Shocks near Jamming

Non-linear sound is an extreme phenomenon typically observed in solids after violent explosions. But granular media are different. Right when they jam, these fragile and disordered solids exhibit a vanishing rigidity and sound speed, so that even tiny mechanical perturbations form supersonic shocks. Here, we perform simulations in which two-dimensional jammed granular packings are dynamically compressed, and demonstrate that the elementary excitations are strongly non-linear shocks, rather than ordinary phonons. We capture the full dependence of the shock speed on pressure and impact intensity by a surprisingly simple analytical model.Comment: Revised version. Accepted for publication in Phys. Rev. Let

On Validating an Astrophysical Simulation Code

We present a case study of validating an astrophysical simulation code. Our study focuses on validating FLASH, a parallel, adaptive-mesh hydrodynamics code for studying the compressible, reactive flows found in many astrophysical environments. We describe the astrophysics problems of interest and the challenges associated with simulating these problems. We describe methodology and discuss solutions to difficulties encountered in verification and validation. We describe verification tests regularly administered to the code, present the results of new verification tests, and outline a method for testing general equations of state. We present the results of two validation tests in which we compared simulations to experimental data. The first is of a laser-driven shock propagating through a multi-layer target, a configuration subject to both Rayleigh-Taylor and Richtmyer-Meshkov instabilities. The second test is a classic Rayleigh-Taylor instability, where a heavy fluid is supported against the force of gravity by a light fluid. Our simulations of the multi-layer target experiments showed good agreement with the experimental results, but our simulations of the Rayleigh-Taylor instability did not agree well with the experimental results. We discuss our findings and present results of additional simulations undertaken to further investigate the Rayleigh-Taylor instability.Comment: 76 pages, 26 figures (3 color), Accepted for publication in the ApJ

The Size Ellect on the Infrared Spectra of Condensed Media Under Conditions of ID, 2D and 3D Dielectric Confinement

A general expression for the dielectric loss spectrum of an absorbing composite medium was obtained from a Maxwell-Garnett general equation. This expression was simplified for the cases of one, two and three dimensional dielectric confinement in both ordered and disordered thin layers, rods (wires) and spheres of absorbing medium which are considered as mesoparticles or mesoscopic molecules. This theoretical approach was verified experimentally using high purity organic liquids with strong absorption bands in the infrared range. Three organic liquids, namely benzene, chloroform and carbon disulphide, were measured in various dielectric confinement configurations using Fourier Transform Infrared (FTIR) spectroscopy with a Grazing Angle attachment GATRTM. A significant shift of the resonant absorption band of liquid mesoparticles was observed for various dielectric confinement geometries which is in good agreement with theoretical predictions. Possible applications of this work include investigations of industrial smoke, toxic aerosols and liquid droplets

Методы детекции специфических для опухолевой ткани однонуклеотидных соматических мутаций в препаратах цДНК из плазмы крови

