Structure simulation with calculated NMR parameters - integrating COSMOS into the CCPN framework.

PubMed

Schneider, Olaf; Fogh, Rasmus H; Sternberg, Ulrich; Klenin, Konstantin; Kondov, Ivan

2012-01-01

The Collaborative Computing Project for NMR (CCPN) has build a software framework consisting of the CCPN data model (with APIs) for NMR related data, the CcpNmr Analysis program and additional tools like CcpNmr FormatConverter. The open architecture allows for the integration of external software to extend the abilities of the CCPN framework with additional calculation methods. Recently, we have carried out the first steps for integrating our software Computer Simulation of Molecular Structures (COSMOS) into the CCPN framework. The COSMOS-NMR force field unites quantum chemical routines for the calculation of molecular properties with a molecular mechanics force field yielding the relative molecular energies. COSMOS-NMR allows introducing NMR parameters as constraints into molecular mechanics calculations. The resulting infrastructure will be made available for the NMR community. As a first application we have tested the evaluation of calculated protein structures using COSMOS-derived 13C Cα and Cβ chemical shifts. In this paper we give an overview of the methodology and a roadmap for future developments and applications.

Moving Beyond the Single Center--Ways to Reinforce Molecular Orbital Theory in an Inorganic Course

ERIC Educational Resources Information Center

Cass, Marion E.; Hollingsworth, William E.

2004-01-01

It is suggested that molecular theory should be taught earlier in the inorganic chemistry curriculum even in the introductory chemistry course in order to integrate molecular orbital arguments more effectively throughout the curriculum. The method of teaching relies on having access to molecular modeling software as having access to such software…

ePMV embeds molecular modeling into professional animation software environments.

PubMed

Johnson, Graham T; Autin, Ludovic; Goodsell, David S; Sanner, Michel F; Olson, Arthur J

2011-03-09

Increasingly complex research has made it more difficult to prepare data for publication, education, and outreach. Many scientists must also wade through black-box code to interface computational algorithms from diverse sources to supplement their bench work. To reduce these barriers we have developed an open-source plug-in, embedded Python Molecular Viewer (ePMV), that runs molecular modeling software directly inside of professional 3D animation applications (hosts) to provide simultaneous access to the capabilities of these newly connected systems. Uniting host and scientific algorithms into a single interface allows users from varied backgrounds to assemble professional quality visuals and to perform computational experiments with relative ease. By enabling easy exchange of algorithms, ePMV can facilitate interdisciplinary research, smooth communication between broadly diverse specialties, and provide a common platform to frame and visualize the increasingly detailed intersection(s) of cellular and molecular biology. Copyright © 2011 Elsevier Ltd. All rights reserved.

Transitioning NWChem to the Next Generation of Manycore Machines

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bylaska, Eric J.; Apra, Edoardo; Kowalski, Karol

The NorthWest Chemistry (NWChem) modeling software is a popular molecular chemistry simulation software that was designed from the start to work on massively parallel processing supercomputers[6, 28, 49]. It contains an umbrella of modules that today includes Self Consistent Field (SCF), second order Mller-Plesset perturbation theory (MP2), Coupled Cluster, multi-conguration selfconsistent eld (MCSCF), selected conguration interaction (CI), tensor contraction engine (TCE) many body methods, density functional theory (DFT), time-dependent density functional theory (TDDFT), real time time-dependent density functional theory, pseudopotential plane-wave density functional theory (PSPW), band structure (BAND), ab initio molecular dynamics, Car-Parrinello molecular dynamics, classical molecular dynamics (MD), QM/MM,more » AIMD/MM, GIAO NMR, COSMO, COSMO-SMD, and RISM solvation models, free energy simulations, reaction path optimization, parallel in time, among other capabilities[ 22]. Moreover new capabilities continue to be added with each new release.« less

ePMV Embeds Molecular Modeling into Professional Animation Software Environments

PubMed Central

Johnson, Graham T.; Autin, Ludovic; Goodsell, David S.; Sanner, Michel F.; Olson, Arthur J.

2011-01-01

SUMMARY Increasingly complex research has made it more difficult to prepare data for publication, education, and outreach. Many scientists must also wade through black-box code to interface computational algorithms from diverse sources to supplement their bench work. To reduce these barriers, we have developed an open-source plug-in, embedded Python Molecular Viewer (ePMV), that runs molecular modeling software directly inside of professional 3D animation applications (hosts) to provide simultaneous access to the capabilities of these newly connected systems. Uniting host and scientific algorithms into a single interface allows users from varied backgrounds to assemble professional quality visuals and to perform computational experiments with relative ease. By enabling easy exchange of algorithms, ePMV can facilitate interdisciplinary research, smooth communication between broadly diverse specialties and provide a common platform to frame and visualize the increasingly detailed intersection(s) of cellular and molecular biology. PMID:21397181

Using the [beta][subscript 2]-Adrenoceptor for Structure-Based Drug Design

ERIC Educational Resources Information Center

Manallack, David T.; Chalmers, David K.; Yuriev, Elizabeth

2010-01-01

The topics of molecular modeling and drug design are studied in a medicinal chemistry course. The recently reported structures of several G protein-coupled receptors (GPCR) with bound ligands have been used to develop a simple computer-based experiment employing molecular-modeling software. Knowledge of the specific interactions between a ligand…

Looking beyond Lewis Structures: A General Chemistry Molecular Modeling Experiment Focusing on Physical Properties and Geometry

ERIC Educational Resources Information Center

Linenberger, Kimberly J.; Cole, Renee S.; Sarkar, Somnath

2011-01-01

We present a guided-inquiry experiment using Spartan Student Version, ready to be adapted and implemented into a general chemistry laboratory course. The experiment provides students an experience with Spartan Molecular Modeling software while discovering the relationships between the structure and properties of molecules. Topics discussed within…

Integrated software environment based on COMKAT for analyzing tracer pharmacokinetics with molecular imaging.

PubMed

Fang, Yu-Hua Dean; Asthana, Pravesh; Salinas, Cristian; Huang, Hsuan-Ming; Muzic, Raymond F

2010-01-01

An integrated software package, Compartment Model Kinetic Analysis Tool (COMKAT), is presented in this report. COMKAT is an open-source software package with many functions for incorporating pharmacokinetic analysis in molecular imaging research and has both command-line and graphical user interfaces. With COMKAT, users may load and display images, draw regions of interest, load input functions, select kinetic models from a predefined list, or create a novel model and perform parameter estimation, all without having to write any computer code. For image analysis, COMKAT image tool supports multiple image file formats, including the Digital Imaging and Communications in Medicine (DICOM) standard. Image contrast, zoom, reslicing, display color table, and frame summation can be adjusted in COMKAT image tool. It also displays and automatically registers images from 2 modalities. Parametric imaging capability is provided and can be combined with the distributed computing support to enhance computation speeds. For users without MATLAB licenses, a compiled, executable version of COMKAT is available, although it currently has only a subset of the full COMKAT capability. Both the compiled and the noncompiled versions of COMKAT are free for academic research use. Extensive documentation, examples, and COMKAT itself are available on its wiki-based Web site, http://comkat.case.edu. Users are encouraged to contribute, sharing their experience, examples, and extensions of COMKAT. With integrated functionality specifically designed for imaging and kinetic modeling analysis, COMKAT can be used as a software environment for molecular imaging and pharmacokinetic analysis.

Modeling of diatomic molecule using the Morse potential and the Verlet algorithm

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fidiani, Elok

Performing molecular modeling usually uses special software for Molecular Dynamics (MD) such as: GROMACS, NAMD, JMOL etc. Molecular dynamics is a computational method to calculate the time dependent behavior of a molecular system. In this work, MATLAB was used as numerical method for a simple modeling of some diatomic molecules: HCl, H{sub 2} and O{sub 2}. MATLAB is a matrix based numerical software, in order to do numerical analysis, all the functions and equations describing properties of atoms and molecules must be developed manually in MATLAB. In this work, a Morse potential was generated to describe the bond interaction betweenmore » the two atoms. In order to analyze the simultaneous motion of molecules, the Verlet Algorithm derived from Newton’s Equations of Motion (classical mechanics) was operated. Both the Morse potential and the Verlet algorithm were integrated using MATLAB to derive physical properties and the trajectory of the molecules. The data computed by MATLAB is always in the form of a matrix. To visualize it, Visualized Molecular Dynamics (VMD) was performed. Such method is useful for development and testing some types of interaction on a molecular scale. Besides, this can be very helpful for describing some basic principles of molecular interaction for educational purposes.« less

MDWiZ: a platform for the automated translation of molecular dynamics simulations.

PubMed

Rusu, Victor H; Horta, Vitor A C; Horta, Bruno A C; Lins, Roberto D; Baron, Riccardo

2014-03-01

A variety of popular molecular dynamics (MD) simulation packages were independently developed in the last decades to reach diverse scientific goals. However, such non-coordinated development of software, force fields, and analysis tools for molecular simulations gave rise to an array of software formats and arbitrary conventions for routine preparation and analysis of simulation input and output data. Different formats and/or parameter definitions are used at each stage of the modeling process despite largely contain redundant information between alternative software tools. Such Babel of languages that cannot be easily and univocally translated one into another poses one of the major technical obstacles to the preparation, translation, and comparison of molecular simulation data that users face on a daily basis. Here, we present the MDWiZ platform, a freely accessed online portal designed to aid the fast and reliable preparation and conversion of file formats that allows researchers to reproduce or generate data from MD simulations using different setups, including force fields and models with different underlying potential forms. The general structure of MDWiZ is presented, the features of version 1.0 are detailed, and an extensive validation based on GROMACS to LAMMPS conversion is presented. We believe that MDWiZ will be largely useful to the molecular dynamics community. Such fast format and force field exchange for a given system allows tailoring the chosen system to a given computer platform and/or taking advantage of a specific capabilities offered by different software engines. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

Department of Defense High Performance Computing Modernization Program. 2006 Annual Report

DTIC Science & Technology

2007-03-01

Department. We successfully completed several software development projects that introduced parallel, scalable production software now in use across the...imagined. They are developing and deploying weather and ocean models that allow our soldiers, sailors, marines and airmen to plan missions more effectively...and to navigate adverse environments safely. They are modeling molecular interactions leading to the development of higher energy fuels, munitions

Development of Continuum-Atomistic Approach for Modeling Metal Irradiation by Heavy Ions

NASA Astrophysics Data System (ADS)

Batgerel, Balt; Dimova, Stefka; Puzynin, Igor; Puzynina, Taisia; Hristov, Ivan; Hristova, Radoslava; Tukhliev, Zafar; Sharipov, Zarif

2018-02-01

Over the last several decades active research in the field of materials irradiation by high-energy heavy ions has been worked out. The experiments in this area are labor-consuming and expensive. Therefore the improvement of the existing mathematical models and the development of new ones based on the experimental data of interaction of high-energy heavy ions with materials are of interest. Presently, two approaches are used for studying these processes: a thermal spike model and molecular dynamics methods. The combination of these two approaches - the continuous-atomistic model - will give the opportunity to investigate more thoroughly the processes of irradiation of materials by high-energy heavy ions. To solve the equations of the continuous-atomistic model, a software package was developed and the block of molecular dynamics software was tested on the heterogeneous cluster HybriLIT.

Complex molecular assemblies at hand via interactive simulations.

PubMed

Delalande, Olivier; Férey, Nicolas; Grasseau, Gilles; Baaden, Marc

2009-11-30

Studying complex molecular assemblies interactively is becoming an increasingly appealing approach to molecular modeling. Here we focus on interactive molecular dynamics (IMD) as a textbook example for interactive simulation methods. Such simulations can be useful in exploring and generating hypotheses about the structural and mechanical aspects of biomolecular interactions. For the first time, we carry out low-resolution coarse-grain IMD simulations. Such simplified modeling methods currently appear to be more suitable for interactive experiments and represent a well-balanced compromise between an important gain in computational speed versus a moderate loss in modeling accuracy compared to higher resolution all-atom simulations. This is particularly useful for initial exploration and hypothesis development for rare molecular interaction events. We evaluate which applications are currently feasible using molecular assemblies from 1900 to over 300,000 particles. Three biochemical systems are discussed: the guanylate kinase (GK) enzyme, the outer membrane protease T and the soluble N-ethylmaleimide-sensitive factor attachment protein receptors complex involved in membrane fusion. We induce large conformational changes, carry out interactive docking experiments, probe lipid-protein interactions and are able to sense the mechanical properties of a molecular model. Furthermore, such interactive simulations facilitate exploration of modeling parameters for method improvement. For the purpose of these simulations, we have developed a freely available software library called MDDriver. It uses the IMD protocol from NAMD and facilitates the implementation and application of interactive simulations. With MDDriver it becomes very easy to render any particle-based molecular simulation engine interactive. Here we use its implementation in the Gromacs software as an example. Copyright 2009 Wiley Periodicals, Inc.

MolPrint3D: Enhanced 3D Printing of Ball-and-Stick Molecular Models

ERIC Educational Resources Information Center

Paukstelis, Paul J.

2018-01-01

The increased availability of noncommercial 3D printers has provided instructors and students improved access to printing technology. However, printing complex ball-and-stick molecular structures faces distinct challenges, including the need for support structures that increase with molecular complexity. MolPrint3D is a software add-on for the…

The structural bioinformatics library: modeling in biomolecular science and beyond.

PubMed

Cazals, Frédéric; Dreyfus, Tom

2017-04-01

Software in structural bioinformatics has mainly been application driven. To favor practitioners seeking off-the-shelf applications, but also developers seeking advanced building blocks to develop novel applications, we undertook the design of the Structural Bioinformatics Library ( SBL , http://sbl.inria.fr ), a generic C ++/python cross-platform software library targeting complex problems in structural bioinformatics. Its tenet is based on a modular design offering a rich and versatile framework allowing the development of novel applications requiring well specified complex operations, without compromising robustness and performances. The SBL involves four software components (1-4 thereafter). For end-users, the SBL provides ready to use, state-of-the-art (1) applications to handle molecular models defined by unions of balls, to deal with molecular flexibility, to model macro-molecular assemblies. These applications can also be combined to tackle integrated analysis problems. For developers, the SBL provides a broad C ++ toolbox with modular design, involving core (2) algorithms , (3) biophysical models and (4) modules , the latter being especially suited to develop novel applications. The SBL comes with a thorough documentation consisting of user and reference manuals, and a bugzilla platform to handle community feedback. The SBL is available from http://sbl.inria.fr. Frederic.Cazals@inria.fr. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

An overview of the utility of population simulation software in molecular ecology.

