PLUMED 2: New feathers for an old bird

Enhancing sampling and analyzing simulations are central issues in molecular simulation. Recently, we introduced PLUMED, an open-source plug-in that provides some of the most popular molecular dynamics (MD) codes with implementations of a variety of different enhanced sampling algorithms and collective variables (CVs). The rapid changes in this field, in particular new directions in enhanced sampling and dimensionality reduction together with new hardware, require a code that is more flexible and more efficient. We therefore present PLUMED 2 here a,complete rewrite of the code in an object-oriented programming language (C++). This new version introduces greater flexibility and greater modularity, which both extends its core capabilities and makes it far easier to add new methods and CVs. It also has a simpler interface with the MD engines and provides a single software library containing both tools and core facilities. Ultimately, the new code better serves the ever-growing community of users and contributors in coping with the new challenges arising in the field.

Program summary

Program title: PLUMED 2

Catalogue identifier: AEEE_v2_0

Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEEE_v2_0.html

Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland

Licensing provisions: Yes

No. of lines in distributed program, including test data, etc.: 700646

No. of bytes in distributed program, including test data, etc.: 6618136

Distribution format: tar.gz

Programming language: ANSI-C++.

Computer: Any computer capable of running an executable produced by a C++ compiler.

Operating system: Linux operating system, Unix OSs.

Has the code been vectorized or parallelized?: Yes, parallelized using MPI.

RAM: Depends on the number of atoms, the method chosen and the collective variables used.

Classification: 3, 7.7, 23. Catalogue identifier of previous version: AEEE_v1_0.

Journal reference of previous version: Comput. Phys. Comm. 180 (2009) 1961.

External routines: GNU libmatheval, Lapack, Bias, MPI. (C) 2013 Elsevier B.V. All rights reserved.

Performance Analysis of Randomized Distributed Space-Time Codes over Composite Gamma/Lognormal Fading Channels

This work investigates the end-to-end performance of randomized distributed space-time codes with complex Gaussian distribution, when employed in a wireless relay network. The relaying nodes are assumed to adopt a decode-and-forward strategy and transmissions are affected by small and large scale fading phenomena. Extremely tight, analytical approximations of the end-to-end symbol error probability and of the end-to-end outage probability are derived and successfully validated through Monte-Carlo simulation. For the high signal-to-noise ratio regime, a simple, closed-form expression for the symbol error probability is further provided.

Novel genetic susceptibility loci for diabetic end-stage renal disease identified through robust naive Bayes classification

Aims/hypothesis: Diabetic nephropathy is a major diabetic complication, and diabetes is the leading cause of end-stage renal disease (ESRD). Family studies suggest a hereditary component for diabetic nephropathy. However, only a few genes have been associated with diabetic nephropathy or ESRD in diabetic patients. Our aim was to detect novel genetic variants associated with diabetic nephropathy and ESRD. Methods: We exploited a novel algorithm, ‘Bag of Naive Bayes’, whose marker selection strategy is complementary to that of conventional genome-wide association models based on univariate association tests. The analysis was performed on a genome-wide association study of 3,464 patients with type 1 diabetes from the Finnish Diabetic Nephropathy (FinnDiane) Study and subsequently replicated with 4,263 type 1 diabetes patients from the Steno Diabetes Centre, the All Ireland-Warren 3-Genetics of Kidneys in Diabetes UK collection (UK–Republic of Ireland) and the Genetics of Kidneys in Diabetes US Study (GoKinD US). Results: Five genetic loci (WNT4/ZBTB40-rs12137135, RGMA/MCTP2-rs17709344, MAPRE1P2-rs1670754, SEMA6D/SLC24A5-rs12917114 and SIK1-rs2838302) were associated with ESRD in the FinnDiane study. An association between ESRD and rs17709344, tagging the previously identified rs12437854 and located between the RGMA and MCTP2 genes, was replicated in independent case–control cohorts. rs12917114 near SEMA6D was associated with ESRD in the replication cohorts under the genotypic model (p < 0.05), and rs12137135 upstream of WNT4 was associated with ESRD in Steno. Conclusions/interpretation: This study supports the previously identified findings on the RGMA/MCTP2 region and suggests novel susceptibility loci for ESRD. This highlights the importance of applying complementary statistical methods to detect novel genetic variants in diabetic nephropathy and, in general, in complex diseases.

