Tensor hypercontraction: A universal technique for the resolution of matrix elements of local, finite-range NN-body potentials in many-body quantum problems

Configuration-space matrix elements of N-body potentials arise naturally and ubiquitously in the Ritz-Galerkin solution of many-body quantum problems. For the common specialization of local, finite-range potentials, we develop the eXact Tensor HyperContraction (X-THC) method, which provides a quantized renormalization of the coordinate-space form of the N-body potential, allowing for a highly separable tensor factorization of the configuration-space matrix elements. This representation allows for substantial computational savings in chemical, atomic, and nuclear physics simulations, particularly with respect to difficult "exchange-like" contractions.Comment: Third version of the manuscript after referee's comments. In press in PRL. Main text: 4 pages, 2 figures, 1 table; Supplemental material (also included): 14 pages, 2 figures, 2 table

Oscillations in meta-generalized-gradient approximation potential energy surfaces for dispersion-bound complexes

© 2009 American Institute of Physics. The electronic version of this article is the complete one and can be found at: http://dx.doi.org/10.1063/1.3177061DOI: 10.1063/1.3177061Meta-generalized-gradient approximations (meta-GGAs) in density-functional theory are exchange-correlation functionals whose integrands depend on local density, density gradient, and also the kinetic-energy density. It has been pointed out by Johnson et al. [Chem. Phys. Lett. 394, 334 (2004) ] that meta-GGA potential energy curves in dispersion-bound complexes are susceptible to spurious oscillations unless very large integration grids are used. This grid sensitivity originates from the saddle-point region of the density near the intermonomer midpoint. Various dimensionless ratios involving the kinetic-energy density, found in typical meta-GGAs, may be ill-behaved in this region. Grid sensitivity thus arises if the midpoint region is sampled by too sparse a grid. For most meta-GGAs, standard grids do not suffice. Care must be taken to avoid this problem when using, or constructing, meta-GGAs

Improvement of the coupled-cluster singles and doubles method via scaling same- and opposite-spin components of the double excitation correlation energy

© 2008 American Institute of Physics. The electronic version of this article is the complete one and can be found at: http://dx.doi.org/10.1063/1.2883974DOI: 10.1063/1.2883974There has been much interest in cost-free improvements to second-order Moller-Plesset perturbation theory (MP2) via scaling the same- and opposite-spin components of the correlation energy (spin-component scaled MP2). By scaling the same- and opposite-spin components of the double excitation correlation energy from the coupled-cluster of single and double excitations (CCSD) method, similar improvements can be achieved. Optimized for a set of 48 reaction energies, scaling factors were determined to be 1.13 and 1.27 for the same- and opposite-spin components, respectively. Preliminary results suggest that the spin-component scaled CCSD (SCS-CCSD) method will outperform all MP2 type methods considered for describing intermolecular interactions. Potential energy curves computed with the SCS-CCSD method for the sandwich benzene dimer and methane dimer reproduce the benchmark CCSD(T) potential curves with errors of only a few hundredths of 1 kcal mol⁻¹ for the minima. The performance of the SCS-CCSD method suggests that it is a reliable, lower cost alternative to the CCSD(T) method

Long term (5 Year) safety of bronchial thermoplasty: Asthma Intervention Research (AIR) trial

<b>Background:</b> Bronchial thermoplasty (BT) is a bronchoscopic procedure that improves asthma control by reducing excess airway smooth muscle. Treated patients have been followed out to 5 years to evaluate long-term safety of this procedure. <br></br> <br></br> <b>Methods:</b> Patients enrolled in the Asthma Intervention Research Trial were on inhaled corticosteroids ≥200 μg beclomethasone or equivalent + long-acting-beta2-agonists and demonstrated worsening of asthma on long-acting-β2-agonist withdrawal. Following initial evaluation at 1 year, subjects were invited to participate in a 4 year safety study. Adverse events (AEs) and spirometry data were used to assess long-term safety out to 5 years post-BT. <br></br> <br></br> <b>Results:</b> 45 of 52 treated and 24 of 49 control group subjects participated in long-term follow-up of 5 years and 3 years respectively. The rate of respiratory adverse events (AEs/subject) was stable in years 2 to 5 following BT (1.2, 1.3, 1.2, and 1.1, respectively,). There was no increase in hospitalizations or emergency room visits for respiratory symptoms in Years 2, 3, 4, and 5 compared to Year 1. The FVC and FEV1 values showed no deterioration over the 5 year period in the BT group. Similar results were obtained for the Control group. <br></br><br></br> <b>Conclusions:</b> The absence of clinical complications (based on AE reporting) and the maintenance of stable lung function (no deterioration of FVC and FEV1) over a 5-year period post-BT in this group of patients with moderate to severe asthma support the long-term safety of the procedure out to 5 years