PubMed

Hoban, Sean

2014-05-01

Stochastic simulation software that simultaneously model genetic, population and environmental processes can inform many topics in molecular ecology. These include forecasting species and community response to environmental change, inferring dispersal ecology, revealing cryptic mating, quantifying past population dynamics, assessing in situ management options and monitoring neutral and adaptive biodiversity change. Advances in population demographic-genetic simulation software, especially with respect to individual life history, landscapes and genetic processes, are transforming and expanding the ways that molecular data can be used. The aim of this review is to explain the roles that such software can play in molecular ecology studies (whether as a principal component or a supporting function) so that researchers can decide whether, when and precisely how simulations can be incorporated into their work. First, I use seven case studies to demonstrate how simulations are employed, their specific advantage/necessity and what alternative or complementary (nonsimulation) approaches are available. I also explain how simulations can be integrated with existing spatial, environmental, historical and genetic data sets. I next describe simulation features that may be of interest to molecular ecologists, such as spatial and behavioural considerations and species' interactions, to provide guidance on how particular simulation capabilities can serve particular needs. Lastly, I discuss the prospect of simulation software in emerging challenges (climate change, biodiversity monitoring, population exploitation) and opportunities (genomics, ancient DNA), in order to emphasize that the scope of simulation-based work is expanding. I also suggest practical considerations, priorities and elements of best practice. This should accelerate the uptake of simulation approaches and firmly embed them as a versatile tool in the molecular ecologist's toolbox. © 2014 John Wiley & Sons Ltd.

Descriptions and Implementations of DL_F Notation: A Natural Chemical Expression System of Atom Types for Molecular Simulations.

PubMed

Yong, Chin W

2016-08-22

DL_F Notation is an easy-to-understand, standardized atom typesetting expression for molecular simulations for a range of organic force field (FF) schemes such as OPLSAA, PCFF, and CVFF. It is implemented within DL_FIELD, a software program that facilitates the setting up of molecular FF models for DL_POLY molecular dynamics simulation software. By making use of the Notation, a single core conversion module (the DL_F conversion Engine) implemented within DL_FIELD can be used to analyze a molecular structure and determine the types of atoms for a given FF scheme. Users only need to provide the molecular input structure in a simple xyz format and DL_FIELD can produce the necessary force field file for DL_POLY automatically. In commensurate with the development concept of DL_FIELD, which placed emphasis on robustness and user friendliness, the Engine provides a single-step solution to setup complex FF models. This allows users to switch from one of the above-mentioned FF seamlessly to another while at the same time provides a consistent atom typing that is expressed in a natural chemical sense.

SYVA: A program to analyze symmetry of molecules based on vector algebra

NASA Astrophysics Data System (ADS)

Gyevi-Nagy, László; Tasi, Gyula

2017-06-01

Symmetry is a useful concept in physics and chemistry. It can be used to find out some simple properties of a molecule or simplify complex calculations. In this paper a simple vector algebraic method is described to determine all symmetry elements of an arbitrary molecule. To carry out the symmetry analysis, a program has been written, which is also capable of generating the framework group of the molecule, revealing the symmetry properties of normal modes of vibration and symmetrizing the structure. To demonstrate the capabilities of the program, it is compared to other common widely used stand-alone symmetry analyzer (SYMMOL, Symmetrizer) and molecular modeling (NWChem, ORCA, MRCC) software. SYVA can generate input files for molecular modeling programs, e.g. Gaussian, using precisely symmetrized molecular structures. Possible applications are also demonstrated by integrating SYVA with the GAMESS and MRCC software.

Fragment-Based Docking: Development of the CHARMMing Web User Interface as a Platform for Computer-Aided Drug Design

PubMed Central

2015-01-01

Web-based user interfaces to scientific applications are important tools that allow researchers to utilize a broad range of software packages with just an Internet connection and a browser.1 One such interface, CHARMMing (CHARMM interface and graphics), facilitates access to the powerful and widely used molecular software package CHARMM. CHARMMing incorporates tasks such as molecular structure analysis, dynamics, multiscale modeling, and other techniques commonly used by computational life scientists. We have extended CHARMMing’s capabilities to include a fragment-based docking protocol that allows users to perform molecular docking and virtual screening calculations either directly via the CHARMMing Web server or on computing resources using the self-contained job scripts generated via the Web interface. The docking protocol was evaluated by performing a series of “re-dockings” with direct comparison to top commercial docking software. Results of this evaluation showed that CHARMMing’s docking implementation is comparable to many widely used software packages and validates the use of the new CHARMM generalized force field for docking and virtual screening. PMID:25151852

Fragment-based docking: development of the CHARMMing Web user interface as a platform for computer-aided drug design.

PubMed

Pevzner, Yuri; Frugier, Emilie; Schalk, Vinushka; Caflisch, Amedeo; Woodcock, H Lee

2014-09-22

Web-based user interfaces to scientific applications are important tools that allow researchers to utilize a broad range of software packages with just an Internet connection and a browser. One such interface, CHARMMing (CHARMM interface and graphics), facilitates access to the powerful and widely used molecular software package CHARMM. CHARMMing incorporates tasks such as molecular structure analysis, dynamics, multiscale modeling, and other techniques commonly used by computational life scientists. We have extended CHARMMing's capabilities to include a fragment-based docking protocol that allows users to perform molecular docking and virtual screening calculations either directly via the CHARMMing Web server or on computing resources using the self-contained job scripts generated via the Web interface. The docking protocol was evaluated by performing a series of "re-dockings" with direct comparison to top commercial docking software. Results of this evaluation showed that CHARMMing's docking implementation is comparable to many widely used software packages and validates the use of the new CHARMM generalized force field for docking and virtual screening.

SWIFT MODELLER: a Java based GUI for molecular modeling.

PubMed

Mathur, Abhinav; Shankaracharya; Vidyarthi, Ambarish S

2011-10-01

MODELLER is command line argument based software which requires tedious formatting of inputs and writing of Python scripts which most people are not comfortable with. Also the visualization of output becomes cumbersome due to verbose files. This makes the whole software protocol very complex and requires extensive study of MODELLER manuals and tutorials. Here we describe SWIFT MODELLER, a GUI that automates formatting, scripting and data extraction processes and present it in an interactive way making MODELLER much easier to use than before. The screens in SWIFT MODELLER are designed keeping homology modeling in mind and their flow is a depiction of its steps. It eliminates the formatting of inputs, scripting processes and analysis of verbose output files through automation and makes pasting of the target sequence as the only prerequisite. Jmol (3D structure visualization tool) has been integrated into the GUI which opens and demonstrates the protein data bank files created by the MODELLER software. All files required and created by the software are saved in a folder named after the work instance's date and time of execution. SWIFT MODELLER lowers the skill level required for the software through automation of many of the steps in the original software protocol, thus saving an enormous amount of time per instance and making MODELLER very easy to work with.

URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries.

PubMed

Drawert, Brian; Engblom, Stefan; Hellander, Andreas

2012-06-22

Experiments in silico using stochastic reaction-diffusion models have emerged as an important tool in molecular systems biology. Designing computational software for such applications poses several challenges. Firstly, realistic lattice-based modeling for biological applications requires a consistent way of handling complex geometries, including curved inner- and outer boundaries. Secondly, spatiotemporal stochastic simulations are computationally expensive due to the fast time scales of individual reaction- and diffusion events when compared to the biological phenomena of actual interest. We therefore argue that simulation software needs to be both computationally efficient, employing sophisticated algorithms, yet in the same time flexible in order to meet present and future needs of increasingly complex biological modeling. We have developed URDME, a flexible software framework for general stochastic reaction-transport modeling and simulation. URDME uses Unstructured triangular and tetrahedral meshes to resolve general geometries, and relies on the Reaction-Diffusion Master Equation formalism to model the processes under study. An interface to a mature geometry and mesh handling external software (Comsol Multiphysics) provides for a stable and interactive environment for model construction. The core simulation routines are logically separated from the model building interface and written in a low-level language for computational efficiency. The connection to the geometry handling software is realized via a Matlab interface which facilitates script computing, data management, and post-processing. For practitioners, the software therefore behaves much as an interactive Matlab toolbox. At the same time, it is possible to modify and extend URDME with newly developed simulation routines. Since the overall design effectively hides the complexity of managing the geometry and meshes, this means that newly developed methods may be tested in a realistic setting already at an early stage of development. In this paper we demonstrate, in a series of examples with high relevance to the molecular systems biology community, that the proposed software framework is a useful tool for both practitioners and developers of spatial stochastic simulation algorithms. Through the combined efforts of algorithm development and improved modeling accuracy, increasingly complex biological models become feasible to study through computational methods. URDME is freely available at http://www.urdme.org.

KinImmerse: Macromolecular VR for NMR ensembles

PubMed Central

Block, Jeremy N; Zielinski, David J; Chen, Vincent B; Davis, Ian W; Vinson, E Claire; Brady, Rachael; Richardson, Jane S; Richardson, David C

2009-01-01

Background In molecular applications, virtual reality (VR) and immersive virtual environments have generally been used and valued for the visual and interactive experience – to enhance intuition and communicate excitement – rather than as part of the actual research process. In contrast, this work develops a software infrastructure for research use and illustrates such use on a specific case. Methods The Syzygy open-source toolkit for VR software was used to write the KinImmerse program, which translates the molecular capabilities of the kinemage graphics format into software for display and manipulation in the DiVE (Duke immersive Virtual Environment) or other VR system. KinImmerse is supported by the flexible display construction and editing features in the KiNG kinemage viewer and it implements new forms of user interaction in the DiVE. Results In addition to molecular visualizations and navigation, KinImmerse provides a set of research tools for manipulation, identification, co-centering of multiple models, free-form 3D annotation, and output of results. The molecular research test case analyzes the local neighborhood around an individual atom within an ensemble of nuclear magnetic resonance (NMR) models, enabling immersive visual comparison of the local conformation with the local NMR experimental data, including target curves for residual dipolar couplings (RDCs). Conclusion The promise of KinImmerse for production-level molecular research in the DiVE is shown by the locally co-centered RDC visualization developed there, which gave new insights now being pursued in wider data analysis. PMID:19222844

Asynchronous Replica Exchange Software for Grid and Heterogeneous Computing.

PubMed

Gallicchio, Emilio; Xia, Junchao; Flynn, William F; Zhang, Baofeng; Samlalsingh, Sade; Mentes, Ahmet; Levy, Ronald M

2015-11-01

Parallel replica exchange sampling is an extended ensemble technique often used to accelerate the exploration of the conformational ensemble of atomistic molecular simulations of chemical systems. Inter-process communication and coordination requirements have historically discouraged the deployment of replica exchange on distributed and heterogeneous resources. Here we describe the architecture of a software (named ASyncRE) for performing asynchronous replica exchange molecular simulations on volunteered computing grids and heterogeneous high performance clusters. The asynchronous replica exchange algorithm on which the software is based avoids centralized synchronization steps and the need for direct communication between remote processes. It allows molecular dynamics threads to progress at different rates and enables parameter exchanges among arbitrary sets of replicas independently from other replicas. ASyncRE is written in Python following a modular design conducive to extensions to various replica exchange schemes and molecular dynamics engines. Applications of the software for the modeling of association equilibria of supramolecular and macromolecular complexes on BOINC campus computational grids and on the CPU/MIC heterogeneous hardware of the XSEDE Stampede supercomputer are illustrated. They show the ability of ASyncRE to utilize large grids of desktop computers running the Windows, MacOS, and/or Linux operating systems as well as collections of high performance heterogeneous hardware devices.

DockoMatic 2.0: high throughput inverse virtual screening and homology modeling.

PubMed

Bullock, Casey; Cornia, Nic; Jacob, Reed; Remm, Andrew; Peavey, Thomas; Weekes, Ken; Mallory, Chris; Oxford, Julia T; McDougal, Owen M; Andersen, Timothy L

2013-08-26

DockoMatic is a free and open source application that unifies a suite of software programs within a user-friendly graphical user interface (GUI) to facilitate molecular docking experiments. Here we describe the release of DockoMatic 2.0; significant software advances include the ability to (1) conduct high throughput inverse virtual screening (IVS); (2) construct 3D homology models; and (3) customize the user interface. Users can now efficiently setup, start, and manage IVS experiments through the DockoMatic GUI by specifying receptor(s), ligand(s), grid parameter file(s), and docking engine (either AutoDock or AutoDock Vina). DockoMatic automatically generates the needed experiment input files and output directories and allows the user to manage and monitor job progress. Upon job completion, a summary of results is generated by Dockomatic to facilitate interpretation by the user. DockoMatic functionality has also been expanded to facilitate the construction of 3D protein homology models using the Timely Integrated Modeler (TIM) wizard. The wizard TIM provides an interface that accesses the basic local alignment search tool (BLAST) and MODELER programs and guides the user through the necessary steps to easily and efficiently create 3D homology models for biomacromolecular structures. The DockoMatic GUI can be customized by the user, and the software design makes it relatively easy to integrate additional docking engines, scoring functions, or third party programs. DockoMatic is a free comprehensive molecular docking software program for all levels of scientists in both research and education.

