Error estimates for solid-state density-functional theory predictions: an overview by means of the ground-state elemental crystals

Predictions of observable properties by density-functional theory calculations (DFT) are used increasingly often in experimental condensed-matter physics and materials engineering as data. These predictions are used to analyze recent measurements, or to plan future experiments. Increasingly more experimental scientists in these fields therefore face the natural question: what is the expected error for such an ab initio prediction? Information and experience about this question is scattered over two decades of literature. The present review aims to summarize and quantify this implicit knowledge. This leads to a practical protocol that allows any scientist - experimental or theoretical - to determine justifiable error estimates for many basic property predictions, without having to perform additional DFT calculations. A central role is played by a large and diverse test set of crystalline solids, containing all ground-state elemental crystals (except most lanthanides). For several properties of each crystal, the difference between DFT results and experimental values is assessed. We discuss trends in these deviations and review explanations suggested in the literature. A prerequisite for such an error analysis is that different implementations of the same first-principles formalism provide the same predictions. Therefore, the reproducibility of predictions across several mainstream methods and codes is discussed too. A quality factor Delta expresses the spread in predictions from two distinct DFT implementations by a single number. To compare the PAW method to the highly accurate APW+lo approach, a code assessment of VASP and GPAW with respect to WIEN2k yields Delta values of 1.9 and 3.3 meV/atom, respectively. These differences are an order of magnitude smaller than the typical difference with experiment, and therefore predictions by APW+lo and PAW are for practical purposes identical.Comment: 27 pages, 20 figures, supplementary material available (v5 contains updated supplementary material

The cytoplasm of living cells: A functional mixture of thousands of components

Inside every living cell is the cytoplasm: a fluid mixture of thousands of different macromolecules, predominantly proteins. This mixture is where most of the biochemistry occurs that enables living cells to function, and it is perhaps the most complex liquid on earth. Here we take an inventory of what is actually in this mixture. Recent genome-sequencing work has given us for the first time at least some information on all of these thousands of components. Having done so we consider two physical phenomena in the cytoplasm: diffusion and possible phase separation. Diffusion is slower in the highly crowded cytoplasm than in dilute solution. Reasonable estimates of this slowdown can be obtained and their consequences explored, for example, monomer-dimer equilibria are established approximately twenty times slower than in a dilute solution. Phase separation in all except exceptional cells appears not to be a problem, despite the high density and so strong protein-protein interactions present. We suggest that this may be partially a byproduct of the evolution of other properties, and partially a result of the huge number of components present.Comment: 11 pages, 1 figure, 1 tabl

Bose-Einstein Condensation in a Harmonic Potential

We examine several features of Bose-Einstein condensation (BEC) in an external harmonic potential well. In the thermodynamic limit, there is a phase transition to a spatial Bose-Einstein condensed state for dimension D greater than or equal to 2. The thermodynamic limit requires maintaining constant average density by weakening the potential while increasing the particle number N to infinity, while of course in real experiments the potential is fixed and N stays finite. For such finite ideal harmonic systems we show that a BEC still occurs, although without a true phase transition, below a certain ``pseudo-critical'' temperature, even for D=1. We study the momentum-space condensate fraction and find that it vanishes as 1/N^(1/2) in any number of dimensions in the thermodynamic limit. In D less than or equal to 2 the lack of a momentum condensation is in accord with the Hohenberg theorem, but must be reconciled with the existence of a spatial BEC in D=2. For finite systems we derive the N-dependence of the spatial and momentum condensate fractions and the transition temperatures, features that may be experimentally testable. We show that the N-dependence of the 2D ideal-gas transition temperature for a finite system cannot persist in the interacting case because it violates a theorem due to Chester, Penrose, and Onsager.Comment: 34 pages, LaTeX, 6 Postscript figures, Submitted to Jour. Low Temp. Phy

Effect of Conjugated Linoleic Acids on Nutritional Status and Lipid Metabolism in Rats Fed Linoleic-Acid-Deprived Diets

