PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models

Markov (state) models (MSMs) and related models of molecular kinetics have recently received a surge of interest as they can systematically reconcile simulation data from either a few long or many short simulations and allow us to analyze the essential metastable structures, thermodynamics, and kinetics of the molecular system under investigation. However, the estimation, validation, and analysis of such models is far from trivial and involves sophisticated and often numerically sensitive methods. In this work we present the opensource Python package PyEMMA (http://pyemma.org) that provides accurate and efficient algorithms for kinetic model construction. PyEMMA can read all common molecular dynamics data formats, helps in the selection of input features, provides easy access to dimension reduction algorithms such as principal component analysis (PCA) and time-lagged independent component analysis (TICA) and clustering algorithms such as k-means, and contains estimators for MSMs, hidden Markov models, and several other models. Systematic model validation and error calculation methods are provided. PyEMMA offers a wealth of analysis functions such that the user can conveniently compute molecular observables of interest. We have derived a systematic and accurate way to coarse-grain MSMs to few states and to illustrate the structures of the metastable states of the system. Plotting functions to produce a manuscript-ready presentation of the results are available. In this work, we demonstrate the features of the software and show new methodological concepts and results produced by PyEMMA

Observing the metal-poor solar neighbourhood: A comparison of galactic chemical evolution predictions

© 2017 The Authors. Atmospheric parameters and chemical compositions for 10 stars with metallicities in the region of -2.2 < [Fe/H] < -0.6 were precisely determined using high-resolution, high signal-tonoise, spectra. For each star, the abundances, for 14-27 elements, were derived using both local thermodynamic equilibrium (LTE) and non-LTE (NLTE) approaches. In particular, differences by assuming LTE or NLTE are about 0.10 dex; depending on [Fe/H], Teff, gravity and element lines used in the analysis. We find that the O abundance has the largest error, ranging from 0.10 and 0.2 dex. The best measured elements are Cr, Fe, and Mn; with errors between 0.03 and 0.11 dex. The stars in our sample were included in previous different observational work. We provide a consistent data analysis. The data dispersion introduced in the literature by different techniques and assumptions used by the different authors is within the observational errors, excepting for HD103095. We compare these results with stellar observations from different data sets and a number of theoretical galactic chemical evolution (GCE) simulations. We find a large scatter in the GCE results, used to study the origin of the elements. Within this scatter as found in previous GCE simulations, we cannot reproduce the evolution of the elemental ratios [Sc/Fe] , [Ti/Fe], and [V/Fe] at different metallicities. The stellar yields from core-collapse supernovae are likely primarily responsible for this discrepancy. Possible solutions and open problems are discussed

Explosive Nucleosynthesis: What we learned and what we still do not understand

This review touches on historical aspects, going back to the early days of nuclear astrophysics, initiated by B$^2$FH and Cameron, discusses (i) the required nuclear input from reaction rates and decay properties up to the nuclear equation of state, continues (ii) with the tools to perform nucleosynthesis calculations and (iii) early parametrized nucleosynthesis studies, before (iv) reliable stellar models became available for the late stages of stellar evolution. It passes then through (v) explosive environments from core-collapse supernovae to explosive events in binary systems (including type Ia supernovae and compact binary mergers), and finally (vi) discusses the role of all these nucleosynthesis production sites in the evolution of galaxies. The focus is put on the comparison of early ideas and present, very recent, understanding.Comment: 11 pages, to appear in Springer Proceedings in Physics (Proc. of Intl. Conf. "Nuclei in the Cosmos XV", LNGS Assergi, Italy, June 2018

How a Diverse Research Ecosystem Has Generated New Rehabilitation Technologies: Review of NIDILRR’s Rehabilitation Engineering Research Centers

Over 50 million United States citizens (1 in 6 people in the US) have a developmental, acquired, or degenerative disability. The average US citizen can expect to live 20% of his or her life with a disability. Rehabilitation technologies play a major role in improving the quality of life for people with a disability, yet widespread and highly challenging needs remain. Within the US, a major effort aimed at the creation and evaluation of rehabilitation technology has been the Rehabilitation Engineering Research Centers (RERCs) sponsored by the National Institute on Disability, Independent Living, and Rehabilitation Research. As envisioned at their conception by a panel of the National Academy of Science in 1970, these centers were intended to take a “total approach to rehabilitation”, combining medicine, engineering, and related science, to improve the quality of life of individuals with a disability. Here, we review the scope, achievements, and ongoing projects of an unbiased sample of 19 currently active or recently terminated RERCs. Specifically, for each center, we briefly explain the needs it targets, summarize key historical advances, identify emerging innovations, and consider future directions. Our assessment from this review is that the RERC program indeed involves a multidisciplinary approach, with 36 professional fields involved, although 70% of research and development staff are in engineering fields, 23% in clinical fields, and only 7% in basic science fields; significantly, 11% of the professional staff have a disability related to their research. We observe that the RERC program has substantially diversified the scope of its work since the 1970’s, addressing more types of disabilities using more technologies, and, in particular, often now focusing on information technologies. RERC work also now often views users as integrated into an interdependent society through technologies that both people with and without disabilities co-use (such as the internet, wireless communication, and architecture). In addition, RERC research has evolved to view users as able at improving outcomes through learning, exercise, and plasticity (rather than being static), which can be optimally timed. We provide examples of rehabilitation technology innovation produced by the RERCs that illustrate this increasingly diversifying scope and evolving perspective. We conclude by discussing growth opportunities and possible future directions of the RERC program

Horizons: Nuclear Astrophysics in the 2020s and Beyond

Nuclear Astrophysics is a field at the intersection of nuclear physics and astrophysics, which seeks to understand the nuclear engines of astronomical objects and the origin of the chemical elements. This white paper summarizes progress and status of the field, the new open questions that have emerged, and the tremendous scientific opportunities that have opened up with major advances in capabilities across an ever growing number of disciplines and subfields that need to be integrated. We take a holistic view of the field discussing the unique challenges and opportunities in nuclear astrophysics in regards to science, diversity, education, and the interdisciplinarity and breadth of the field. Clearly nuclear astrophysics is a dynamic field with a bright future that is entering a new era of discovery opportunities.Comment: 96 pages. Submitted to Journal of Physics