An Overview of Mesoscale Modeling Software for Energetic Materials Research

DTIC Science & Technology

2010-03-01

12 2.9 Large-scale Atomic/Molecular Massively Parallel Simulator ( LAMMPS ...13 Table 10. LAMMPS summary...extensive reviews, lectures and workshops are available on multiscale modeling of materials applications (76-78). • Multi-phase mixtures of

Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perkins, Stephen J.; Wright, David W.; Zhang, Hailiang

2016-10-14

The capabilities of current computer simulations provide a unique opportunity to model small-angle scattering (SAS) data at the atomistic level, and to include other structural constraints ranging from molecular and atomistic energetics to crystallography, electron microscopy and NMR. This extends the capabilities of solution scattering and provides deeper insights into the physics and chemistry of the systems studied. Realizing this potential, however, requires integrating the experimental data with a new generation of modelling software. To achieve this, the CCP-SAS collaboration (http://www.ccpsas.org/) is developing open-source, high-throughput and user-friendly software for the atomistic and coarse-grained molecular modelling of scattering data. Robust state-of-the-artmore » molecular simulation engines and molecular dynamics and Monte Carlo force fields provide constraints to the solution structure inferred from the small-angle scattering data, which incorporates the known physical chemistry of the system. The implementation of this software suite involves a tiered approach in whichGenAppprovides the deployment infrastructure for running applications on both standard and high-performance computing hardware, andSASSIEprovides a workflow framework into which modules can be plugged to prepare structures, carry out simulations, calculate theoretical scattering data and compare results with experimental data.GenAppproduces the accessible web-based front end termedSASSIE-web, andGenAppandSASSIEalso make community SAS codes available. Applications are illustrated by case studies: (i) inter-domain flexibility in two- to six-domain proteins as exemplified by HIV-1 Gag, MASP and ubiquitin; (ii) the hinge conformation in human IgG2 and IgA1 antibodies; (iii) the complex formed between a hexameric protein Hfq and mRNA; and (iv) synthetic `bottlebrush' polymers.« less

Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS).

PubMed

Perkins, Stephen J; Wright, David W; Zhang, Hailiang; Brookes, Emre H; Chen, Jianhan; Irving, Thomas C; Krueger, Susan; Barlow, David J; Edler, Karen J; Scott, David J; Terrill, Nicholas J; King, Stephen M; Butler, Paul D; Curtis, Joseph E

2016-12-01

The capabilities of current computer simulations provide a unique opportunity to model small-angle scattering (SAS) data at the atomistic level, and to include other structural constraints ranging from molecular and atomistic energetics to crystallography, electron microscopy and NMR. This extends the capabilities of solution scattering and provides deeper insights into the physics and chemistry of the systems studied. Realizing this potential, however, requires integrating the experimental data with a new generation of modelling software. To achieve this, the CCP-SAS collaboration (http://www.ccpsas.org/) is developing open-source, high-throughput and user-friendly software for the atomistic and coarse-grained molecular modelling of scattering data. Robust state-of-the-art molecular simulation engines and molecular dynamics and Monte Carlo force fields provide constraints to the solution structure inferred from the small-angle scattering data, which incorporates the known physical chemistry of the system. The implementation of this software suite involves a tiered approach in which GenApp provides the deployment infrastructure for running applications on both standard and high-performance computing hardware, and SASSIE provides a workflow framework into which modules can be plugged to prepare structures, carry out simulations, calculate theoretical scattering data and compare results with experimental data. GenApp produces the accessible web-based front end termed SASSIE-web , and GenApp and SASSIE also make community SAS codes available. Applications are illustrated by case studies: (i) inter-domain flexibility in two- to six-domain proteins as exemplified by HIV-1 Gag, MASP and ubiquitin; (ii) the hinge conformation in human IgG2 and IgA1 antibodies; (iii) the complex formed between a hexameric protein Hfq and mRNA; and (iv) synthetic 'bottlebrush' polymers.

Computer aided drug design

NASA Astrophysics Data System (ADS)

Jain, A.

2017-08-01

Computer based method can help in discovery of leads and can potentially eliminate chemical synthesis and screening of many irrelevant compounds, and in this way, it save time as well as cost. Molecular modeling systems are powerful tools for building, visualizing, analyzing and storing models of complex molecular structure that can help to interpretate structure activity relationship. The use of various techniques of molecular mechanics and dynamics and software in Computer aided drug design along with statistics analysis is powerful tool for the medicinal chemistry to synthesis therapeutic and effective drugs with minimum side effect.

Genetic Testing Registry

MedlinePlus

... Splign Vector Alignment Search Tool (VAST) All Data & Software Resources... Domains & Structures BioSystems Cn3D Conserved Domain Database (CDD) Conserved Domain Search Service (CD Search) Structure (Molecular Modeling Database) Vector Alignment ...

Implementation of Shifted Periodic Boundary Conditions in the Large-Scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) Software

DTIC Science & Technology

2015-08-01

Atomic/Molecular Massively Parallel Simulator ( LAMMPS ) Software by N Scott Weingarten and James P Larentzos Approved for...Massively Parallel Simulator ( LAMMPS ) Software by N Scott Weingarten Weapons and Materials Research Directorate, ARL James P Larentzos Engility...Shifted Periodic Boundary Conditions in the Large-Scale Atomic/Molecular Massively Parallel Simulator ( LAMMPS ) Software 5a. CONTRACT NUMBER 5b

DockoMatic 2.0: High Throughput Inverse Virtual Screening and Homology Modeling

PubMed Central

Bullock, Casey; Cornia, Nic; Jacob, Reed; Remm, Andrew; Peavey, Thomas; Weekes, Ken; Mallory, Chris; Oxford, Julia T.; McDougal, Owen M.; Andersen, Timothy L.

2013-01-01

DockoMatic is a free and open source application that unifies a suite of software programs within a user-friendly Graphical User Interface (GUI) to facilitate molecular docking experiments. Here we describe the release of DockoMatic 2.0; significant software advances include the ability to: (1) conduct high throughput Inverse Virtual Screening (IVS); (2) construct 3D homology models; and (3) customize the user interface. Users can now efficiently setup, start, and manage IVS experiments through the DockoMatic GUI by specifying a receptor(s), ligand(s), grid parameter file(s), and docking engine (either AutoDock or AutoDock Vina). DockoMatic automatically generates the needed experiment input files and output directories, and allows the user to manage and monitor job progress. Upon job completion, a summary of results is generated by Dockomatic to facilitate interpretation by the user. DockoMatic functionality has also been expanded to facilitate the construction of 3D protein homology models using the Timely Integrated Modeler (TIM) wizard. The wizard TIM provides an interface that accesses the basic local alignment search tool (BLAST) and MODELLER programs, and guides the user through the necessary steps to easily and efficiently create 3D homology models for biomacromolecular structures. The DockoMatic GUI can be customized by the user, and the software design makes it relatively easy to integrate additional docking engines, scoring functions, or third party programs. DockoMatic is a free comprehensive molecular docking software program for all levels of scientists in both research and education. PMID:23808933

Evaluating the solution from MrBUMP and BALBES

PubMed Central

Keegan, Ronan M.; Long, Fei; Fazio, Vincent J.; Winn, Martyn D.; Murshudov, Garib N.; Vagin, Alexei A.

2011-01-01

Molecular replacement is one of the key methods used to solve the problem of determining the phases of structure factors in protein structure solution from X-ray image diffraction data. Its success rate has been steadily improving with the development of improved software methods and the increasing number of structures available in the PDB for use as search models. Despite this, in cases where there is low sequence identity between the target-structure sequence and that of its set of possible homologues it can be a difficult and time-consuming chore to isolate and prepare the best search model for molecular replacement. MrBUMP and BALBES are two recent developments from CCP4 that have been designed to automate and speed up the process of determining and preparing the best search models and putting them through molecular replacement. Their intention is to provide the user with a broad set of results using many search models and to highlight the best of these for further processing. An overview of both programs is presented along with a description of how best to use them, citing case studies and the results of large-scale testing of the software. PMID:21460449

Towards Archetypes-Based Software Development

NASA Astrophysics Data System (ADS)

Piho, Gunnar; Roost, Mart; Perkins, David; Tepandi, Jaak

We present a framework for the archetypes based engineering of domains, requirements and software (Archetypes-Based Software Development, ABD). An archetype is defined as a primordial object that occurs consistently and universally in business domains and in business software systems. An archetype pattern is a collaboration of archetypes. Archetypes and archetype patterns are used to capture conceptual information into domain specific models that are utilized by ABD. The focus of ABD is on software factories - family-based development artefacts (domain specific languages, patterns, frameworks, tools, micro processes, and others) that can be used to build the family members. We demonstrate the usage of ABD for developing laboratory information management system (LIMS) software for the Clinical and Biomedical Proteomics Group, at the Leeds Institute of Molecular Medicine, University of Leeds.

Modeling of DNA and Protein Organization Levels with Cn3D Software

ERIC Educational Resources Information Center

Stasinakis, Panagiotis K.; Nicolaou, Despoina

2017-01-01

The molecular structure of living organisms and the complex interactions amongst its components are the basis for the diversity observed at the macroscopic level. Proteins and nucleic acids are some of the major molecular components, and play a key role in several biological functions, such as those of development and evolution. This article…

National Center for Biotechnology Information

MedlinePlus

... Splign Vector Alignment Search Tool (VAST) All Data & Software Resources... Domains & Structures BioSystems Cn3D Conserved Domain Database (CDD) Conserved Domain Search Service (CD Search) Structure (Molecular Modeling Database) Vector Alignment ...

Modeling Carbon and Hydrocarbon Molecular Structures in EZTB

NASA Technical Reports Server (NTRS)

Lee, Seungwon; vonAllmen, Paul

2007-01-01

A software module that models the electronic and mechanical aspects of hydrocarbon molecules and carbon molecular structures on the basis of first principles has been written for incorporation into, and execution within, the Easy (Modular) Tight-Binding (EZTB) software infrastructure, which is summarized briefly in the immediately preceding article. Of particular interest, this module can model carbon crystals and nanotubes characterized by various coordinates and containing defects, without need to adjust parameters of the physical model. The module has been used to study the changes in electronic properties of carbon nanotubes, caused by bending of the nanotubes, for potential utility as the basis of a nonvolatile, electriccharge- free memory devices. For example, in one application of the module, it was found that an initially 50-nmlong carbon, (10,10)-chirality nanotube, which is a metallic conductor when straight, becomes a semiconductor with an energy gap of .3 meV when bent to a lateral displacement of 4 nm at the middle.

Diamond-like nanoparticles influence on flavonoids transport: molecular modelling

NASA Astrophysics Data System (ADS)

Plastun, Inna L.; Agandeeva, Ksenia E.; Bokarev, Andrey N.; Zenkin, Nikita S.

2017-03-01

Intermolecular interaction of diamond-like nanoparticles and flavonoids is investigated by numerical simulation. Using molecular modelling by the density functional theory method, we analyze hydrogen bonds formation and their influence on IR - spectra and structure of molecular complex which is formed due to interaction between flavonoids and nanodiamonds surrounded with carboxylic groups. Enriched adamantane (1,3,5,7 - adamantanetetracarboxylic acid) is used as an example of diamond-like nanoparticles. Intermolecular forces and structure of hydrogen bonds are investigated. IR - spectra and structure parameters of quercetin - adamantanetetracarboxylic acid molecular complex are obtained by numerical simulation using the Gaussian software complex. Received data coincide well with experimental results. Intermolecular interactions and hydrogen bonding structure in the obtained molecular complex are examined. Possibilities of flavonoids interaction with DNA at the molecular level are also considered.

PyEvolve: a toolkit for statistical modelling of molecular evolution.

PubMed

Butterfield, Andrew; Vedagiri, Vivek; Lang, Edward; Lawrence, Cath; Wakefield, Matthew J; Isaev, Alexander; Huttley, Gavin A

2004-01-05

Examining the distribution of variation has proven an extremely profitable technique in the effort to identify sequences of biological significance. Most approaches in the field, however, evaluate only the conserved portions of sequences - ignoring the biological significance of sequence differences. A suite of sophisticated likelihood based statistical models from the field of molecular evolution provides the basis for extracting the information from the full distribution of sequence variation. The number of different problems to which phylogeny-based maximum likelihood calculations can be applied is extensive. Available software packages that can perform likelihood calculations suffer from a lack of flexibility and scalability, or employ error-prone approaches to model parameterisation. Here we describe the implementation of PyEvolve, a toolkit for the application of existing, and development of new, statistical methods for molecular evolution. We present the object architecture and design schema of PyEvolve, which includes an adaptable multi-level parallelisation schema. The approach for defining new methods is illustrated by implementing a novel dinucleotide model of substitution that includes a parameter for mutation of methylated CpG's, which required 8 lines of standard Python code to define. Benchmarking was performed using either a dinucleotide or codon substitution model applied to an alignment of BRCA1 sequences from 20 mammals, or a 10 species subset. Up to five-fold parallel performance gains over serial were recorded. Compared to leading alternative software, PyEvolve exhibited significantly better real world performance for parameter rich models with a large data set, reducing the time required for optimisation from approximately 10 days to approximately 6 hours. PyEvolve provides flexible functionality that can be used either for statistical modelling of molecular evolution, or the development of new methods in the field. The toolkit can be used interactively or by writing and executing scripts. The toolkit uses efficient processes for specifying the parameterisation of statistical models, and implements numerous optimisations that make highly parameter rich likelihood functions solvable within hours on multi-cpu hardware. PyEvolve can be readily adapted in response to changing computational demands and hardware configurations to maximise performance. PyEvolve is released under the GPL and can be downloaded from http://cbis.anu.edu.au/software.