This study aims to investigate the effect of conjugated linoleic acid (CLA) on nutritional parameters and triacylglycerol (TAG) regulation in male Wistar rats fed linoleic acid (LA)-deprived (−LA) diets compared to LA-enriched (+LA) diets. In both +LA and −LA groups, CLA are incorporated into the tissues, showing higher levels in the adipose tissue. However, different metabolic and nutritional effects are observed depending on the LA status. CLA markedly reduces fat depots in the −LA group, associated with an increased lipoprotein lipase (LPL) and lipogenic enzyme activities as compensatory mechanisms. Moreover, CLA restores the hepatic TAG levels in −LA animals, associated with a normalized triacylglycerol-secretion rate (TAG-SR), an increased lipogenic enzyme activity and higher mRNA levels of fatty acid synthase. Serum TAG levels are not affected by CLA in the +LA group. However, in the −LA group, CLA decreases the TAG levels associated with a reduced TAG-SR and a higher adipose tissue LPL activity. Thus, the CLA effects on the nutritional parameters and TAG metabolism differs depending on the LA status. CLA causes certain beneficial biological and nutritional effects in LA-deprived but not in LA-enriched animals. Practical Applications: The approach by the authors involve growing animals in healthy physiological conditions fed with diets containing recommended levels of dietary fats, moderate amounts of commercial CLA mixture obtained from industrial synthesis (equimolecular amounts of 9c,11t- and 10t,12c-isomers), and unbalanced LA levels. These variables constitute a situation observed in the human population. The present study might contribute to understanding the role of CLA on nutritional parameters and TAG metabolism depending on the nutritional milieu. Conjugated linoleic acid effects on nutritional parameters and triacylglycerol metabolism in rats fed linoleic-acid-enriched and linoleic-acid-deprived diets are determined.Fil: Fariña, Ana Clara. Universidad Nacional del Litoral. Facultad de Bioquímica y Ciencias Biológicas. Departamento de Ciencias Biológicas. Cátedra de Bromatología y Nutrición; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe; ArgentinaFil: Lavandera, Jimena Veronica. Universidad Nacional del Litoral. Facultad de Bioquímica y Ciencias Biológicas. Departamento de Ciencias Biológicas. Cátedra de Bromatología y Nutrición; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe; ArgentinaFil: González, Marcela Aída. Universidad Nacional del Litoral. Facultad de Bioquímica y Ciencias Biológicas. Departamento de Ciencias Biológicas. Cátedra de Bromatología y Nutrición; ArgentinaFil: Bernal, Claudio Adrian. Universidad Nacional del Litoral. Facultad de Bioquímica y Ciencias Biológicas. Departamento de Ciencias Biológicas. Cátedra de Bromatología y Nutrición; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe; Argentin

Independence in CLP Languages

Studying independence of goals has proven very useful in the context of logic programming. In particular, it has provided a formal basis for powerful automatic parallelization tools, since independence ensures that two goals may be evaluated in parallel while preserving correctness and eciency. We extend the concept of independence to constraint logic programs (CLP) and prove that it also ensures the correctness and eciency of the parallel evaluation of independent goals. Independence for CLP languages is more complex than for logic programming as search space preservation is necessary but no longer sucient for ensuring correctness and eciency. Two additional issues arise. The rst is that the cost of constraint solving may depend upon the order constraints are encountered. The second is the need to handle dynamic scheduling. We clarify these issues by proposing various types of search independence and constraint solver independence, and show how they can be combined to allow dierent optimizations, from parallelism to intelligent backtracking. Sucient conditions for independence which can be evaluated \a priori" at run-time are also proposed. Our study also yields new insights into independence in logic programming languages. In particular, we show that search space preservation is not only a sucient but also a necessary condition for ensuring correctness and eciency of parallel execution

Pair creation: back-reactions and damping

We solve the quantum Vlasov equation for fermions and bosons, incorporating spontaneous pair creation in the presence of back-reactions and collisions. Pair creation is initiated by an external impulse field and the source term is non-Markovian. A simultaneous solution of Maxwell's equation in the presence of feedback yields an internal current and electric field that exhibit plasma oscillations with a period tau_pl. Allowing for collisions, these oscillations are damped on a time-scale, tau_r, determined by the collision frequency. Plasma oscillations cannot affect the early stages of the formation of a quark-gluon plasma unless tau_r >> tau_pl and tau_pl approx. 1/Lambda_QCD approx 1 fm/c.Comment: 16 pages, 6 figure, REVTEX, epsfig.st

The agency of liminality: army wives in the DR Congo and the tactical reversal of militarization

