Performance optimisation of inertial confinement fusion codes using mini-applications

Despite the recent successes of nuclear energy researchers, the scientific community still remains some distance from being able to create controlled, self-sustaining fusion reactions. Inertial Confinement Fusion (ICF) techniques represent one possible option to surpass this barrier, with scientific simulation playing a leading role in guiding and supporting their development. The simulation of such techniques allows for safe and efficient investigation of laser design and pulse shaping, as well as providing insight into the reaction as a whole. The research presented here focuses on the simulation code EPOCH, a fully relativistic particle-in-cell plasma physics code concerned with faithfully recreating laser-plasma interactions at scale. A significant challenge in developing large codes like EPOCH is maintaining effective scientific delivery on successive generations of high-performance computing architecture. To support this process, we adopt the use of mini-applications -- small code proxies that encapsulate important computational properties of their larger parent counterparts. Through the development of a mini-application for EPOCH (called miniEPOCH), we investigate a variety of the performance features exhibited in EPOCH, expose opportunities for optimisation and increased scientific capability, and offer our conclusions to guide future changes to similar ICF codes

Mini-app driven optimisation of inertial confinement fusion codes

In September 2013, the large laser-based inertial confinement fusion device housed in the National Ignition Facility at Lawrence Livermore National Laboratory, was widely acclaimed to have achieved a milestone in controlled fusion – successfully initiating a reaction that resulted in the release of more energy than the fuel absorbed. Despite this success, we remain some distance from being able to create controlled, self-sustaining fusion reactions. Inertial Confinement Fusion (ICF) represents one leading design for the generation of energy by nuclear fusion. Since the 1950s, ICF has been supported by computing simulations, providing the mathematical foundations for pulse shaping, lasers, and material shells needed to ensure effective and efficient implosion. The research presented here focuses on one such simulation code, EPOCH, a fully relativistic particle-in-cell plasma physics code, developed by a leading network of over 30 UK researchers. A significant challenge in developing large codes like EPOCH is maintaining effective scientific delivery on successive generations of high-performance computing architecture. To support this process, we adopt the use of mini-applications – small code proxies that encapsulate important computational properties of their larger parent counterparts. Through the development of a miniapp for EPOCH (called miniEPOCH), we investigate known timestep scaling issues within EPOCH and explore possible optimisations: (i) Employing loop fission to increase levels of vectorisation; (ii) Enforcing particle ordering to allow the exploitation of domain specific knowledge and, (iii) Changing underlying data storage to improve memory locality. When applied to EPOCH, these improvements represent a 2.02× speed-up in the core algorithm and a 1.55× speed-up to the overall application runtime, when executed on EPCC’s Cray XC30 ARCHER platform

A Nanoflare Distribution Generated by Repeated Relaxations Triggered by Kink Instability

Context: It is thought likely that vast numbers of nanoflares are responsible for the corona having a temperature of millions of degrees. Current observational technologies lack the resolving power to confirm the nanoflare hypothesis. An alternative approach is to construct a magnetohydrodynamic coronal loop model that has the ability to predict nanoflare energy distributions. Aims: This paper presents the initial results generated by such a model. It predicts heating events with a range of sizes, depending on where the instability threshold for linear kink modes is encountered. The aims are to calculate the distribution of event energies and to investigate whether kink instability can be predicted from a single parameter. Methods: The loop is represented as a straight line-tied cylinder. The twisting caused by random photospheric motions is captured by two parameters, representing the ratio of current density to field strength for specific regions of the loop. Dissipation of the loop's magnetic energy begins during the nonlinear stage of the instability, which develops as a consequence of current sheet reconnection. After flaring, the loop evolves to the state of lowest energy where, in accordance with relaxation theory, the ratio of current to field is constant throughout the loop and helicity is conserved. Results: The results suggest that instability cannot be predicted by any simple twist-derived property reaching a critical value. The model is applied such that the loop undergoes repeated episodes of instability followed by energy-releasing relaxation. Hence, an energy distribution of the nanoflares produced is collated. Conclusions: The final energy distribution features two nanoflare populations that follow different power laws. The power law index for the higher energy population is more than sufficient for coronal heating.Comment: 13 pages, 18 figure

The Flare-energy Distributions Generated by Kink-unstable Ensembles of Zero-net-current Coronal Loops

It has been proposed that the million degree temperature of the corona is due to the combined effect of barely-detectable energy releases, so called nanoflares, that occur throughout the solar atmosphere. Alas, the nanoflare density and brightness implied by this hypothesis means that conclusive verification is beyond present observational abilities. Nevertheless, we investigate the plausibility of the nanoflare hypothesis by constructing a magnetohydrodynamic (MHD) model that can derive the energy of a nanoflare from the nature of an ideal kink instability. The set of energy-releasing instabilities is captured by an instability threshold for linear kink modes. Each point on the threshold is associated with a unique energy release and so we can predict a distribution of nanoflare energies. When the linear instability threshold is crossed, the instability enters a nonlinear phase as it is driven by current sheet reconnection. As the ensuing flare erupts and declines, the field transitions to a lower energy state, which is modelled by relaxation theory, i.e., helicity is conserved and the ratio of current to field becomes invariant within the loop. We apply the model so that all the loops within an ensemble achieve instability followed by energy-releasing relaxation. The result is a nanoflare energy distribution. Furthermore, we produce different distributions by varying the loop aspect ratio, the nature of the path to instability taken by each loop and also the level of radial expansion that may accompany loop relaxation. The heating rate obtained is just sufficient for coronal heating. In addition, we also show that kink instability cannot be associated with a critical magnetic twist value for every point along the instability threshold