A Software Architecture for the Construction and Management of Real-Time Virtual Worlds

DTIC Science & Technology

1993-06-01

University of California, Berkeley [FUNK921. The second improvement was the addition of a radiosity light model. The use of radiosity and its use of diffuse...the viewpoint is stationary, the coarse polygon model is replaced by progressively more complex radiosity lit scenes. The area of molecular modeling

Rosetta3: An Object-Oriented Software Suite for the Simulation and Design of Macromolecules

PubMed Central

Leaver-Fay, Andrew; Tyka, Michael; Lewis, Steven M.; Lange, Oliver F.; Thompson, James; Jacak, Ron; Kaufman, Kristian; Renfrew, P. Douglas; Smith, Colin A.; Sheffler, Will; Davis, Ian W.; Cooper, Seth; Treuille, Adrien; Mandell, Daniel J.; Richter, Florian; Ban, Yih-En Andrew; Fleishman, Sarel J.; Corn, Jacob E.; Kim, David E.; Lyskov, Sergey; Berrondo, Monica; Mentzer, Stuart; Popović, Zoran; Havranek, James J.; Karanicolas, John; Das, Rhiju; Meiler, Jens; Kortemme, Tanja; Gray, Jeffrey J.; Kuhlman, Brian; Baker, David; Bradley, Philip

2013-01-01

We have recently completed a full re-architecturing of the Rosetta molecular modeling program, generalizing and expanding its existing functionality. The new architecture enables the rapid prototyping of novel protocols by providing easy to use interfaces to powerful tools for molecular modeling. The source code of this rearchitecturing has been released as Rosetta3 and is freely available for academic use. At the time of its release, it contained 470,000 lines of code. Counting currently unpublished protocols at the time of this writing, the source includes 1,285,000 lines. Its rapid growth is a testament to its ease of use. This document describes the requirements for our new architecture, justifies the design decisions, sketches out central classes, and highlights a few of the common tasks that the new software can perform. PMID:21187238

ReaDDy - A Software for Particle-Based Reaction-Diffusion Dynamics in Crowded Cellular Environments

PubMed Central

Schöneberg, Johannes; Noé, Frank

2013-01-01

We introduce the software package ReaDDy for simulation of detailed spatiotemporal mechanisms of dynamical processes in the cell, based on reaction-diffusion dynamics with particle resolution. In contrast to other particle-based reaction kinetics programs, ReaDDy supports particle interaction potentials. This permits effects such as space exclusion, molecular crowding and aggregation to be modeled. The biomolecules simulated can be represented as a sphere, or as a more complex geometry such as a domain structure or polymer chain. ReaDDy bridges the gap between small-scale but highly detailed molecular dynamics or Brownian dynamics simulations and large-scale but little-detailed reaction kinetics simulations. ReaDDy has a modular design that enables the exchange of the computing core by efficient platform-specific implementations or dynamical models that are different from Brownian dynamics. PMID:24040218

Lacosamide derivatives with anticonvulsant activity as carbonic anhydrase inhibitors. Molecular modeling, docking and QSAR analysis.

PubMed

Garro Martinez, Juan C; Vega-Hissi, Esteban G; Andrada, Matías F; Duchowicz, Pablo R; Torrens, Francisco; Estrada, Mario R

2014-01-01

Lacosamide is an anticonvulsant drug which presents carbonic anhydrase inhibition. In this paper, we analyzed the apparent relationship between both activities performing a molecular modeling, docking and QSAR studies on 18 lacosamide derivatives with known anticonvulsant activity. Docking results suggested the zinc-binding site of carbonic anhydrase is a possible target of lacosamide and lacosamide derivatives making favorable Van der Waals interactions with Asn67, Gln92, Phe131 and Thr200. The mathematical models revealed a poor relationship between the anticonvulsant activity and molecular descriptors obtained from DFT and docking calculations. However, a QSAR model was developed using Dragon software descriptors. The statistic parameters of the model are: correlation coefficient, R=0.957 and standard deviation, S=0.162. Our results provide new valuable information regarding the relationship between both activities and contribute important insights into the essential molecular requirements for the anticonvulsant activity.

Integrating Computational Chemistry into the Physical Chemistry Curriculum

ERIC Educational Resources Information Center

Johnson, Lewis E.; Engel, Thomas

2011-01-01

Relatively few undergraduate physical chemistry programs integrate molecular modeling into their quantum mechanics curriculum owing to concerns about limited access to computational facilities, the cost of software, and concerns about increasing the course material. However, modeling exercises can be integrated into an undergraduate course at a…

QSAR as a random event: modeling of nanoparticles uptake in PaCa2 cancer cells.

PubMed

Toropov, Andrey A; Toropova, Alla P; Puzyn, Tomasz; Benfenati, Emilio; Gini, Giuseppina; Leszczynska, Danuta; Leszczynski, Jerzy

2013-06-01

Quantitative structure-property/activity relationships (QSPRs/QSARs) are a tool to predict various endpoints for various substances. The "classic" QSPR/QSAR analysis is based on the representation of the molecular structure by the molecular graph. However, simplified molecular input-line entry system (SMILES) gradually becomes most popular representation of the molecular structure in the databases available on the Internet. Under such circumstances, the development of molecular descriptors calculated directly from SMILES becomes attractive alternative to "classic" descriptors. The CORAL software (http://www.insilico.eu/coral) is provider of SMILES-based optimal molecular descriptors which are aimed to correlate with various endpoints. We analyzed data set on nanoparticles uptake in PaCa2 pancreatic cancer cells. The data set includes 109 nanoparticles with the same core but different surface modifiers (small organic molecules). The concept of a QSAR as a random event is suggested in opposition to "classic" QSARs which are based on the only one distribution of available data into the training and the validation sets. In other words, five random splits into the "visible" training set and the "invisible" validation set were examined. The SMILES-based optimal descriptors (obtained by the Monte Carlo technique) for these splits are calculated with the CORAL software. The statistical quality of all these models is good. Copyright © 2013 Elsevier Ltd. All rights reserved.

High-Resolution Spectroscopic Database for the NASA Earth Observing System Program

NASA Technical Reports Server (NTRS)

Rothman, Laurence S.; Starr, David (Technical Monitor)

2002-01-01

The purpose of this project is to develop and enhance the HITRAN molecular spectroscopic database and associated software to support the observational programs of the Earth Observing System (EOS). In particular, the focus is on the EOS projects: the Atmospheric Infrared Sounder (AIRS), the High-Resolution Dynamics Limb Sounder (HIRDLS), Measurements of Pollution in the Troposphere (MOPITT), the Tropospheric Emission Spectrometer (TES), and the Stratospheric Aerosol and Gas Experiment (SAGE III). The data requirements of these programs in terms of spectroscopy are varied, but usually call for additional spectral parameters or improvements to existing molecular bands. In addition, cross-section data for heavier molecular species must be expanded and made amenable to modeling in remote sensing. The effort in the project also includes developing software and distribution to make access, manipulation, and use of HITRAN functional to the EOS program.

Small Business Innovations

NASA Technical Reports Server (NTRS)

1995-01-01

The PER-Force Handcontroller was originally developed for the International Space Station under a Johnson Space Center Small Business Innovation Research (SBIR) contract. Produced by Cybernet Systems Corporation, the unit is a force-reflecting system that manipulates robots or objects by "feel." The Handcontroller moves in six degrees of freedom, with real and virtual reality forces simulated by a 3-D molecular modeling software package. It is used in molecular modeling in metallurgy applications, satellite docking research, and in research on military unmanned ground vehicles.

Modeling Complex Workflow in Molecular Diagnostics

PubMed Central

Gomah, Mohamed E.; Turley, James P.; Lu, Huimin; Jones, Dan

2010-01-01

One of the hurdles to achieving personalized medicine has been implementing the laboratory processes for performing and reporting complex molecular tests. The rapidly changing test rosters and complex analysis platforms in molecular diagnostics have meant that many clinical laboratories still use labor-intensive manual processing and testing without the level of automation seen in high-volume chemistry and hematology testing. We provide here a discussion of design requirements and the results of implementation of a suite of lab management tools that incorporate the many elements required for use of molecular diagnostics in personalized medicine, particularly in cancer. These applications provide the functionality required for sample accessioning and tracking, material generation, and testing that are particular to the evolving needs of individualized molecular diagnostics. On implementation, the applications described here resulted in improvements in the turn-around time for reporting of more complex molecular test sets, and significant changes in the workflow. Therefore, careful mapping of workflow can permit design of software applications that simplify even the complex demands of specialized molecular testing. By incorporating design features for order review, software tools can permit a more personalized approach to sample handling and test selection without compromising efficiency. PMID:20007844

Assessment of atmospheric distribution of polycyclic aromatic hydrocarbons using a molecular structure model

NASA Astrophysics Data System (ADS)

Turk Sekulić, Maja; Okuka, Marija; Šenk, Nevena; Radonić, Jelena; Vojinović Miloradov, Mirjana; Vidicki, Branko

2013-07-01

In this paper, a comparison of experimentally obtained and SPARC software v4.6 modelled values of gas/particle partitioning coefficients was conducted to determine whether the evaluation of atmospheric distribution of PAH molecules can be performed using a molecular structure model. Partitioning coefficients were calculated for sixteen EPA PAHs, in thirty-nine samples of ambient air collected at nineteen urban, industrial, highly contaminated and background sites in the Republic of Serbia and Bosnia and Herzegovina. For obtaining samples of ambient air, the conventional high volume (Hi-Vol) methodology was applied, whereby gaseous and particulate phase data collection was conducted simultaneously by glass fibre filters (GFFs) and polyurethane foam filters (PUFs). The best prediction was for PAHs with 5 or more rings (benzo(b)fluoranthene, benzo(k)fluoranthene, benzo(a)pyrene, indeno(1,2,3-cd)perylene and benzo(ghi)perylene). For evaluating the applicability of SPARC software predictions of gas/particle partitioning coefficients for the existing conditions, the results were compared with those obtained by applying other frequently used and highly ranked theoretical models of phase distributions, namely Junge-Pankow adsorption model, KOA absorption model, Dachs-Eisenreich dual model and PP-LFER model.

SMOG 2: A Versatile Software Package for Generating Structure-Based Models.

PubMed

Noel, Jeffrey K; Levi, Mariana; Raghunathan, Mohit; Lammert, Heiko; Hayes, Ryan L; Onuchic, José N; Whitford, Paul C

2016-03-01

Molecular dynamics simulations with coarse-grained or simplified Hamiltonians have proven to be an effective means of capturing the functionally important long-time and large-length scale motions of proteins and RNAs. Originally developed in the context of protein folding, structure-based models (SBMs) have since been extended to probe a diverse range of biomolecular processes, spanning from protein and RNA folding to functional transitions in molecular machines. The hallmark feature of a structure-based model is that part, or all, of the potential energy function is defined by a known structure. Within this general class of models, there exist many possible variations in resolution and energetic composition. SMOG 2 is a downloadable software package that reads user-designated structural information and user-defined energy definitions, in order to produce the files necessary to use SBMs with high performance molecular dynamics packages: GROMACS and NAMD. SMOG 2 is bundled with XML-formatted template files that define commonly used SBMs, and it can process template files that are altered according to the needs of each user. This computational infrastructure also allows for experimental or bioinformatics-derived restraints or novel structural features to be included, e.g. novel ligands, prosthetic groups and post-translational/transcriptional modifications. The code and user guide can be downloaded at http://smog-server.org/smog2.

Molecular radiotherapy: the NUKFIT software for calculating the time-integrated activity coefficient.

PubMed

Kletting, P; Schimmel, S; Kestler, H A; Hänscheid, H; Luster, M; Fernández, M; Bröer, J H; Nosske, D; Lassmann, M; Glatting, G

2013-10-01

Calculation of the time-integrated activity coefficient (residence time) is a crucial step in dosimetry for molecular radiotherapy. However, available software is deficient in that it is either not tailored for the use in molecular radiotherapy and/or does not include all required estimation methods. The aim of this work was therefore the development and programming of an algorithm which allows for an objective and reproducible determination of the time-integrated activity coefficient and its standard error. The algorithm includes the selection of a set of fitting functions from predefined sums of exponentials and the choice of an error model for the used data. To estimate the values of the adjustable parameters an objective function, depending on the data, the parameters of the error model, the fitting function and (if required and available) Bayesian information, is minimized. To increase reproducibility and user-friendliness the starting values are automatically determined using a combination of curve stripping and random search. Visual inspection, the coefficient of determination, the standard error of the fitted parameters, and the correlation matrix are provided to evaluate the quality of the fit. The functions which are most supported by the data are determined using the corrected Akaike information criterion. The time-integrated activity coefficient is estimated by analytically integrating the fitted functions. Its standard error is determined assuming Gaussian error propagation. The software was implemented using MATLAB. To validate the proper implementation of the objective function and the fit functions, the results of NUKFIT and SAAM numerical, a commercially available software tool, were compared. The automatic search for starting values was successfully tested for reproducibility. The quality criteria applied in conjunction with the Akaike information criterion allowed the selection of suitable functions. Function fit parameters and their standard error estimated by using SAAM numerical and NUKFIT showed differences of <1%. The differences for the time-integrated activity coefficients were also <1% (standard error between 0.4% and 3%). In general, the application of the software is user-friendly and the results are mathematically correct and reproducible. An application of NUKFIT is presented for three different clinical examples. The software tool with its underlying methodology can be employed to objectively and reproducibly estimate the time integrated activity coefficient and its standard error for most time activity data in molecular radiotherapy.

