Implementation of the SU(2) Hamiltonian Symmetry for the DMRG Algorithm

In the Density Matrix Renormalization Group (DMRG) algorithm, Hamiltonian symmetries play an important role. Using symmetries, the matrix representation of the Hamiltonian can be blocked. Diagonalizing each matrix block is more efficient than diagonalizing the original matrix. This paper explains how the the DMRG++ code has been extended to handle the non-local SU(2) symmetry in a model independent way. Improvements in CPU times compared to runs with only local symmetries are discussed for the one-orbital Hubbard model, and for a two-orbital Hubbard model for iron-based superconductors. The computational bottleneck of the algorithm and the use of shared memory parallelization are also addressed.Comment: elsarticle, 1 figur

Mobile MoCap: Retroreflector Localization On-The-Go

Motion capture (MoCap) through tracking retroreflectors obtains high precision pose estimation, which is frequently used in robotics. Unlike MoCap, fiducial marker-based tracking methods do not require a static camera setup to perform relative localization. Popular pose-estimating systems based on fiducial markers have lower localization accuracy than MoCap. As a solution, we propose Mobile MoCap, a system that employs inexpensive near-infrared cameras for precise relative localization in dynamic environments. We present a retroreflector feature detector that performs 6-DoF (six degrees-of-freedom) tracking and operates with minimal camera exposure times to reduce motion blur. To evaluate different localization techniques in a mobile robot setup, we mount our Mobile MoCap system, as well as a standard RGB camera, onto a precision-controlled linear rail for the purposes of retroreflective and fiducial marker tracking, respectively. We benchmark the two systems against each other, varying distance, marker viewing angle, and relative velocities. Our stereo-based Mobile MoCap approach obtains higher position and orientation accuracy than the fiducial approach. The code for Mobile MoCap is implemented in ROS 2 and made publicly available at https://github.com/RIVeR-Lab/mobile_mocap

Predicting how drug molecules bind to their protein targets

There have been substantial advances in the application of molecular modelling and simulation to drug discovery in recent years, as massive increases in computer power are coupled with continued development in the underlying methods and understanding of how to apply them. Here, we survey recent advances in one particular area — predicting how a known ligand binds to a particular protein. We focus on the four contributing classes of calculation: predicting where a binding site is on a protein; characterizing where chemical functional groups will bind to that site; molecular docking to generate a binding mode for a ligand and dynamics simulations to refine that pose and allow for protein conformation change. Examples of successful application are provided for each class

Dynamic undocking and the quasi-bound state as tools for drug discovery

There is a pressing need for new technologies that improve the efficacy and efficiency of drug discovery. Structure-based methods have contributed towards this goal but they focus on predicting the binding affinity of protein–ligand complexes, which is notoriously difficult. We adopt an alternative approach that evaluates structural, rather than thermodynamic, stability. As bioactive molecules present a static binding mode, we devised dynamic undocking (DUck), a fast computational method to calculate the work necessary to reach a quasi-bound state at which the ligand has just broken the most important native contact with the receptor. This non-equilibrium property is surprisingly effective in virtual screening because true ligands form more-resilient interactions than decoys. Notably, DUck is orthogonal to docking and other ‘thermodynamic’ methods. We demonstrate the potential of the docking–undocking combination in a fragment screening against the molecular chaperone and oncology target Hsp90, for which we obtain novel chemotypes and a hit rate that approaches 40

rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids

Identification of chemical compounds with specific biological activities is an important step in both chemical biology and drug discovery. When the structure of the intended target is available, one approach is to use molecular docking programs to assess the chemical complementarity of small molecules with the target; such calculations provide a qualitative measure of affinity that can be used in virtual screening (VS) to rank order a list of compounds according to their potential to be active. rDock is a molecular docking program developed at Vernalis for high-throughput VS (HTVS) applications. Evolved from RiboDock, the program can be used against proteins and nucleic acids, is designed to be computationally very efficient and allows the user to incorporate additional constraints and information as a bias to guide docking. This article provides an overview of the program structure and features and compares rDock to two reference programs, AutoDock Vina (open source) and Schrodinger's Glide (commercial). In terms of computational speed for VS, rDock is faster than Vina and comparable to Glide. For binding mode prediction, rDock and Vina are superior to Glide. The VS performance of rDock is significantly better than Vina, but inferior to Glide for most systems unless pharmacophore constraints are used; in that case rDock and Glide are of equal performance. The program is released under the Lesser General Public License and is freely available for download, together with the manuals, example files and the complete test sets, at http://rdock.sourceforge.net

A giant comet-like cloud of hydrogen escaping the warm Neptune-mass exoplanet GJ 436b