Towards a consensus around standards for smartphone apps and digital mental health

Mental disorders impact one in four people worldwide, yet access to care is challenging for those who suffer from them1. Mental health apps offer the potential to overcome access barriers for the nearly three billion people projected to own a smartphone by 2020. Although there are over 10,000 mental health apps commercially available, there are few resources available to help end users (patients, clinicians and health care organizations) to evaluate the quality and suitability of these products. Thus, there is an urgent need for an agreement about appropriate standards, principles and practices in research and evaluation of these tools.We represent leaders in mHealth research, industry and health care systems from around the globe, and we seek here to promote consensus on implementing these standards and principles for the evaluation of mental health apps. At a minimum, standards should include consideration of: a) data safety and privacy, b) effectiveness, c) user experience/adherence, d) data integration. Our consensus on the challenges and recommendations in each of these areas is presented below

The Energy Computation Paradox and ab initio Protein Folding

The routine prediction of three-dimensional protein structure from sequence remains a challenge in computational biochemistry. It has been intuited that calculated energies from physics-based scoring functions are able to distinguish native from nonnative folds based on previous performance with small proteins and that conformational sampling is the fundamental bottleneck to successful folding. We demonstrate that as protein size increases, errors in the computed energies become a significant problem. We show, by using error probability density functions, that physics-based scores contain significant systematic and random errors relative to accurate reference energies. These errors propagate throughout an entire protein and distort its energy landscape to such an extent that modern scoring functions should have little chance of success in finding the free energy minima of large proteins. Nonetheless, by understanding errors in physics-based score functions, they can be reduced in a post-hoc manner, improving accuracy in energy computation and fold discrimination

Guidelines for Genome-Scale Analysis of Biological Rhythms

Genome biology approaches have made enormous contributions to our understanding of biological rhythms, particularly in identifying outputs of the clock, including RNAs, proteins, and metabolites, whose abundance oscillates throughout the day. These methods hold significant promise for future discovery, particularly when combined with computational modeling. However, genome-scale experiments are costly and laborious, yielding “big data” that are conceptually and statistically difficult to analyze. There is no obvious consensus regarding design or analysis. Here we discuss the relevant technical considerations to generate reproducible, statistically sound, and broadly useful genome-scale data. Rather than suggest a set of rigid rules, we aim to codify principles by which investigators, reviewers, and readers of the primary literature can evaluate the suitability of different experimental designs for measuring different aspects of biological rhythms. We introduce CircaInSilico, a web-based application for generating synthetic genome biology data to benchmark statistical methods for studying biological rhythms. Finally, we discuss several unmet analytical needs, including applications to clinical medicine, and suggest productive avenues to address them

Psi4

Psi4 is an ab initio electronic structure program providing methods such as Hartree-Fock, density functional theory, configuration interaction, and coupled-cluster theory. The 1.1 release represents a major update meant to automate complex tasks, such as geometry optimization using complete-basis-set extrapolation or focal-point methods. Conversion of the top-level code to a Python module means that Psi4 can now be used in complex workflows alongside other Python tools. Several new features have been added with the aid of libraries providing easy access to techniques such as density fitting, Cholesky decomposition, and Laplace denominators. The build system has been completely rewritten to simplify interoperability with independent, reusable software components for quantum chemistry. Finally, a wide range of new theoretical methods and analyses have been added to the code base, including functional-group and open-shell symmetry adapted perturbation theory, density-fitted coupled cluster with frozen natural orbitals, orbital-optimized perturbation and coupled-cluster methods (e.g., OO-MP2 and OO-LCCD), density-fitted multiconfigurational self-consistent field, density cumulant functional theory, algebraic-diagrammatic construction excited states, improvements to the geometry optimizer, and the "X2C" approach to relativistic corrections, among many other improvements