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

PubMed Central

Pronk, Sander; Páll, Szilárd; Schulz, Roland; Larsson, Per; Bjelkmar, Pär; Apostolov, Rossen; Shirts, Michael R.; Smith, Jeremy C.; Kasson, Peter M.; van der Spoel, David; Hess, Berk; Lindahl, Erik

2013-01-01

Motivation: Molecular simulation has historically been a low-throughput technique, but faster computers and increasing amounts of genomic and structural data are changing this by enabling large-scale automated simulation of, for instance, many conformers or mutants of biomolecules with or without a range of ligands. At the same time, advances in performance and scaling now make it possible to model complex biomolecular interaction and function in a manner directly testable by experiment. These applications share a need for fast and efficient software that can be deployed on massive scale in clusters, web servers, distributed computing or cloud resources. Results: Here, we present a range of new simulation algorithms and features developed during the past 4 years, leading up to the GROMACS 4.5 software package. The software now automatically handles wide classes of biomolecules, such as proteins, nucleic acids and lipids, and comes with all commonly used force fields for these molecules built-in. GROMACS supports several implicit solvent models, as well as new free-energy algorithms, and the software now uses multithreading for efficient parallelization even on low-end systems, including windows-based workstations. Together with hand-tuned assembly kernels and state-of-the-art parallelization, this provides extremely high performance and cost efficiency for high-throughput as well as massively parallel simulations. Availability: GROMACS is an open source and free software available from http://www.gromacs.org. Contact: erik.lindahl@scilifelab.se Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23407358

Binding Energy Calculation of Patchouli Alcohol Isomer Cyclooxygenase Complexes Suggested as COX-1/COX-2 Selective Inhibitor

PubMed Central

Mahdi, Chanif; Nurdiana, Nurdiana; Kikuchi, Takheshi; Fatchiyah, Fatchiyah

2014-01-01

To understand the structural features that dictate the selectivity of the two isoforms of the prostaglandin H2 synthase (PGHS/COX), the three-dimensional (3D) structure of COX-1/COX-2 was assessed by means of binding energy calculation of virtual molecular dynamic with using ligand alpha-Patchouli alcohol isomers. Molecular interaction studies with COX-1 and COX-2 were done using the molecular docking tools by Hex 8.0. Interactions were further visualized by using Discovery Studio Client 3.5 software tool. The binding energy of molecular interaction was calculated by AMBER12 and Virtual Molecular Dynamic 1.9.1 software. The analysis of the alpha-Patchouli alcohol isomer compounds showed that all alpha-Patchouli alcohol isomers were suggested as inhibitor of COX-1 and COX-2. Collectively, the scoring binding energy calculation (with PBSA Model Solvent) of alpha-Patchouli alcohol isomer compounds (CID442384, CID6432585, CID3080622, CID10955174, and CID56928117) was suggested as candidate for a selective COX-1 inhibitor and CID521903 as nonselective COX-1/COX-2. PMID:25484897

Modeling Molecules

NASA Technical Reports Server (NTRS)

2000-01-01

The molecule modeling method known as Multibody Order (N) Dynamics, or MBO(N)D, was developed by Moldyn, Inc. at Goddard Space Flight Center through funding provided by the SBIR program. The software can model the dynamics of molecules through technology which stimulates low-frequency molecular motions and properties, such as movements among a molecule's constituent parts. With MBO(N)D, a molecule is substructured into a set of interconnected rigid and flexible bodies. These bodies replace the computation burden of mapping individual atoms. Moldyn's technology cuts computation time while increasing accuracy. The MBO(N)D technology is available as Insight II 97.0 from Molecular Simulations, Inc. Currently the technology is used to account for forces on spacecraft parts and to perform molecular analyses for pharmaceutical purposes. It permits the solution of molecular dynamics problems on a moderate workstation, as opposed to on a supercomputer.

Separation and purification of thymopentin with molecular imprinting membrane by solid phase extraction disks.

PubMed

Wang, Chaoli; Hu, Xiaoling; Guan, Ping; Wu, Danfeng; Qian, Liwei; Li, Ji; Song, Renyuan

2015-01-01

The synthesis and performance of molecularly imprinted membranes (MIMs) as a solid phase extraction packing materials for the separation and purification of thymopentin from crude samples was described. In order to increase structural selectivity and imprinting efficiency, surface-initiated ATRP and ionic liquid (1-vinyl-3-ethyl acetate imidazolium chloride) were used to prepare molecularly imprinting membranes. The results demonstrated that solid phase extraction disks stuffed by MIMs with ionic liquids as functional monomer demonstrated high isolation and purification of performance to the thymopentin. The molecular recognition of thymopentin was analyzed by using molecular modeling software. Copyright © 2014 Elsevier B.V. All rights reserved.

LIQUID: an-open source software for identifying lipids in LC-MS/MS-based lipidomics data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kyle, Jennifer E.; Crowell, Kevin L.; Casey, Cameron P.

2017-01-31

We introduce an open-source software, LIQUID, for semi-automated processing and visualization of LC-MS/MS based lipidomics data. LIQUID provides users with the capability to process high throughput data and contains a customizable target library and scoring model per project needs. The graphical user interface provides visualization of multiple lines of spectral evidence for each lipid identification, allowing rapid examination of data for making confident identifications of lipid molecular species.

A Computational Systems Biology Software Platform for Multiscale Modeling and Simulation: Integrating Whole-Body Physiology, Disease Biology, and Molecular Reaction Networks

PubMed Central

Eissing, Thomas; Kuepfer, Lars; Becker, Corina; Block, Michael; Coboeken, Katrin; Gaub, Thomas; Goerlitz, Linus; Jaeger, Juergen; Loosen, Roland; Ludewig, Bernd; Meyer, Michaela; Niederalt, Christoph; Sevestre, Michael; Siegmund, Hans-Ulrich; Solodenko, Juri; Thelen, Kirstin; Telle, Ulrich; Weiss, Wolfgang; Wendl, Thomas; Willmann, Stefan; Lippert, Joerg

2011-01-01

Today, in silico studies and trial simulations already complement experimental approaches in pharmaceutical R&D and have become indispensable tools for decision making and communication with regulatory agencies. While biology is multiscale by nature, project work, and software tools usually focus on isolated aspects of drug action, such as pharmacokinetics at the organism scale or pharmacodynamic interaction on the molecular level. We present a modeling and simulation software platform consisting of PK-Sim® and MoBi® capable of building and simulating models that integrate across biological scales. A prototypical multiscale model for the progression of a pancreatic tumor and its response to pharmacotherapy is constructed and virtual patients are treated with a prodrug activated by hepatic metabolization. Tumor growth is driven by signal transduction leading to cell cycle transition and proliferation. Free tumor concentrations of the active metabolite inhibit Raf kinase in the signaling cascade and thereby cell cycle progression. In a virtual clinical study, the individual therapeutic outcome of the chemotherapeutic intervention is simulated for a large population with heterogeneous genomic background. Thereby, the platform allows efficient model building and integration of biological knowledge and prior data from all biological scales. Experimental in vitro model systems can be linked with observations in animal experiments and clinical trials. The interplay between patients, diseases, and drugs and topics with high clinical relevance such as the role of pharmacogenomics, drug–drug, or drug–metabolite interactions can be addressed using this mechanistic, insight driven multiscale modeling approach. PMID:21483730

JAMI: a Java library for molecular interactions and data interoperability.

PubMed

Sivade Dumousseau, M; Koch, M; Shrivastava, A; Alonso-López, D; De Las Rivas, J; Del-Toro, N; Combe, C W; Meldal, B H M; Heimbach, J; Rappsilber, J; Sullivan, J; Yehudi, Y; Orchard, S

2018-04-11

A number of different molecular interactions data download formats now exist, designed to allow access to these valuable data by diverse user groups. These formats include the PSI-XML and MITAB standard interchange formats developed by Molecular Interaction workgroup of the HUPO-PSI in addition to other, use-specific downloads produced by other resources. The onus is currently on the user to ensure that a piece of software is capable of read/writing all necessary versions of each format. This problem may increase, as data providers strive to meet ever more sophisticated user demands and data types. A collaboration between EMBL-EBI and the University of Cambridge has produced JAMI, a single library to unify standard molecular interaction data formats such as PSI-MI XML and PSI-MITAB. The JAMI free, open-source library enables the development of molecular interaction computational tools and pipelines without the need to produce different versions of software to read different versions of the data formats. Software and tools developed on top of the JAMI framework are able to integrate and support both PSI-MI XML and PSI-MITAB. The use of JAMI avoids the requirement to chain conversions between formats in order to reach a desired output format and prevents code and unit test duplication as the code becomes more modular. JAMI's model interfaces are abstracted from the underlying format, hiding the complexity and requirements of each data format from developers using JAMI as a library.

DiffPy-CMI-Python libraries for Complex Modeling Initiative

DOE Office of Scientific and Technical Information (OSTI.GOV)

Billinge, Simon; Juhas, Pavol; Farrow, Christopher

2014-02-01

Software to manipulate and describe crystal and molecular structures and set up structural refinements from multiple experimental inputs. Calculation and simulation of structure derived physical quantities. Library for creating customized refinements of atomic structures from available experimental and theoretical inputs.

A component-based software environment for visualizing large macromolecular assemblies.

PubMed

Sanner, Michel F

2005-03-01

The interactive visualization of large biological assemblies poses a number of challenging problems, including the development of multiresolution representations and new interaction methods for navigating and analyzing these complex systems. An additional challenge is the development of flexible software environments that will facilitate the integration and interoperation of computational models and techniques from a wide variety of scientific disciplines. In this paper, we present a component-based software development strategy centered on the high-level, object-oriented, interpretive programming language: Python. We present several software components, discuss their integration, and describe some of their features that are relevant to the visualization of large molecular assemblies. Several examples are given to illustrate the interoperation of these software components and the integration of structural data from a variety of experimental sources. These examples illustrate how combining visual programming with component-based software development facilitates the rapid prototyping of novel visualization tools.

An undergraduate laboratory activity on molecular dynamics simulations.

PubMed

Spitznagel, Benjamin; Pritchett, Paige R; Messina, Troy C; Goadrich, Mark; Rodriguez, Juan

2016-01-01

Vision and Change [AAAS, 2011] outlines a blueprint for modernizing biology education by addressing conceptual understanding of key concepts, such as the relationship between structure and function. The document also highlights skills necessary for student success in 21st century Biology, such as the use of modeling and simulation. Here we describe a laboratory activity that allows students to investigate the dynamic nature of protein structure and function through the use of a modeling technique known as molecular dynamics (MD). The activity takes place over two lab periods that are 3 hr each. The first lab period unpacks the basic approach behind MD simulations, beginning with the kinematic equations that all bioscience students learn in an introductory physics course. During this period students are taught rudimentary programming skills in Python while guided through simple modeling exercises that lead up to the simulation of the motion of a single atom. In the second lab period students extend concepts learned in the first period to develop skills in the use of expert MD software. Here students simulate and analyze changes in protein conformation resulting from temperature change, solvation, and phosphorylation. The article will describe how these activities can be carried out using free software packages, including Abalone and VMD/NAMD. © 2016 The International Union of Biochemistry and Molecular Biology.

The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable

PubMed Central

2016-01-01

Reconstructing and understanding the Human Physiome virtually is a complex mathematical problem, and a highly demanding computational challenge. Mathematical models spanning from the molecular level through to whole populations of individuals must be integrated, then personalized. This requires interoperability with multiple disparate and geographically separated data sources, and myriad computational software tools. Extracting and producing knowledge from such sources, even when the databases and software are readily available, is a challenging task. Despite the difficulties, researchers must frequently perform these tasks so that available knowledge can be continually integrated into the common framework required to realize the Human Physiome. Software and infrastructures that support the communities that generate these, together with their underlying standards to format, describe and interlink the corresponding data and computer models, are pivotal to the Human Physiome being realized. They provide the foundations for integrating, exchanging and re-using data and models efficiently, and correctly, while also supporting the dissemination of growing knowledge in these forms. In this paper, we explore the standards, software tooling, repositories and infrastructures that support this work, and detail what makes them vital to realizing the Human Physiome. PMID:27051515

The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable.

PubMed

Nickerson, David; Atalag, Koray; de Bono, Bernard; Geiger, Jörg; Goble, Carole; Hollmann, Susanne; Lonien, Joachim; Müller, Wolfgang; Regierer, Babette; Stanford, Natalie J; Golebiewski, Martin; Hunter, Peter

2016-04-06

Reconstructing and understanding the Human Physiome virtually is a complex mathematical problem, and a highly demanding computational challenge. Mathematical models spanning from the molecular level through to whole populations of individuals must be integrated, then personalized. This requires interoperability with multiple disparate and geographically separated data sources, and myriad computational software tools. Extracting and producing knowledge from such sources, even when the databases and software are readily available, is a challenging task. Despite the difficulties, researchers must frequently perform these tasks so that available knowledge can be continually integrated into the common framework required to realize the Human Physiome. Software and infrastructures that support the communities that generate these, together with their underlying standards to format, describe and interlink the corresponding data and computer models, are pivotal to the Human Physiome being realized. They provide the foundations for integrating, exchanging and re-using data and models efficiently, and correctly, while also supporting the dissemination of growing knowledge in these forms. In this paper, we explore the standards, software tooling, repositories and infrastructures that support this work, and detail what makes them vital to realizing the Human Physiome.

Infrared and Raman Spectroscopy: A Discovery-Based Activity for the General Chemistry Curriculum

ERIC Educational Resources Information Center

Borgsmiller, Karen L.; O'Connell, Dylan J.; Klauenberg, Kathryn M.; Wilson, Peter M.; Stromberg, Christopher J.

2012-01-01

A discovery-based method is described for incorporating the concepts of IR and Raman spectroscopy into the general chemistry curriculum. Students use three sets of springs to model the properties of single, double, and triple covalent bonds. Then, Gaussian 03W molecular modeling software is used to illustrate the relationship between bond…

Scientific Use Cases for the Virtual Atomic and Molecular Data Center

NASA Astrophysics Data System (ADS)

Dubernet, M. L.; Aboudarham, J.; Ba, Y. A.; Boiziot, M.; Bottinelli, S.; Caux, E.; Endres, C.; Glorian, J. M.; Henry, F.; Lamy, L.; Le Sidaner, P.; Møller, T.; Moreau, N.; Rénié, C.; Roueff, E.; Schilke, P.; Vastel, C.; Zwoelf, C. M.

2014-12-01

VAMDC Consortium is a worldwide consortium which federates interoperable Atomic and Molecular databases through an e-science infrastructure. The contained data are of the highest scientific quality and are crucial for many applications: astrophysics, atmospheric physics, fusion, plasma and lighting technologies, health, etc. In this paper we present astrophysical scientific use cases in relation to the use of the VAMDC e-infrastructure. Those will cover very different applications such as: (i) modeling the spectra of interstellar objects using the myXCLASS software tool implemented in the Common Astronomy Software Applications package (CASA) or using the CASSIS software tool, in its stand-alone version or implemented in the Herschel Interactive Processing Environment (HIPE); (ii) the use of Virtual Observatory tools accessing VAMDC databases; (iii) the access of VAMDC from the Paris solar BASS2000 portal; (iv) the combination of tools and database from the APIS service (Auroral Planetary Imaging and Spectroscopy); (v) combination of heterogeneous data for the application to the interstellar medium from the SPECTCOL tool.