Exoplanets orbiting close to their parent stars could lose some fraction of their atmospheres because of the extreme irradiation. Atmospheric mass loss primarily affects low-mass exoplanets, leading to suggest that hot rocky planets might have begun as Neptune-like, but subsequently lost all of their atmospheres; however, no confident measurements have hitherto been available. The signature of this loss could be observed in the ultraviolet spectrum, when the planet and its escaping atmosphere transit the star, giving rise to deeper and longer transit signatures than in the optical spectrum. Here we report that in the ultraviolet the Neptune-mass exoplanet GJ 436b (also known as Gliese 436b) has transit depths of 56.3 +/- 3.5% (1 sigma), far beyond the 0.69% optical transit depth. The ultraviolet transits repeatedly start ~2 h before, and end >3 h after the ~1 h optical transit, which is substantially different from one previous claim (based on an inaccurate ephemeris). We infer from this that the planet is surrounded and trailed by a large exospheric cloud composed mainly of hydrogen atoms. We estimate a mass-loss rate in the range of ~10^8-10^9 g/s, which today is far too small to deplete the atmosphere of a Neptune-like planet in the lifetime of the parent star, but would have been much greater in the past.Comment: Published in Nature on 25 June 2015. Preprint is 28 pages, 12 figures, 2 table

Functional Alterations in Cerebellar Functional Connectivity in Anxiety Disorders

Adolescents with anxiety disorders exhibit excessive emotional and somatic arousal. Neuroimaging studies have shown abnormal cerebral cortical activation and connectivity in this patient population. The specific role of cerebellar output circuitry, specifically the dentate nuclei (DN), in adolescent anxiety disorders remains largely unexplored. Resting-state functional connectivity analyses have parcellated the DN, the major output nuclei of the cerebellum, into three functional territories (FTs) that include default-mode, salience-motor, and visual networks. The objective of this study was to understand whether FTs of the DN are implicated in adolescent anxiety disorders. Forty-one adolescents (mean age 15.19 ± 0.82, 26 females) with one or more anxiety disorders and 55 age- and gender-matched healthy controls completed resting-state fMRI scans and a self-report survey on anxiety symptoms. Seed-to-voxel functional connectivity analyses were performed using the FTs from DN parcellation. Brain connectivity metrics were then correlated with State-Trait Anxiety Inventory (STAI) measures within each group. Adolescents with an anxiety disorder showed significant hyperconnectivity between salience-motor DN FT and cerebral cortical salience-motor regions compared to controls. Salience-motor FT connectivity with cerebral cortical sensorimotor regions was significantly correlated with STAI-trait scores in HC (R2 = 0.41). Here, we report DN functional connectivity differences in adolescents diagnosed with anxiety, as well as in HC with variable degrees of anxiety traits. These observations highlight the relevance of DN as a potential clinical and sub-clinical marker of anxiety

Variations in disability and quality of life with age and sex between eight Lower and Middle Income Countries:data from the INDEPTH WHO-SAGE collaboration

Background: Disability and quality of life are key outcomes for older people. Little is known about how these measures vary with age and gender across lower income and middle-income countries; such information is necessary to tailor health and social care policy to promote healthy ageing and minimise disability. Methods: We analysed data from participants aged 50 years and over from health and demographic surveillance system sites of the International Network for the Demographic Evaluation of Populations and their Health Network in Ghana, Kenya, Tanzania, South Africa, Vietnam, India, Indonesia and Bangladesh, using an abbreviated version of the WHO Study on global AGEing survey instrument. We used the eight-item WHO Quality of Life (WHOQoL) tool to measure quality of life and theWHO Disability Assessment Schedule, version 2 (WHODAS-II) tool to measure disability. We collected selected health status measures via the survey instrument and collected demographic and socioeconomic data from linked surveillance site information. We performed regression analyses to quantify differences between countries in the relationship between age, gender and both quality of life and disability, and we used anchoring vignettes to account for differences in interpretation of disability severity. Results: We included 43 935 individuals in the analysis. Mean age was 63.7 years (SD 9.7) and 24 434 (55.6%) were women. In unadjusted analyses across all countries, WHOQoL scores worsened by 0.13 points (95% CI 0.12 to 0.14) per year increase in age and WHODAS scores worsened by 0.60 points (95% CI 0.57 to 0.64). WHODAS-II and WHOQoL scores varied markedly between countries, as did the gradient of scores with increasing age. In regression analyses, differences were not fully explained by age, socioeconomic status, marital status, education or health factors. Differences in disability scores between countries were not explained by differences in anchoring vignette responses. Conclusions: The relationship between age, sex and both disability and quality of life varies between countries. The findings may guide tailoring of interventions to individual country needs, although these associations require further study

Body size and shape changes and the risk of diabetes in the Diabetes Prevention Program