Introduction. Liquid biopsy is considered as a minimally invasive method of molecular genetic analysis that can be used for early diagnosis, prognosis of disease development, monitoring of residual disease or treatment outcomes, and selection of optimal drug therapy schemes for a patient. Along with the development of tests based on the study of panels of oncologically significant genes or their regions, for various forms of genetically heterogeneous tumors a promising approach could be the use as an object of liquid biopsy of an individual spectrum of somatic mutations of a particular patient that can be detected on the basis of high-throughput sequencing of tumor tissue.Aim. To determine the applicability of different methods for detecting single-nucleotide somatic mutations detected in tumor tissue of a particular patient in cDNA preparations from blood plasma obtained before surgical removal of the tumor and to evaluate the possibility of quantifying the proportion of the alternative variant in the total pool of cDNA. Materials and methods. We used normal and tumor tissue, as well as blood plasma samples from patients with hepatocellular carcinoma, and various methods for detecting single-nucleotide somatic mutations: real-time polymerase chain reaction (PCR) with intercalating dye or with TaqMan probes, droplet digital PCR and high-throughput sequencing of target amplicons.Results. Using the example of a somatic mutation in the TLN1 gene detected in tumor tissue of a patient with hepatocellular carcinoma, methods were developed and tested, each of which allows specific detection of the mutant variant in small amounts (2 ng) of cDNA from the blood plasma of the same patient. The use of droplet PCR and target amplicon sequencing methods allowed us to quantify the proportion of the mutant variant in the total cDNA pool, which was 19.7 and 23.5 %, respectively.Conclusion. Among the methods investigated, droplet digital PCR and targeted amplicon sequencing allow not only reliable detection of mutant variants in small amounts of cDNA, but also adequate quantification, which is particularly important for the development of ways to monitor tumor growth during treatment. The close values of the proportion of mutant variants in cDNA detected by these methods indicate the accuracy of quantitative analysis and the possibility of their use for cross-validation of the results obtained.Введение. Жидкостная биопсия рассматривается как малоинвазивный способ проведения молекулярно-генетического анализа, который может быть использован для ранней диагностики, прогноза течения заболевания, мониторинга остаточной болезни или результатов лечения, а также выбора оптимальных для пациента схем лекарственной терапии. Наряду с разработкой тестов, основанных на исследовании панелей онкологически значимых генов или их участков, для различных форм генетически гетерогенных опухолей перспективным подходом может стать использование в качестве объекта жидкостной биопсии индивидуального спектра соматических мутаций конкретного больного, которые могут быть выявлены с помощью высокопроизводительного секвенирования опухолевой ткани.Цель исследования - определить возможность использования различных методов детекции однонуклеотидных соматических мутаций, выявленных в опухолевой ткани конкретного пациента, в препаратах циркулирующей ДНК (цДНК) из плазмы крови, полученных до хирургического удаления опухоли, и выявить возможность количественной оценки доли альтернативного варианта в общем пуле цДНК.Материалы и методы. В работе использованы препараты нормальной и опухолевой тканей, плазмы крови пациентов с гепатоцеллюлярной карциномой, а также различные методы детекции однонуклеотидных соматических мутаций: полимеразная цепная реакция (ПЦР) в реальном времени с интеркалирующим красителем или с зондами TaqMan, капельная цифровая ПЦР и высокопроизводительное секвенирование таргетных ампликонов.Результаты. На примере соматической мутации в гене TLN1, выявленной в опухолевой ткани пациента с гепатоцеллюлярной карциномой, разработаны и апробированы методы, каждый из которых позволяет специфично детектировать мутантный вариант в малых количествах (2 нг) цДНК из плазмы крови того же пациента. использование капельной ПЦР и секвенирования таргетных ампликонов позволило провести количественную оценку долей мутантного варианта в общем пуле цДНК, которые составили 19,7 и 23,5 % соответственно.Заключение. Капельная цифровая ПЦР и таргетное секвенирование ампликонов позволяют не только надежно детектировать мутантные варианты в малых количествах цДНК, но и адекватно проводить их количественную оценку, что особенно важно для разработки способов мониторинга опухолевого роста в процессе лечения. Близкие значения доли мутантного варианта в цДНК, детектированной этими методами, свидетельствуют о точности количественного анализа и возможности их использования для кросс-валидации получаемых результатов

Non-Standard Errors

In statistics, samples are drawn from a population in a data-generating process (DGP). Standard errors measure the uncertainty in estimates of population parameters. In science, evidence is generated to test hypotheses in an evidence-generating process (EGP). We claim that EGP variation across researchers adds uncertainty: Non-standard errors (NSEs). We study NSEs by letting 164 teams test the same hypotheses on the same data. NSEs turn out to be sizable, but smaller for better reproducible or higher rated research. Adding peer-review stages reduces NSEs. We further find that this type of uncertainty is underestimated by participants

Roadmap on dynamics of molecules and clusters in the gas phase

This roadmap article highlights recent advances, challenges and future prospects in studies of the dynamics of molecules and clusters in the gas phase. It comprises nineteen contributions by scientists with leading expertise in complementary experimental and theoretical techniques to probe the dynamics on timescales spanning twenty order of magnitudes, from attoseconds to minutes and beyond, and for systems ranging in complexity from the smallest (diatomic) molecules to clusters and nanoparticles. Combining some of these techniques opens up new avenues to unravel hitherto unexplored reaction pathways and mechanisms, and to establish their significance in, e.g. radiotherapy and radiation damage on the nanoscale, astrophysics, astrochemistry and atmospheric science

Non-standard errors

In statistics, samples are drawn from a population in a data-generating process (DGP). Standard errors measure the uncertainty in estimates of population parameters. In science, evidence is generated to test hypotheses in an evidence generating process (EGP). We claim that EGP variation across researchers adds uncertainty: Non-standard errors (NSEs). We study NSEs by letting 164 teams test the same hypotheses on the same data. NSEs turn out to be sizable, but smaller for better reproducible or higher rated research. Adding peer-review stages reduces NSEs. We further find that this type of uncertainty is underestimated by participants