The display of molecular models with the Ames Interactive Modeling System (AIMS)

NASA Technical Reports Server (NTRS)

Egan, J. T.; Hart, J.; Burt, S. K.; Macelroy, R. D.

1982-01-01

A visualization of molecular models can lead to a clearer understanding of the models. Sophisticated graphics devices supported by minicomputers make it possible for the chemist to interact with the display of a very large model, altering its structure. In addition to user interaction, the need arises also for other ways of displaying information. These include the production of viewgraphs, film presentation, as well as publication quality prints of various models. To satisfy these needs, the display capability of the Ames Interactive Modeling System (AIMS) has been enhanced to provide a wide range of graphics and plotting capabilities. Attention is given to an overview of the AIMS system, graphics hardware used by the AIMS display subsystem, a comparison of graphics hardware, the representation of molecular models, graphics software used by the AIMS display subsystem, the display of a model obtained from data stored in molecule data base, a graphics feature for obtaining single frame permanent copy displays, and a feature for producing multiple frame displays.

The PyRosetta Toolkit: a graphical user interface for the Rosetta software suite.

PubMed

Adolf-Bryfogle, Jared; Dunbrack, Roland L

2013-01-01

The Rosetta Molecular Modeling suite is a command-line-only collection of applications that enable high-resolution modeling and design of proteins and other molecules. Although extremely useful, Rosetta can be difficult to learn for scientists with little computational or programming experience. To that end, we have created a Graphical User Interface (GUI) for Rosetta, called the PyRosetta Toolkit, for creating and running protocols in Rosetta for common molecular modeling and protein design tasks and for analyzing the results of Rosetta calculations. The program is highly extensible so that developers can add new protocols and analysis tools to the PyRosetta Toolkit GUI.

Molecular modeling of lipase binding to a substrate-water interface.

PubMed

Gruber, Christian C; Pleiss, Jürgen

2012-01-01

Interactions of lipases with hydrophobic substrate-water interfaces are of great interest to design improved lipase variants and engineer reaction conditions. This chapter describes the necessary steps to carry out molecular dynamics simulations of Candida antarctica lipase B at tributyrin-water interface using the GROMACS simulation software. Special attention is drawn to the preparation of the protein and the substrate-water interface and to the analysis of the obtained trajectory.

Early Experiences Porting the NAMD and VMD Molecular Simulation and Analysis Software to GPU-Accelerated OpenPOWER Platforms

PubMed Central

Stone, John E.; Hynninen, Antti-Pekka; Phillips, James C.; Schulten, Klaus

2017-01-01

All-atom molecular dynamics simulations of biomolecules provide a powerful tool for exploring the structure and dynamics of large protein complexes within realistic cellular environments. Unfortunately, such simulations are extremely demanding in terms of their computational requirements, and they present many challenges in terms of preparation, simulation methodology, and analysis and visualization of results. We describe our early experiences porting the popular molecular dynamics simulation program NAMD and the simulation preparation, analysis, and visualization tool VMD to GPU-accelerated OpenPOWER hardware platforms. We report our experiences with compiler-provided autovectorization and compare with hand-coded vector intrinsics for the POWER8 CPU. We explore the performance benefits obtained from unique POWER8 architectural features such as 8-way SMT and its value for particular molecular modeling tasks. Finally, we evaluate the performance of several GPU-accelerated molecular modeling kernels and relate them to other hardware platforms. PMID:29202130

pyPcazip: A PCA-based toolkit for compression and analysis of molecular simulation data

NASA Astrophysics Data System (ADS)

Shkurti, Ardita; Goni, Ramon; Andrio, Pau; Breitmoser, Elena; Bethune, Iain; Orozco, Modesto; Laughton, Charles A.

The biomolecular simulation community is currently in need of novel and optimised software tools that can analyse and process, in reasonable timescales, the large generated amounts of molecular simulation data. In light of this, we have developed and present here pyPcazip: a suite of software tools for compression and analysis of molecular dynamics (MD) simulation data. The software is compatible with trajectory file formats generated by most contemporary MD engines such as AMBER, CHARMM, GROMACS and NAMD, and is MPI parallelised to permit the efficient processing of very large datasets. pyPcazip is a Unix based open-source software (BSD licenced) written in Python.

Extension of the AMBER molecular dynamics software to Intel's Many Integrated Core (MIC) architecture

NASA Astrophysics Data System (ADS)

Needham, Perri J.; Bhuiyan, Ashraf; Walker, Ross C.

2016-04-01

We present an implementation of explicit solvent particle mesh Ewald (PME) classical molecular dynamics (MD) within the PMEMD molecular dynamics engine, that forms part of the AMBER v14 MD software package, that makes use of Intel Xeon Phi coprocessors by offloading portions of the PME direct summation and neighbor list build to the coprocessor. We refer to this implementation as pmemd MIC offload and in this paper present the technical details of the algorithm, including basic models for MPI and OpenMP configuration, and analyze the resultant performance. The algorithm provides the best performance improvement for large systems (>400,000 atoms), achieving a ∼35% performance improvement for satellite tobacco mosaic virus (1,067,095 atoms) when 2 Intel E5-2697 v2 processors (2 ×12 cores, 30M cache, 2.7 GHz) are coupled to an Intel Xeon Phi coprocessor (Model 7120P-1.238/1.333 GHz, 61 cores). The implementation utilizes a two-fold decomposition strategy: spatial decomposition using an MPI library and thread-based decomposition using OpenMP. We also present compiler optimization settings that improve the performance on Intel Xeon processors, while retaining simulation accuracy.

relaxGUI: a new software for fast and simple NMR relaxation data analysis and calculation of ps-ns and μs motion of proteins.

PubMed

Bieri, Michael; d'Auvergne, Edward J; Gooley, Paul R

2011-06-01

Investigation of protein dynamics on the ps-ns and μs-ms timeframes provides detailed insight into the mechanisms of enzymes and the binding properties of proteins. Nuclear magnetic resonance (NMR) is an excellent tool for studying protein dynamics at atomic resolution. Analysis of relaxation data using model-free analysis can be a tedious and time consuming process, which requires good knowledge of scripting procedures. The software relaxGUI was developed for fast and simple model-free analysis and is fully integrated into the software package relax. It is written in Python and uses wxPython to build the graphical user interface (GUI) for maximum performance and multi-platform use. This software allows the analysis of NMR relaxation data with ease and the generation of publication quality graphs as well as color coded images of molecular structures. The interface is designed for simple data analysis and management. The software was tested and validated against the command line version of relax.

Integrating Computational Chemistry into a Course in Classical Thermodynamics

ERIC Educational Resources Information Center

Martini, Sheridan R.; Hartzell, Cynthia J.

2015-01-01

Computational chemistry is commonly addressed in the quantum mechanics course of undergraduate physical chemistry curricula. Since quantum mechanics traditionally follows the thermodynamics course, there is a lack of curricula relating computational chemistry to thermodynamics. A method integrating molecular modeling software into a semester long…

An Educational Software for Simulating the Sample Size of Molecular Marker Experiments

ERIC Educational Resources Information Center

Helms, T. C.; Doetkott, C.

2007-01-01

We developed educational software to show graduate students how to plan molecular marker experiments. These computer simulations give the students feedback on the precision of their experiments. The objective of the software was to show students using a hands-on approach how: (1) environmental variation influences the range of the estimates of the…

Applied Computational Chemistry for the Blind and Visually Impaired

ERIC Educational Resources Information Center

Wedler, Henry B.; Cohen, Sarah R.; Davis, Rebecca L.; Harrison, Jason G.; Siebert, Matthew R.; Willenbring, Dan; Hamann, Christian S.; Shaw, Jared T.; Tantillo, Dean J.

2012-01-01

We describe accommodations that we have made to our applied computational-theoretical chemistry laboratory to provide access for blind and visually impaired students interested in independent investigation of structure-function relationships. Our approach utilizes tactile drawings, molecular model kits, existing software, Bash and Perl scripts…

QuBiLS-MAS, open source multi-platform software for atom- and bond-based topological (2D) and chiral (2.5D) algebraic molecular descriptors computations.

PubMed

Valdés-Martiní, José R; Marrero-Ponce, Yovani; García-Jacas, César R; Martinez-Mayorga, Karina; Barigye, Stephen J; Vaz d'Almeida, Yasser Silveira; Pham-The, Hai; Pérez-Giménez, Facundo; Morell, Carlos A

2017-06-07

In previous reports, Marrero-Ponce et al. proposed algebraic formalisms for characterizing topological (2D) and chiral (2.5D) molecular features through atom- and bond-based ToMoCoMD-CARDD (acronym for Topological Molecular Computational Design-Computer Aided Rational Drug Design) molecular descriptors. These MDs codify molecular information based on the bilinear, quadratic and linear algebraic forms and the graph-theoretical electronic-density and edge-adjacency matrices in order to consider atom- and bond-based relations, respectively. These MDs have been successfully applied in the screening of chemical compounds of different therapeutic applications ranging from antimalarials, antibacterials, tyrosinase inhibitors and so on. To compute these MDs, a computational program with the same name was initially developed. However, this in house software barely offered the functionalities required in contemporary molecular modeling tasks, in addition to the inherent limitations that made its usability impractical. Therefore, the present manuscript introduces the QuBiLS-MAS (acronym for Quadratic, Bilinear and N-Linear mapS based on graph-theoretic electronic-density Matrices and Atomic weightingS) software designed to compute topological (0-2.5D) molecular descriptors based on bilinear, quadratic and linear algebraic forms for atom- and bond-based relations. The QuBiLS-MAS module was designed as standalone software, in which extensions and generalizations of the former ToMoCoMD-CARDD 2D-algebraic indices are implemented, considering the following aspects: (a) two new matrix normalization approaches based on double-stochastic and mutual probability formalisms; (b) topological constraints (cut-offs) to take into account particular inter-atomic relations; (c) six additional atomic properties to be used as weighting schemes in the calculation of the molecular vectors; (d) four new local-fragments to consider molecular regions of interest; (e) number of lone-pair electrons in chemical structure defined by diagonal coefficients in matrix representations; and (f) several aggregation operators (invariants) applied over atom/bond-level descriptors in order to compute global indices. This software permits the parallel computation of the indices, contains a batch processing module and data curation functionalities. This program was developed in Java v1.7 using the Chemistry Development Kit library (version 1.4.19). The QuBiLS-MAS software consists of two components: a desktop interface (GUI) and an API library allowing for the easy integration of the latter in chemoinformatics applications. The relevance of the novel extensions and generalizations implemented in this software is demonstrated through three studies. Firstly, a comparative Shannon's entropy based variability study for the proposed QuBiLS-MAS and the DRAGON indices demonstrates superior performance for the former. A principal component analysis reveals that the QuBiLS-MAS approach captures chemical information orthogonal to that codified by the DRAGON descriptors. Lastly, a QSAR study for the binding affinity to the corticosteroid-binding globulin using Cramer's steroid dataset is carried out. From these analyses, it is revealed that the QuBiLS-MAS approach for atom-pair relations yields similar-to-superior performance with regard to other QSAR methodologies reported in the literature. Therefore, the QuBiLS-MAS approach constitutes a useful tool for the diversity analysis of chemical compound datasets and high-throughput screening of structure-activity data.

Homology Modeling and Molecular Docking for the Science Curriculum

ERIC Educational Resources Information Center

McDougal, Owen M.; Cornia, Nic; Sambasivarao, S. V.; Remm, Andrew; Mallory, Chris; Oxford, Julia Thom; Maupin, C. Mark; Andersen, Tim

2014-01-01

DockoMatic 2.0 is a powerful open source software program (downloadable from sourceforge.net) that allows users to utilize a readily accessible computational tool to explore biomolecules and their interactions. This manuscript describes a practical tutorial for use in the undergraduate curriculum that introduces students to macromolecular…

ITRAQ MASS SPECTROMETRIC PROTEOMIC APPLICATIONS FOR IN VIVO TOXICOLOGY STUDIES OF AMPHIBIAN SPECIES: DATA HANDLING AND INTERPRETATION USING PEPTIDE-TAGGING SOFTWARE

EPA Science Inventory

This addresses the USEPA's need for a cost effective, non-mammalian screening assay for thyroid axis disrupting chemicals; a multi-endpoint strategy combining molecular and in vivo protocols in an amphibian model is being applied at MED Duluth.

A new candidate of calcium channel blocker in silico from Tectona grandis for treatment of gestational hypertension

NASA Astrophysics Data System (ADS)

Azizah, A.; Suselo, Y. H.; Muthmainah, M.; Indarto, D.

2018-05-01

Gestational Hypertension is one of the three main causes of maternal mortality in Indonesia. Nifedipine which blockes the Cav1.2 calcium channel has frequently been used to treat gestational hypertension. However the efficacy of nifedipine has not been established yet and the prevalence of gestational hypertension is still high (27.1 %). Indonesian herbal plants have potential to be developed as natural drugs. Molecular docking, a computational method, is very often used to depict interaction between molecules and target receptor This study was therefore to identify Indonesian herbal plants that could inhibit the calcium channel in silico. This was a bioinformatics study with molecular docking approach. Three-dimensional structure of human calcium channel Cav1.2 was determined by modelling with rabbit calcium channel (ID:5GJW) as template and using the SWISS MODEL software. Nifedipine was used as a standard ligand and obtained from ZINC database with the access code ZINC19594578. Active compounds of Indonesian herbal plants were registered in HerbalDB database and their molecular structure was obtained from PubChem. Binding affinity of human Cav1.2 model-ligand complexes were assesed using AutoDock Vina 1.1.2 software and visualization of molecular conformation used Chimera 1.10 and PyMol 1.3 softwares. The Lipinsky’s rules of five were used to determine active compounds which fullfilled drug criteria. The human Cav1-2 model had 72.35% sequence identity with rabbit Cav1.1. Nifedipine bound to the human Cav1.2 model with -2.1 kcal/mol binding affinity and had binding sites at Gln1060, Phe1129, Ser1132, and Ile1173 residues. A lower binding affinity was observed in 8 phytochemicals but only obtusifolin 2-glucoside (-2.2 kcal/mol) had similar binding sites as nifedipin did. In addition, obtusifolin 2-glucoside met the Lipinsky criteria and the molecule conformation was similar with nifedipine. From the HerbalDB database, obtusifolin 2-glucoside is found in Tectona grandis. Obtusifolin 2-glucoside computationally becomes a potensial candidate of calcium channel blocker. In vitro assays should be performed to evaluate the antagonist effect of obtusifolin 2-glucoside on calcium channel Cav1.2.