Tunnel spoil classification and applicability of lime addition in weak formations for muck reuse

Tunnel construction planning requires careful consideration of the spoil management part, as this involves environmental, economic and legal requirements. In this paper a methodological approach that considers the interaction between technical and geological factors in determining the features of the resulting muck is proposed. This gives indications about the required treatments as well as laboratory and field characterisation tests to be performed to assess muck recovery alternatives. While this reuse is an opportunity for excavations in good quality homogeneous grounds (e.g. granitic mass), it is critical for complex formation. This approach has been validated, at present, for three different geo-materials resulting from a tunnel excavation carried out with a large diameter Earth Pressure Balance Shield (EPB) through a complex geological succession. Physical parameters and technological features of the three materials have been assessed, according to their valorisation potential, for defining re-utilisation patterns. The methodology proved to be effective and the laboratory tests carried out on the three materials allowed the suitability and treatment effectiveness for each muck recovery strategy to be defined. © 2014 Elsevier Ltd.

The distribution of COPD in UK general practice using the new GOLD classification

The new Global Initiative for Chronic Obstructive Lung Disease (GOLD) 2011 document recommends a combined assessment of chronic obstructive pulmonary disease (COPD) based on current symptoms and future risk.

A large database of primary-care COPD patients across the UK was used to determine COPD distribution and characteristics according to the new GOLD classification. 80 general practices provided patients with a Read code diagnosis of COPD. Electronic and hand searches of patient medical records were undertaken, optimising data capture.

Data for 9219 COPD patients were collected. For the 6283 patients with both forced expiratory volume in 1 s (FEV1) and modified Medical Research Council scores (mean¡SD age 69.2¡10.6 years, body mass index 27.3¡6.2 kg?m-2), GOLD 2011 group distributions were: A (low risk and fewer symptoms) 36.1%, B (low risk and more symptoms) 19.1%, C (high risk and fewer symptoms) 19.6% and D (high risk and more symptoms) 25.3%. This is in contrast with GOLD 2007 stage classification: I (mild) 17.1%, II (moderate) 52.2%, III (severe) 25.5% and IV (very severe) 5.2%. 20% of patients with FEV1 o50% predicted had more than two exacerbations in the previous 12 months. 70% of patients with FEV1 ,50% pred had fewer than two exacerbations in the previous 12 months.

This database, representative of UK primary-care COPD patients, identified greater proportions of patients in the mildest and most severe categories upon comparing 2011 versus 2007 GOLD classifications. Discordance between airflow limitation severity and exacerbation risk was observed.

Enabling Complexity-Performance Trade-Offs for Successive Cancellation Decoding of Polar Codes

Polar codes are one of the most recent advancements in coding theory and they have attracted significant interest. While they are provably capacity achieving over various channels, they have seen limited practical applications. Unfortunately, the successive nature of successive cancellation based decoders hinders fine-grained adaptation of the decoding complexity to design constraints and operating conditions. In this paper, we propose a systematic method for enabling complexity-performance trade-offs by constructing polar codes based on an optimization problem which minimizes the complexity under a suitably defined mutual information based performance constraint. Moreover, a low-complexity greedy algorithm is proposed in order to solve the optimization problem efficiently for very large code lengths.

Prediction of integral type failures in semiconductor manufacturing through classification methods

Smart management of maintenances has become fundamental in manufacturing environments in order to decrease downtime and costs associated with failures. Predictive Maintenance (PdM) systems based on Machine Learning (ML) techniques have the possibility with low added costs of drastically decrease failures-related expenses; given the increase of availability of data and capabilities of ML tools, PdM systems are becoming really popular, especially in semiconductor manufacturing. A PdM module based on Classification methods is presented here for the prediction of integral type faults that are related to machine usage and stress of equipment parts. The module has been applied to an important class of semiconductor processes, ion-implantation, for the prediction of ion-source tungsten filament breaks. The PdM has been tested on a real production dataset. © 2013 IEEE.