MPL mutations in myeloproliferative disorders: analysis of the PT-1 cohort

Activating mutations of MPL exon 10 have been described in a minority of patients with idiopathic myelofibrosis (IMF) or essential thrombocythemia (ET), but their prevalence and clinical significance are unclear. Here we demonstrate that MPL mutations outside exon 10 are uncommon in platelet cDNA and identify 4 different exon 10 mutations in granulocyte DNA from a retrospective cohort of 200 patients with ET or IMF. Allelespecific polymerase chain reaction was then used to genotype 776 samples from patients with ET entered into the PT-1 studies. MPL mutations were identified in 8.5% of JAK2 V617F ؊ patients and a single V617F ؉ patient. Patients carrying the W515K allele had a significantly higher allele burden than did those with the W515L allele, suggesting a functional difference between the 2 variants. Compared with V617F ؉ ET patients, those with MPL mutations displayed lower hemoglobin and higher platelet levels at diagnosis, higher serum erythropoietin levels, endogenous megakaryocytic but not erythroid colony growth, and reduced bone marrow erythroid and overall cellularity. Compared with V617F ؊ patients, those with MPL mutations were older with reduced bone marrow cellularity but could not be identified as a discrete clinicopathologic subgroup. MPL mutations lacked prognostic significance with respect to thrombosis, major hemorrhage, myelofibrotic transformation or survival. (Blood

Riboflavin Ameliorates Cisplatin Induced Toxicities under Photoillumination

BACKGROUND: Cisplatin is an effective anticancer drug that elicits many side effects mainly due to induction of oxidative and nitrosative stresses during prolonged chemotherapy. The severity of these side effects consequently restricts its clinical use under long term treatment. Riboflavin is an essential vitamin used in various metabolic redox reactions in the form of flavin adenine dinucleotide and flavin mononucleotide. Besides, it has excellent photosensitizing property that can be used to ameliorate these toxicities in mice under photodynamic therapy. METHODS AND FINDINGS: Riboflavin, cisplatin and their combinations were given to the separate groups of mice under photoilluminated condition under specific treatment regime. Their kidney and liver were excised for comet assay and histopathological studies. Furthermore, Fourier Transform Infrared Spectroscopy of riboflavin-cisplatin combination in vitro was also conducted to investigate any possible interaction between the two compounds. Their comet assay and histopathological examination revealed that riboflavin in combination with cisplatin was able to protect the tissues from cisplatin induced toxicities and damages. Moreover, Fourier Transform Infrared Spectroscopy analysis of the combination indicated a strong molecular interaction among their constituent groups that may be assigned for the protective effect of the combination in the treated animals. CONCLUSION: Inclusion of riboflavin diminishes cisplatin induced toxicities which may possibly make the cisplatin-riboflavin combination, an effective treatment strategy under chemoradiotherapy in pronouncing its antineoplastic activity and sensitivity towards the cancer cells as compared to cisplatin alone

Barriers to Non-Viral Vector-Mediated Gene Delivery in the Nervous System

Efficient methods for cell line transfection are well described, but, for primary neurons, a high-yield method different from those relying on viral vectors is lacking. Viral transfection has several drawbacks, such as the complexity of vector preparation, safety concerns, and the generation of immune and inflammatory responses when used in vivo. However, one of the main problems for the use of non-viral gene vectors for neuronal transfection is their low efficiency when compared with viral vectors. Transgene expression, or siRNA delivery mediated by non-viral vectors, is the result of multiple processes related to cellular membrane crossing, intracellular traffic, and/or nuclear delivery of the genetic material cargo. This review will deal with the barriers that different nanoparticles (cationic lipids, polyethyleneimine, dendrimers and carbon nanotubes) must overcome to efficiently deliver their cargo to central nervous system cells, including internalization into the neurons, interaction with intracellular organelles such as lysosomes, and transport across the nuclear membrane of the neuron in the case of DNA transfection. Furthermore, when used in vivo, the nanoparticles should efficiently cross the blood-brain barrier to reach the target cells in the brain

Probing the Behaviors of Gold Nanorods in Metastatic Breast Cancer Cells Based on UV-vis-NIR Absorption Spectroscopy

In this work, behaviors of positively-charged AuNRs in a highly metastatic tumor cell line MDA-MB-231 are examined based on UV-vis-NIR absorption spectroscopy in combination with inductively coupled plasma mass spectrometry (ICP-MS), transmission electron microscopy (TEM) and dark-field microscopic observation. It is found that characteristic surface plasmon resonance (SPR) peaks of AuNRs can be detected using spectroscopic method within living cells that have taken up AuNRs. The peak area of transverse SPR band is shown to be proportionally related to the amount of AuNRs in the cells determined with ICP-MS, which suggests a facile and real time quantification method for AuNRs in living cells. The shape of longitudinal SPR band in UV-vis-NIR spectrum reflects the aggregation state of AuNRs in the cells during the incubation period, which is proved by TEM and microscopic observations. Experimental results reveal that AuNRs are internalized by the cells rapidly; the accumulation, distribution and aggregation of AuNRs in the cells compartments are time and dose dependent. The established spectroscopic analysis method can not only monitor the behaviors of AuNRs in living cells but may also be helpful in choosing the optimum laser stimulation wavelength for anti-tumor thermotherapy