Towards better modelling of drug-loading in solid lipid nanoparticles: Molecular dynamics, docking experiments and Gaussian Processes machine learning.

PubMed

Hathout, Rania M; Metwally, Abdelkader A

2016-11-01

This study represents one of the series applying computer-oriented processes and tools in digging for information, analysing data and finally extracting correlations and meaningful outcomes. In this context, binding energies could be used to model and predict the mass of loaded drugs in solid lipid nanoparticles after molecular docking of literature-gathered drugs using MOE® software package on molecularly simulated tripalmitin matrices using GROMACS®. Consequently, Gaussian processes as a supervised machine learning artificial intelligence technique were used to correlate the drugs' descriptors (e.g. M.W., xLogP, TPSA and fragment complexity) with their molecular docking binding energies. Lower percentage bias was obtained compared to previous studies which allows the accurate estimation of the loaded mass of any drug in the investigated solid lipid nanoparticles by just projecting its chemical structure to its main features (descriptors). Copyright © 2016 Elsevier B.V. All rights reserved.

Gesture Interaction Browser-Based 3D Molecular Viewer.

PubMed

Virag, Ioan; Stoicu-Tivadar, Lăcrămioara; Crişan-Vida, Mihaela

2016-01-01

The paper presents an open source system that allows the user to interact with a 3D molecular viewer using associated hand gestures for rotating, scaling and panning the rendered model. The novelty of this approach is that the entire application is browser-based and doesn't require installation of third party plug-ins or additional software components in order to visualize the supported chemical file formats. This kind of solution is suitable for instruction of users in less IT oriented environments, like medicine or chemistry. For rendering various molecular geometries our team used GLmol (a molecular viewer written in JavaScript). The interaction with the 3D models is made with Leap Motion controller that allows real-time tracking of the user's hand gestures. The first results confirmed that the resulting application leads to a better way of understanding various types of translational bioinformatics related problems in both biomedical research and education.

From UNIX to PC via X-Windows: Molecular Modeling for the General Chemistry Lab

NASA Astrophysics Data System (ADS)

Pavia, Donald; Wicholas, Mark

1997-04-01

The emphasis of molecular modeling in the undergraduate curriculum has generally been directed toward sophomore organic and higher-level chemistry instruction, especially when UNIX systems are used. When developing plans for incorporating molecular modeling into the curriculum, we decided to also include it in our first-year general chemistry course. Modeling would serve primarily as a visualization tool to augment the general chemistry coverage of bonding and structure. Our first thoughts were rather naive: we would set up a number of workstations and somehow get our general chemistry students, as many as 480 in one academic quarter, directly onto these machines at some time in a 1-2 week period during their weekly 3-hour lab. Further exploration of our options revealed that a better approach was to use PCs as dummy terminals for UNIX workstations. Described below are the hardware and software for this venture and the modeling experiment done by our students in general chemistry.

SketchBio: a scientist's 3D interface for molecular modeling and animation.

PubMed

Waldon, Shawn M; Thompson, Peter M; Hahn, Patrick J; Taylor, Russell M

2014-10-30

Because of the difficulties involved in learning and using 3D modeling and rendering software, many scientists hire programmers or animators to create models and animations. This both slows the discovery process and provides opportunities for miscommunication. Working with multiple collaborators, a tool was developed (based on a set of design goals) to enable them to directly construct models and animations. SketchBio is presented, a tool that incorporates state-of-the-art bimanual interaction and drop shadows to enable rapid construction of molecular structures and animations. It includes three novel features: crystal-by-example, pose-mode physics, and spring-based layout that accelerate operations common in the formation of molecular models. Design decisions and their consequences are presented, including cases where iterative design was required to produce effective approaches. The design decisions, novel features, and inclusion of state-of-the-art techniques enabled SketchBio to meet all of its design goals. These features and decisions can be incorporated into existing and new tools to improve their effectiveness.

Large Eddy Simulation (LES) of Particle-Laden Temporal Mixing Layers

NASA Technical Reports Server (NTRS)

Bellan, Josette; Radhakrishnan, Senthilkumaran

2012-01-01

High-fidelity models of plume-regolith interaction are difficult to develop because of the widely disparate flow conditions that exist in this process. The gas in the core of a rocket plume can often be modeled as a time-dependent, high-temperature, turbulent, reacting continuum flow. However, due to the vacuum conditions on the lunar surface, the mean molecular path in the outer parts of the plume is too long for the continuum assumption to remain valid. Molecular methods are better suited to model this region of the flow. Finally, granular and multiphase flow models must be employed to describe the dust and debris that are displaced from the surface, as well as how a crater is formed in the regolith. At present, standard commercial CFD (computational fluid dynamics) software is not capable of coupling each of these flow regimes to provide an accurate representation of this flow process, necessitating the development of custom software. This software solves the fluid-flow-governing equations in an Eulerian framework, coupled with the particle transport equations that are solved in a Lagrangian framework. It uses a fourth-order explicit Runge-Kutta scheme for temporal integration, an eighth-order central finite differencing scheme for spatial discretization. The non-linear terms in the governing equations are recast in cubic skew symmetric form to reduce aliasing error. The second derivative viscous terms are computed using eighth-order narrow stencils that provide better diffusion for the highest resolved wave numbers. A fourth-order Lagrange interpolation procedure is used to obtain gas-phase variable values at the particle locations.

NanoDesign: Concepts and Software for a Nanotechnology Based on Functionalized Fullerenes

NASA Technical Reports Server (NTRS)

Globus, Al; Jaffe, Richard; Chancellor, Marisa K. (Technical Monitor)

1996-01-01

Eric Drexler has proposed a hypothetical nanotechnology based on diamond and investigated the properties of such molecular systems. While attractive, diamonoid nanotechnology is not physically accessible with straightforward extensions of current laboratory techniques. We propose a nanotechnology based on functionalized fullerenes and investigate carbon nanotube based gears with teeth added via a benzyne reaction known to occur with C60. The gears are single-walled carbon nanotubes with appended coenzyme groups for teeth. Fullerenes are in widespread laboratory use and can be functionalized in many ways. Companion papers computationally demonstrate the properties of these gears (they appear to work) and the accessibility of the benzyne/nanotube reaction. This paper describes the molecular design techniques and rationale as well as the software that implements these design techniques. The software is a set of persistent C++ objects controlled by TCL command scripts. The c++/tcl interface is automatically generated by a software system called tcl_c++ developed by the author and described here. The objects keep track of different portions of the molecular machinery to allow different simulation techniques and boundary conditions to be applied as appropriate. This capability has been required to demonstrate (computationally) our gear's feasibility. A new distributed software architecture featuring a WWW universal client, CORBA distributed objects, and agent software is under consideration. The software architecture is intended to eventually enable a widely disbursed group to develop complex simulated molecular machines.

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald.

PubMed

Salomon-Ferrer, Romelia; Götz, Andreas W; Poole, Duncan; Le Grand, Scott; Walker, Ross C

2013-09-10

We present an implementation of explicit solvent all atom classical molecular dynamics (MD) within the AMBER program package that runs entirely on CUDA-enabled GPUs. First released publicly in April 2010 as part of version 11 of the AMBER MD package and further improved and optimized over the last two years, this implementation supports the three most widely used statistical mechanical ensembles (NVE, NVT, and NPT), uses particle mesh Ewald (PME) for the long-range electrostatics, and runs entirely on CUDA-enabled NVIDIA graphics processing units (GPUs), providing results that are statistically indistinguishable from the traditional CPU version of the software and with performance that exceeds that achievable by the CPU version of AMBER software running on all conventional CPU-based clusters and supercomputers. We briefly discuss three different precision models developed specifically for this work (SPDP, SPFP, and DPDP) and highlight the technical details of the approach as it extends beyond previously reported work [Götz et al., J. Chem. Theory Comput. 2012, DOI: 10.1021/ct200909j; Le Grand et al., Comp. Phys. Comm. 2013, DOI: 10.1016/j.cpc.2012.09.022].We highlight the substantial improvements in performance that are seen over traditional CPU-only machines and provide validation of our implementation and precision models. We also provide evidence supporting our decision to deprecate the previously described fully single precision (SPSP) model from the latest release of the AMBER software package.

The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button.

PubMed

Swertz, Morris A; Dijkstra, Martijn; Adamusiak, Tomasz; van der Velde, Joeri K; Kanterakis, Alexandros; Roos, Erik T; Lops, Joris; Thorisson, Gudmundur A; Arends, Danny; Byelas, George; Muilu, Juha; Brookes, Anthony J; de Brock, Engbert O; Jansen, Ritsert C; Parkinson, Helen

2010-12-21

There is a huge demand on bioinformaticians to provide their biologists with user friendly and scalable software infrastructures to capture, exchange, and exploit the unprecedented amounts of new *omics data. We here present MOLGENIS, a generic, open source, software toolkit to quickly produce the bespoke MOLecular GENetics Information Systems needed. The MOLGENIS toolkit provides bioinformaticians with a simple language to model biological data structures and user interfaces. At the push of a button, MOLGENIS' generator suite automatically translates these models into a feature-rich, ready-to-use web application including database, user interfaces, exchange formats, and scriptable interfaces. Each generator is a template of SQL, JAVA, R, or HTML code that would require much effort to write by hand. This 'model-driven' method ensures reuse of best practices and improves quality because the modeling language and generators are shared between all MOLGENIS applications, so that errors are found quickly and improvements are shared easily by a re-generation. A plug-in mechanism ensures that both the generator suite and generated product can be customized just as much as hand-written software. In recent years we have successfully evaluated the MOLGENIS toolkit for the rapid prototyping of many types of biomedical applications, including next-generation sequencing, GWAS, QTL, proteomics and biobanking. Writing 500 lines of model XML typically replaces 15,000 lines of hand-written programming code, which allows for quick adaptation if the information system is not yet to the biologist's satisfaction. Each application generated with MOLGENIS comes with an optimized database back-end, user interfaces for biologists to manage and exploit their data, programming interfaces for bioinformaticians to script analysis tools in R, Java, SOAP, REST/JSON and RDF, a tab-delimited file format to ease upload and exchange of data, and detailed technical documentation. Existing databases can be quickly enhanced with MOLGENIS generated interfaces using the 'ExtractModel' procedure. The MOLGENIS toolkit provides bioinformaticians with a simple model to quickly generate flexible web platforms for all possible genomic, molecular and phenotypic experiments with a richness of interfaces not provided by other tools. All the software and manuals are available free as LGPLv3 open source at http://www.molgenis.org.

Systems Biology-Driven Hypotheses Tested In Vivo: The Need to Advancing Molecular Imaging Tools.

PubMed

Verma, Garima; Palombo, Alessandro; Grigioni, Mauro; La Monaca, Morena; D'Avenio, Giuseppe

2018-01-01

Processing and interpretation of biological images may provide invaluable insights on complex, living systems because images capture the overall dynamics as a "whole." Therefore, "extraction" of key, quantitative morphological parameters could be, at least in principle, helpful in building a reliable systems biology approach in understanding living objects. Molecular imaging tools for system biology models have attained widespread usage in modern experimental laboratories. Here, we provide an overview on advances in the computational technology and different instrumentations focused on molecular image processing and analysis. Quantitative data analysis through various open source software and algorithmic protocols will provide a novel approach for modeling the experimental research program. Besides this, we also highlight the predictable future trends regarding methods for automatically analyzing biological data. Such tools will be very useful to understand the detailed biological and mathematical expressions under in-silico system biology processes with modeling properties.

A theoretical-electron-density databank using a model of real and virtual spherical atoms.

PubMed

Nassour, Ayoub; Domagala, Slawomir; Guillot, Benoit; Leduc, Theo; Lecomte, Claude; Jelsch, Christian

2017-08-01

A database describing the electron density of common chemical groups using combinations of real and virtual spherical atoms is proposed, as an alternative to the multipolar atom modelling of the molecular charge density. Theoretical structure factors were computed from periodic density functional theory calculations on 38 crystal structures of small molecules and the charge density was subsequently refined using a density model based on real spherical atoms and additional dummy charges on the covalent bonds and on electron lone-pair sites. The electron-density parameters of real and dummy atoms present in a similar chemical environment were averaged on all the molecules studied to build a database of transferable spherical atoms. Compared with the now-popular databases of transferable multipolar parameters, the spherical charge modelling needs fewer parameters to describe the molecular electron density and can be more easily incorporated in molecular modelling software for the computation of electrostatic properties. The construction method of the database is described. In order to analyse to what extent this modelling method can be used to derive meaningful molecular properties, it has been applied to the urea molecule and to biotin/streptavidin, a protein/ligand complex.

Applications of molecular modeling in coal research

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carlson, G.A.; Faulon, J.L.

Over the past several years, molecular modeling has been applied to study various characteristics of coal molecular structures. Powerful workstations coupled with molecular force-field-based software packages have been used to study coal and coal-related molecules. Early work involved determination of the minimum-energy three-dimensional conformations of various published coal structures (Given, Wiser, Solomon and Shinn), and the dominant role of van der Waals and hydrogen bonding forces in defining the energy-minimized structures. These studies have been extended to explore various physical properties of coal structures, including density, microporosity, surface area, and fractal dimension. Other studies have related structural characteristics to cross-linkmore » density and have explored small molecule interactions with coal. Finally, recent studies using a structural elucidation (molecular builder) technique have constructed statistically diverse coal structures based on quantitative and qualitative data on coal and its decomposition products. This technique is also being applied to study coalification processes based on postulated coalification chemistry.« less

Multiresolution molecular mechanics: Implementation and efficiency

NASA Astrophysics Data System (ADS)

Biyikli, Emre; To, Albert C.