The inherently unstable boundaries between military and civilian worlds have emerged as a main object of study within the field of critical military studies. This article sheds light on the (re)production of these boundaries by attending to a group that rarely features in the debates on the military/civilian divide: army wives in a ‘non-Northern’ context, more specifically the Democratic Republic of the Congo (DRC). Drawing upon the ‘analytical toolbox’ of governmentality, we explore how civilian and military positionalities are called upon, articulated and subverted in the governing and self-governing of Congolese army wives. We show the decisive importance of these wives’ civilian-military ‘in betweenness’ both in efforts to govern them and in their exercise of agency, in particular The inherently unstable boundaries between military and civilian worlds have emerged as a main object of study within the field of critical military studies. This article sheds light on the (re)production of these boundaries by attending to a group that rarely features in the debates on the military/civilian divide: army wives in a ‘non-Northern’ context, more specifically the Democratic Republic of the Congo (DRC). Drawing upon the ‘analytical toolbox’ of governmentality, we explore how civilian and military positionalities are called upon, articulated, and subverted in the governing and self-governing of Congolese army wives. We show the decisive importance of these wives’ civilian–military ‘in-betweenness’ both in efforts to govern them and in their exercise of agency, in particular the ways in which they ‘tactically reverse’ militarization. The article also demonstrates the dispersed nature of the governing arrangements surrounding army wives, highlighting the vital role of ‘the civilian’ as well as the ‘agency of those being militarized’ within processes of militarization. By foregrounding the relevance of studying Congolese army wives and their militarization with an analytical toolbox often reserved for so called ‘advanced militaries/societies’, and by revealing numerous similarities between the Congolese and ‘Northern’ contexts, the article also sets out to counter the Euro/US-centrism and ‘theoretical discrimination’ that mark present-day (critical) military studies

The Quantum Vlasov Equation and its Markov Limit

The adiabatic particle number in mean field theory obeys a quantum Vlasov equation which is nonlocal in time. For weak, slowly varying electric fields this particle number can be identified with the single particle distribution function in phase space, and its time rate of change is the appropriate effective source term for the Boltzmann-Vlasov equation. By analyzing the evolution of the particle number we exhibit the time structure of the particle creation process in a constant electric field, and derive the local form of the source term due to pair creation. In order to capture the secular Schwinger creation rate, the source term requires an asymptotic expansion which is uniform in time, and whose longitudinal momentum dependence can be approximated by a delta function only on long time scales. The local Vlasov source term amounts to a kind of Markov limit of field theory, where information about quantum phase correlations in the created pairs is ignored and a reversible Hamiltonian evolution is replaced by an irreversible kinetic one. This replacement has a precise counterpart in the density matrix description, where it corresponds to disregarding the rapidly varying off-diagonal terms in the adiabatic number basis and treating the more slowly varying diagonal elements as the probabilities of creating pairs in a stochastic process. A numerical comparison between the quantum and local kinetic approaches to the dynamical backreaction problem shows remarkably good agreement, even in quite strong electric fields, over a large range of times.Comment: 49 pages, RevTex/LaTeX2e, 8 .eps figures included in 404KB .gz file (~3MB total uncompressed). Replacement added \tightenpages command to reduce from 67 to 49 p

Modeling key pathological features of frontotemporal dementia with C9ORF72 repeat expansion in iPSC-derived human neurons

The recently identified GGGGCC repeat expansion in the noncoding region of C9ORF72 is the most common pathogenic mutation in patients with frontotemporal dementia (FTD) or amyotrophic lateral sclerosis (ALS). We generated a human neuronal model and investigated the pathological phenotypes of human neurons containing GGGGCC repeat expansions. Skin biopsies were obtained from two subjects who had \u3e 1,000 GGGGCC repeats in C9ORF72 and their respective fibroblasts were used to generate multiple induced pluripotent stem cell (iPSC) lines. After extensive characterization, two iPSC lines from each subject were selected, differentiated into postmitotic neurons, and compared with control neurons to identify disease-relevant phenotypes. Expanded GGGGCC repeats exhibit instability during reprogramming and neuronal differentiation of iPSCs. RNA foci containing GGGGCC repeats were present in some iPSCs, iPSC-derived human neurons and primary fibroblasts. The percentage of cells with foci and the number of foci per cell appeared to be determined not simply by repeat length but also by other factors. These RNA foci do not seem to sequester several major RNA-binding proteins. Moreover, repeat-associated non-ATG (RAN) translation products were detected in human neurons with GGGGCC repeat expansions and these neurons showed significantly elevated p62 levels and increased sensitivity to cellular stress induced by autophagy inhibitors. Our findings demonstrate that key neuropathological features of FTD/ALS with GGGGCC repeat expansions can be recapitulated in iPSC-derived human neurons and also suggest that compromised autophagy function may represent a novel underlying pathogenic mechanism