) are responsible for them, and what is the biological outcome of these phosphorylations, however, have not been fully investigated. In this study we demonstrate that RPA2 hyperphosphorylation occurs primarily in response to genotoxic stresses that cause high levels of DNA double-strand breaks (DSBs) and that the DNA-dependent protein kinase complex (DNA-PK) is responsible for the modifications in vivo. Alteration of S4, S8 of RPA2 to alanines, which prevent phosphorylations at these sites, caused increased mitotic entry with concomitant increases in RAD51 foci and homologous recombination. Taken together, our results demonstrate that RPA2 hyperphosphorylation by DNA-PK in response to DSBs blocks unscheduled homologous recombination and delays mitotic entry. This pathway thus permits cells to repair DNA damage properly and increase cell viability

The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species.

In biology and biomedicine, relating phenotypic outcomes with genetic variation and environmental factors remains a challenge: patient phenotypes may not match known diseases, candidate variants may be in genes that haven’t been characterized, research organisms may not recapitulate human or veterinary diseases, environmental factors affecting disease outcomes are unknown or undocumented, and many resources must be queried to find potentially significant phenotypic associations. The Monarch Initiative (https://monarchinitiative.org) integrates information on genes, variants, genotypes, phenotypes and diseases in a variety of species, and allows powerful ontology-based search. We develop many widely adopted ontologies that together enable sophisticated computational analysis, mechanistic discovery and diagnostics of Mendelian diseases. Our algorithms and tools are widely used to identify animal models of human disease through phenotypic similarity, for differential diagnostics and to facilitate translational research. Launched in 2015, Monarch has grown with regards to data (new organisms, more sources, better modeling); new API and standards; ontologies (new Mondo unified disease ontology, improvements to ontologies such as HPO and uPheno); user interface (a redesigned website); and community development. Monarch data, algorithms and tools are being used and extended by resources such as GA4GH and NCATS Translator, among others, to aid mechanistic discovery and diagnostics

Nearly Perfect Fluidity: From Cold Atomic Gases to Hot Quark Gluon Plasmas

Shear viscosity is a measure of the amount of dissipation in a simple fluid. In kinetic theory shear viscosity is related to the rate of momentum transport by quasi-particles, and the uncertainty relation suggests that the ratio of shear viscosity eta to entropy density s in units of hbar/k_B is bounded by a constant. Here, hbar is Planck's constant and k_B is Boltzmann's constant. A specific bound has been proposed on the basis of string theory where, for a large class of theories, one can show that eta/s is greater or equal to hbar/(4 pi k_B). We will refer to a fluid that saturates the string theory bound as a perfect fluid. In this review we summarize theoretical and experimental information on the properties of the three main classes of quantum fluids that are known to have values of eta/s that are smaller than hbar/k_B. These fluids are strongly coupled Bose fluids, in particular liquid helium, strongly correlated ultracold Fermi gases, and the quark gluon plasma. We discuss the main theoretical approaches to transport properties of these fluids: kinetic theory, numerical simulations based on linear response theory, and holographic dualities. We also summarize the experimental situation, in particular with regard to the observation of hydrodynamic behavior in ultracold Fermi gases and the quark gluon plasma.Comment: 76 pages, 11 figures, review article, extensive revision

Does Foreign Direct Investment Stimulate New Firm Creation? In Search of Spillovers through Industrial and Geographical Linkages

This paper examines the spillover effects of inward foreign direct investment (FDI) on the entrepreneurial activities of new firm creation through both industrial and geographical linkages. Using a dataset of 44,434 newly created small firms in 234 regions of South Korea in 2000–2004, this study finds that while the spillover impacts of FDI in the low-tech industry are positive and significant across almost all four possible combinations of the intra-/inter-regional and intra-/inter-sectoral channels, the impacts in the high-tech industry are largely intra-sectoral within the host region and across neighboring regions. Moreover, all statistically significant spillover effects follow an inverted ‘U’-shaped curvilinear trend

Gender and Management: new directions in research and continuing patterns in practice

This is the author’s version of the following article. The definitive version is available at www.interscience.wiley.com:Adelina Broadbridge and Jeff Hearn, Gender and management: New directions in research and continuing patterns in practice, 2008, British Journal of Management, (19), s1, 38-49. http://dx.doi.org/10.1111/j.1467-8551.2008.00570.xCopyright: British Academy of Management, Blackwell Publishing Ltdhttp://www.blackwellpublishing.com