Biasing crystallization in fused silica: An assessment of optimal metadynamics parameters

Metadynamics (MetaD) is a useful technique to study rare events such as crystallization. It has been only recently applied to study nucleation and crystallization in glass-forming liquids such as silicates, but the optimal set of parameters to drive crystallization and obtain converged free energy surfaces is still unexplored. In this work, we systematically investigated the effects of the simulation conditions to efficiently study the thermodynamics and mechanism of crystallization in highly viscous systems. As a prototype system, we used fused silica, which easily crystallizes to β-cristobalite through MetaD simulations, owing to its simple microstructure. We investigated the influence of the height, width, and bias factor used to define the biasing Gaussian potential, as well as the effects of the temperature and system size on the results. Among these parameters, the bias factor and temperature seem to be most effective in sampling the free energy landscape of melt to crystal transition and reaching convergence more quickly. We also demonstrate that the temperature rescaling from T > Tm is a reliable approach to recover free energy surfaces below Tm, provided that the temperature gap is below 600 K and the configurational space has been properly sampled. Finally, albeit a complete crystallization is hard to achieve with large simulation boxes, these can be reliably and effectively exploited to study the first stages of nucleation

Arenavirus reverse genetics: New approaches for the investigation of arenavirus biology and development of antiviral strategies

AbstractSeveral arenaviruses, chiefly Lassa virus, cause hemorrhagic fever disease in humans and pose a significant public health problem in their endemic regions. On the other hand the prototypic arenavirus LCMV is a superb workhorse for the investigation of virus–host interactions and associated disease. The development of novel antiviral strategies to combat pathogenic arenaviruses would be facilitated by a detailed understanding of the arenavirus molecular and cell biology. To this end, the development of reverse genetic systems for several arenaviruses has provided investigators with novel and powerful approaches to dissect the functions of arenavirus proteins and their interactions with host factors required to complete each of the steps of the virus life cycle, as well as to cause disease

Disclosing crystal nucleation mechanism in lithium disilicate glass through molecular dynamics simulations and free-energy calculations

Unraveling detailed mechanism of crystal nucleation from amorphous materials is challenging for both experimental and theoretical approaches. In this study, we have examined two methods to understand the initial stage of crystal precipitation from lithium disilicate glasses using molecular dynamics simulations. One of the methods is a modified exploring method to find structurally similar crystalline clusters in the glass models, enabling us to find three different embryos, such as Li2Si2O5 (LS2), Li2SiO3 (LS) and Li3PO4 (LP), in the 33Li2O·66SiO2·1P2O5 glass (LS2P1), in which P2O5 is added as a nucleating agent. Interestingly, LS2 and LP crystals were found inside the LS2P1 glass while LS crystal appeared on the glass surface, which agrees with experimental observations. The other method is free energy calculation using a subnano-scale spherical crystal embedded in the glass model. This method, which we called Free-Energy Seeding Method (FESM), allows us to evaluate free energy change as a function of crystal radius and to identify critical size of the crystal precipitation. The free energy profiles for LS and LS2 crystal nuclei in the LS2 glass models possess maximum energy at a critical radius as expected by classical nucleation theory. Furthermore, the critical radius and the energy barrier height agree well with recent experimental investigation, proving the applicability of this method to design glass–ceramics by atomistic modeling

The GRB 071112C: A Case Study of Different Mechanisms in X-ray and Optical Temporal Evolution

We present the study on GRB 071112C X-ray and optical light curves. In these two wavelength ranges, we have found different temporal properties. The R-band light curve showed an initial rise followed by a single power-law decay, while the X-ray light curve was described by a single power-law decay plus a flare-like feature. Our analysis shows that the observed temporal evolution cannot be described by the external shock model in which the X-ray and optical emission are produced by the same emission mechanism. No significant color changes in multi-band light curves and a reasonable value of the initial Lorentz factor ({\Gamma}0 = 275 \pm 20) in a uniform ISM support the afterglow onset scenario as the correct interpretation for the early R-band rise. The result suggests the optical flux is dominated by afterglow. Our further investigations show that the X-ray flux could be created by an additional feature related to energy injection and X-ray afterglow. Different theoretical interpretations indicate the additional feature in X-ray can be explained by either late internal dissipation or local inverse-Compton scattering in the external shock.Comment: 20 pages, 3 figures, accepted for publication in Ap