Prezentowane badanie przeprowadzono w celu sprawdzenia hipotezy, zgodnie z którą ryzyko rozwoju cukrzycy typu 2 zmniejsza się wraz z redukcją masy ciała i otyłości brzusznej. Do badania Diabetes Prevention Program (DPP) włączono osoby, u których rozpoznawano upośledzoną tolerancję glukozy, i zakwalifikowano je do grup otrzymujących placebo lub metforminę albo wprowadzono tylko modyfikację stylu życia. U uczestników badania określono wzrost, masę ciała oraz zmierzono tkankę tłuszczową na poziomie L2-L3 i L4-L5 za pomocą tomografii komputerowej na początku badania oraz po roku. Zastosowano modele proporcjonalnego ryzyka Coxa w celu oceny, zależnie od płci, wpływu zmiany tych parametrów w ciągu roku na rozwój cukrzycy w okresie dalszej obserwacji, którą prowadzono u 758 osób. Modyfikacja stylu życia doprowadziła do redukcji trzewnej tkanki tłuszczowej na poziomie L2-L3 (mężczyźni: -24,3%; kobiety: -18,2%) oraz na poziomie L4-L5 (mężczyźni: -22,4%, kobiety: -17,8%), tkanki tłuszczowej podskórnej na poziomie L2-L3 (mężczyźni: -15,7%, kobiety: -11,4%) i L4-L5 (mężczyźni: -16,7%, kobiety: -11,9%), do zmniejszenia masy ciała (mężczyźni: -8,2%, kobiety: -7,8%), wskaźnika masy ciała (mężczyźni: -8,2%, kobiety: -7,8%) oraz obwodu talii (mężczyźni: -7,5%, kobiety -6,1%). W grupie otrzymującej metforminę zaobserwowano redukcję masy ciała (-2,9%) i obniżenie wskaźnika masy ciała (-2,9%) u mężczyzn oraz zmniejszenie ilości podskórnej tkanki tłuszczowej (-3,6% na poziomie L2-L3 i -4,7% na poziomie L4-L5), masy ciała (-3,3%), wskaźnika masy ciała (-3,3%) oraz obwodu talii (-2,8%) u kobiet. Zmniejszenie ryzyka rozwoju cukrzycy poprzez zmianę stylu życia wiązało się z redukcją masy ciała, wskaźnika masy ciała oraz rozkładu tkanki tłuszczowej po skorygowaniu względem wieku oraz pochodzenia etnicznego (ustalano je na podstawie informacji uzyskanej od uczestników). Zmniejszenie ryzyka rozwoju cukrzycy poprzez zmianę stylu życia może nastąpić zarówno poprzez wpływ na całą tkankę tłuszczową, jak i brzuszną tkankę tłuszczową; wpływ metforminy wydawał się niezależny od zmian tkanki tłuszczowej.The researchers conducted this study to test the hypothesis that risk of type 2 diabetes is less following reductions in body size and central adiposity. The Diabetes Prevention Program (DPP) recruited and randomized individuals with impaired glucose tolerance to treatment with placebo, metformin, or lifestyle modification. Height, weight, waist circumference, and subcutaneous and visceral fat at L2-L3 and L4-L5 by computed tomography were measured at baseline and at 1 year. Cox proportional hazards models assessed by sex the effect of change in these variables over the 1st year of intervention upon development of diabetes over subsequent follow- up in a subset of 758 participants. Lifestyle reduced visceral fat at L2-L3 (men -24.3%, women -18.2%) and at L4-L5 (men -22.4%, women -17.8%), subcutaneous fat at L2-L3 (men -15.7%, women -11.4%) and at L4-L5 (men -16.7%, women -11.9%), weight (men –8.2%, women –7.8%), BMI (men -8.2%, women -7.8%), and waist circumference (men -7.5%, women -6.1%). Metformin reduced weight (-2.9%) and BMI (-2.9%) in men and subcutaneous fat (-3.6% at L2-L3 and -4.7% at L4-L5), weight (-3.3%), BMI (-3.3%), and waist circumference (-2.8%) in women. Decreased diabetes risk by lifestyle intervention was associated with reductions of body weight, BMI, and central body fat distribution after adjustment for age and self-reported ethnicity. Reduced diabetes risk with lifestyle intervention may have been through effects upon both overall body fat and central body fat but with metformin appeared to be independent of body fat

The deep-pocket effect of internal capital markets

We provide evidence that incumbent and entrant firms' access to business group deep pockets affects entry patterns in product markets. Relying on a unique French data set on business groups, our paper shows that entry in manufacturing industries is negatively related to the cash hoarded by incumbent-affiliated groups, and positively related to entrant groups' cash. In line with theoretical predictions, we find that the impact on entry of group cash holdings is more important in environments where financial constraints are pronounced and in more financially dependent sectors. The cash holdings of incumbent and entrant groups also affect the survival rate of entrants in the 3 to 5 year post-entry window. Overall, our findings suggest that internal capital markets operate within corporate groups and affect the product market behavior of affiliated firms by mitigating financial constraints