Early (<<0.3 day) R-band light curve of the optical afterglow of GRB030329

We observed the optical afterglow of the bright gamma-ray burst GRB030329 on the nights of 2003 March 29, using the Kiso observatory (the University of Tokyo) 1.05 m Schmidt telescope. Data were taken from March 29 13:21:26 UT to 17:43:16 (0.072 to 0.253 days after the burst), using an $Rc$-band filter. The obtained $Rc$-band light curve has been fitted successfully by a single power law function with decay index of $0.891\pm0.004$. These results remain unchanged when incorporating two early photometric data points at 0.065 and 0.073 days, reported by Price et al.(2003) using the SSO 40 inch telescope, and further including RTT150 data (Burenin et al. 2003) covering at about 0.3 days. Over the period of 0.065-0.285 days after the burst, any deviation from the power-law decay is smaller than $\pm$0.007 mag. The temporal structure reported by Uemura et al. (2003) does not show up in our $R$-band light curve.Comment: 9 pages, 2 figures, 1 table, accepted for publication in ApJ

Design and Performance of the Wide-Field X-Ray Monitor on Board the High-Energy Transient Explorer 2

The Wide-field X-ray Monitor (WXM) is one of the scientific instruments carried on the High Energy Transient Explorer 2 (HETE-2) satellite launched on 2000 October 9. HETE-2 is an international mission consisting of a small satellite dedicated to provide broad-band observations and accurate localizations of gamma-ray bursts (GRBs). A unique feature of this mission is its capability to determine and transmit GRB coordinates in almost real-time through the burst alert network. The WXM consists of three elements: four identical Xe-filled one-dimensional position-sensitive proportional counters, two sets of one-dimensional coded apertures, and the main electronics. The WXM counters are sensitive to X-rays between 2 keV and 25 keV within a field-of-view of about 1.5 sr, with a total detector area of about 350 cm$^2$. The in-flight triggering and localization capability can produce a real-time GRB location of several to 30 arcmin accuracy, with a limiting sensitivity of $10^{-7}$ erg cm$^{-2}$. In this report, the details of the mechanical structure, electronics, on-board software, ground and in-flight calibration, and in-flight performance of the WXM are discussed.Comment: 28 pages, 24 figure

Observations of the Prompt Gamma-Ray Emission of GRB 070125

The long, bright gamma-ray burst GRB 070125 was localized by the Interplanetary Network. We present light curves of the prompt gamma-ray emission as observed by Konus-WIND, RHESSI, Suzaku-WAM, and \textit{Swift}-BAT. We detail the results of joint spectral fits with Konus and RHESSI data. The burst shows moderate hard-to-soft evolution in its multi-peaked emission over a period of about one minute. The total burst fluence as observed by Konus is $1.79 \times 10^{-4}$ erg/cm$^2$ (20 keV--10 MeV). Using the spectroscopic redshift $z=1.548$, we find that the burst is consistent with the ``Amati'' $E_{peak,i}-E_{iso}$ correlation. Assuming a jet opening angle derived from broadband modeling of the burst afterglow, GRB 070125 is a significant outlier to the ``Ghirlanda'' $E_{peak,i}-E_\gamma$ correlation. Its collimation-corrected energy release $E_\gamma = 2.5 \times 10^{52}$ ergs is the largest yet observed.Comment: 25 pages, 6 figures; accepted for publication in ApJ. Improved spectral fits and energetics estimate

Optical Classification of Gamma-Ray Bursts in the Swift Era

We propose a new method for the classification of optically dark gamma-ray bursts (GRBs), based on the X-ray and optical-to-X-ray spectral indices of GRB afterglows, and utilizing the spectral capabilities of Swift. This method depends less on model assumptions than previous methods, and can be used as a quick diagnostic tool to identify optically sub-luminous bursts. With this method we can also find GRBs that are extremely bright at optical wavelengths. We show that the previously suggested correlation between the optical darkness and the X-ray/gamma-ray brightness is merely an observational selection effect.Comment: 6 pages, 3 figures; accepted for publication in Ap