2017-01-01

Atomistic/continuum coupling methods combine accurate atomistic methods and efficient continuum methods to simulate the behavior of highly ordered crystalline systems. Coupled methods utilize the advantages of both approaches to simulate systems at a lower computational cost, while retaining the accuracy associated with atomistic methods. Many concurrent atomistic/continuum coupling methods have been proposed in the past; however, their true computational efficiency has not been demonstrated. The present work presents an efficient implementation of a concurrent coupling method called the Multiresolution Molecular Mechanics (MMM) for serial, parallel, and adaptive analysis. First, we present the features of the software implemented along with the associated technologies. The scalability of the software implementation is demonstrated, and the competing effects of multiscale modeling and parallelization are discussed. Then, the algorithms contributing to the efficiency of the software are presented. These include algorithms for eliminating latent ghost atoms from calculations and measurement-based dynamic balancing of parallel workload. The efficiency improvements made by these algorithms are demonstrated by benchmark tests. The efficiency of the software is found to be on par with LAMMPS, a state-of-the-art Molecular Dynamics (MD) simulation code, when performing full atomistic simulations. Speed-up of the MMM method is shown to be directly proportional to the reduction of the number of the atoms visited in force computation. Finally, an adaptive MMM analysis on a nanoindentation problem, containing over a million atoms, is performed, yielding an improvement of 6.3-8.5 times in efficiency, over the full atomistic MD method. For the first time, the efficiency of a concurrent atomistic/continuum coupling method is comprehensively investigated and demonstrated.

Models for twistable elastic polymers in Brownian dynamics, and their implementation for LAMMPS.

PubMed

Brackley, C A; Morozov, A N; Marenduzzo, D

2014-04-07

An elastic rod model for semi-flexible polymers is presented. Theory for a continuum rod is reviewed, and it is shown that a popular discretised model used in numerical simulations gives the correct continuum limit. Correlation functions relating to both bending and twisting of the rod are derived for both continuous and discrete cases, and results are compared with numerical simulations. Finally, two possible implementations of the discretised model in the multi-purpose molecular dynamics software package LAMMPS are described.

3D molecular models of whole HIV-1 virions generated with cellPACK

PubMed Central

Goodsell, David S.; Autin, Ludovic; Forli, Stefano; Sanner, Michel F.; Olson, Arthur J.

2014-01-01

As knowledge of individual biological processes grows, it becomes increasingly useful to frame new findings within their larger biological contexts in order to generate new systems-scale hypotheses. This report highlights two major iterations of a whole virus model of HIV-1, generated with the cellPACK software. cellPACK integrates structural and systems biology data with packing algorithms to assemble comprehensive 3D models of cell-scale structures in molecular detail. This report describes the biological data, modeling parameters and cellPACK methods used to specify and construct editable models for HIV-1. Anticipating that cellPACK interfaces under development will enable researchers from diverse backgrounds to critique and improve the biological models, we discuss how cellPACK can be used as a framework to unify different types of data across all scales of biology. PMID:25253262

Creating and Using a Consumer Chemical Molecular Graphics Database: The "Molecule of the Day" - A Great Way To Begin Your Lecture

NASA Astrophysics Data System (ADS)

Scharberg, Maureen A.; Cox, Oran E.; Barelli, Carl A.

1997-07-01

"The Molecule of the Day" consumer chemical database has been created to allow introductory chemistry students to explore molecular structures of chemicals in household products, and to provide opportunities in molecular modeling for undergraduate chemistry students. Before class begins, an overhead transparency is displayed which shows a three-dimensional molecular structure of a household chemical, and lists relevant features and uses of this chemical. Within answers to questionnaires, students have commented that this molecular graphics database has helped them to visually connect the microscopic structure of a molecule with its physical and chemical properties, as well as its uses in consumer products. It is anticipated that this database will be incorporated into a navigational software package such as Netscape.

{Semantic metadata application for information resources systematization in water spectroscopy} A.Fazliev (1), A.Privezentsev (1), J.Tennyson (2) (1) Institute of Atmospheric Optics SB RAS, Tomsk, Russia, (2) University College London, London, UK (faz@iao

NASA Astrophysics Data System (ADS)

Fazliev, A.

2009-04-01

The information and knowledge layers of information-computational system for water spectroscopy are described. Semantic metadata for all the tasks of domain information model that are the basis of the layers have been studied. The principle of semantic metadata determination and mechanisms of the usage during information systematization in molecular spectroscopy has been revealed. The software developed for the work with semantic metadata is described as well. Formation of domain model in the framework of Semantic Web is based on the use of explicit specification of its conceptualization or, in other words, its ontologies. Formation of conceptualization for molecular spectroscopy was described in Refs. 1, 2. In these works two chains of task are selected for zeroth approximation for knowledge domain description. These are direct tasks chain and inverse tasks chain. Solution schemes of these tasks defined approximation of data layer for knowledge domain conceptualization. Spectroscopy tasks solutions properties lead to a step-by-step extension of molecular spectroscopy conceptualization. Information layer of information system corresponds to this extension. An advantage of molecular spectroscopy model designed in a form of tasks chain is actualized in the fact that one can explicitly define data and metadata at each step of solution of these molecular spectroscopy chain tasks. Metadata structure (tasks solutions properties) in knowledge domain also has form of a chain in which input data and metadata of the previous task become metadata of the following tasks. The term metadata is used in its narrow sense: metadata are the properties of spectroscopy tasks solutions. Semantic metadata represented with the help of OWL 3 are formed automatically and they are individuals of classes (A-box). Unification of T-box and A-box is an ontology that can be processed with the help of inference engine. In this work we analyzed the formation of individuals of molecular spectroscopy applied ontologies as well as the software used for their creation by means of OWL DL language. The results of this work are presented in a form of an information layer and a knowledge layer in W@DIS information system 4. 1 FORMATION OF INDIVIDUALS OF WATER SPECTROSCOPY APPLIED ONTOLOGY Applied tasks ontology contains explicit description of input an output data of physical tasks solved in two chains of molecular spectroscopy tasks. Besides physical concepts, related to spectroscopy tasks solutions, an information source, which is a key concept of knowledge domain information model, is also used. Each solution of knowledge domain task is linked to the information source which contains a reference on published task solution, molecule and task solution properties. Each information source allows us to identify a certain knowledge domain task solution contained in the information system. Water spectroscopy applied ontology classes are formed on the basis of molecular spectroscopy concepts taxonomy. They are defined by constrains on properties of the selected conceptualization. Extension of applied ontology in W@DIS information system is actualized according to two scenarios. Individuals (ontology facts or axioms) formation is actualized during the task solution upload in the information system. Ontology user operation that implies molecular spectroscopy taxonomy and individuals is performed solely by the user. For this purpose Protege ontology editor was used. For the formation, processing and visualization of knowledge domain tasks individuals a software was designed and implemented. Method of individual formation determines the sequence of steps of created ontology individuals' generation. Tasks solutions properties (metadata) have qualitative and quantitative values. Qualitative metadata are regarded as metadata describing qualitative side of a task such as solution method or other information that can be explicitly specified by object properties of OWL DL language. Quantitative metadata are metadata that describe quantitative properties of task solution such as minimal and maximal data value or other information that can be explicitly obtained by programmed algorithmic operations. These metadata are related to DatatypeProperty properties of OWL specification language Quantitative metadata can be obtained automatically during data upload into information system. Since ObjectProperty values are objects, processing of qualitative metadata requires logical constraints. In case of the task solved in W@DIS ICS qualitative metadata can be formed automatically (for example in spectral functions calculation task). The used methods of translation of qualitative metadata into quantitative is characterized as roughened representation of knowledge in knowledge domain. The existence of two ways of data obtainment is a key moment in the formation of applied ontology of molecular spectroscopy task. experimental method (metadata for experimental data contain description of equipment, experiment conditions and so on) on the initial stage and inverse task solution on the following stages; calculation method (metadata for calculation data are closely related to the metadata used for the description of physical and mathematical models of molecular spectroscopy) 2 SOFTWARE FOR ONTOLOGY OPERATION Data collection in water spectroscopy information system is organized in a form of workflow that contains such operations as information source creation, entry of bibliographic data on publications, formation of uploaded data schema an so on. Metadata are generated in information source as well. Two methods are used for their formation: automatic metadata generation and manual metadata generation (performed by user). Software implementation of support of actions related to metadata formation is performed by META+ module. Functions of META+ module can be divided into two groups. The first groups contains the functions necessary to software developer while the second one the functions necessary to a user of the information system. META+ module functions necessary to the developer are: 1. creation of taxonomy (T-boxes) of applied ontology classes of knowledge domain tasks; 2. creation of instances of task classes; 3. creation of data schemes of tasks in a form of an XML-pattern and based on XML-syntax. XML-pattern is developed for instances generator and created according to certain rules imposed on software generator implementation. 4. implementation of metadata values calculation algorithms; 5. creation of a request interface and additional knowledge processing function for the solution of these task; 6. unification of the created functions and interfaces into one information system The following sequence is universal for the generation of task classes' individuals that form chains. Special interfaces for user operations management are designed for software developer in META+ module. There are means for qualitative metadata values updating during data reuploading to information source. The list of functions necessary to end user contains: - data sets visualization and editing, taking into account their metadata, e.g.: display of unique number of bands in transitions for a certain data source; - export of OWL/RDF models from information system to the environment in XML-syntax; - visualization of instances of classes of applied ontology tasks on molecular spectroscopy; - import of OWL/RDF models into the information system and their integration with domain vocabulary; - formation of additional knowledge of knowledge domain for the construction of ontological instances of task classes using GTML-formats and their processing; - formation of additional knowledge in knowledge domain for the construction of instances of task classes, using software algorithm for data sets processing; - function of semantic search implementation using an interface that formulates questions in a form of related triplets in order for getting an adequate answer. 3 STRUCTURE OF META+ MODULE META+ software module that provides the above functions contains the following components: - a knowledge base that stores semantic metadata and taxonomies of information system; - software libraries POWL and RAP 5 created by third-party developer and providing access to ontological storage; - function classes and libraries that form the core of the module and perform the tasks of formation, storage and visualization of classes instances; - configuration files and module patterns that allow one to adjust and organize operation of different functional blocks; META+ module also contains scripts and patterns implemented according to the rules of W@DIS information system development environment. - scripts for interaction with environment by means of the software core of information system. These scripts provide organizing web-oriented interactive communication; - patterns for the formation of functionality visualization realized by the scripts Software core of scientific information-computational system W@DIS is created with the help of MVC (Model - View - Controller) design pattern that allows us to separate logic of application from its representation. It realizes the interaction of three logical components, actualizing interactivity with the environment via Web and performing its preprocessing. Functions of «Controller» logical component are realized with the help of scripts designed according to the rules imposed by software core of the information system. Each script represents a definite object-oriented class with obligatory class method of script initiation called "start". Functions of actualization of domain application operation results representation (i.e. "View" component) are sets of HTML-patterns that allow one to visualize the results of domain applications operation with the help of additional constructions processed by software core of the system. Besides the interaction with the software core of the scientific information system this module also deals with configuration files of software core and its database. Such organization of work provides closer integration with software core and deeper and more adequate connection in operating system support. 4 CONCLUSION In this work the problems of semantic metadata creation in information system oriented on information representation in the area of molecular spectroscopy have been discussed. The described method of semantic metadata and functions formation as well as realization and structure of META+ module have been described. Architecture of META+ module is closely related to the existing software of "Molecular spectroscopy" scientific information system. Realization of the module is performed with the use of modern approaches to Web-oriented applications development. It uses the existing applied interfaces. The developed software allows us to: - perform automatic metadata annotation of calculated tasks solutions directly in the information system; - perform automatic annotation of metadata on the solution of tasks on task solution results uploading outside the information system forming an instance of the solved task on the basis of entry data; - use ontological instances of task solution for identification of data in information tasks of viewing, comparison and search solved by information system; - export applied tasks ontologies for the operation with them by external means; - solve the task of semantic search according to the pattern and using question-answer type interface. 5 ACKNOWLEDGEMENT The authors are grateful to RFBR for the financial support of development of distributed information system for molecular spectroscopy. REFERENCES A.D.Bykov, A.Z. Fazliev, N.N.Filippov, A.V. Kozodoev, A.I.Privezentsev, L.N.Sinitsa, M.V.Tonkov and M.Yu.Tretyakov, Distributed information system on atmospheric spectroscopy // Geophysical Research Abstracts, SRef-ID: 1607-7962/gra/EGU2007-A-01906, 2007, v. 9, p. 01906. A.I.Prevezentsev, A.Z. Fazliev Applied task ontology for molecular spectroscopy information resources systematization. The Proceedings of 9th Russian scientific conference "Electronic libraries: advanced methods and technologies, electronic collections" - RCDL'2007, Pereslavl Zalesskii, 2007, part.1, 2007, P.201-210. OWL Web Ontology Language Semantics and Abstract Syntax, W3C Recommendation 10 February 2004, http://www.w3.org/TR/2004/REC-owl-semantics-20040210/ W@DIS information system, http://wadis.saga.iao.ru RAP library, http://www4.wiwiss.fu-berlin.de/bizer/rdfapi/.

Molecular Modeling on the PC (by Matthew F. Schlecht)

NASA Astrophysics Data System (ADS)

Rioux, Reviewed Frank

2000-06-01

"Computeraided molecular modeling doesn't exist for its own sake, but to contribute to scientific endeavor, and enable the scientist to work smarter." This is the last sentence of Schlecht's preface and it says something very important about contemporary scientific research in the academic and industrial venues. Owing to the accelerating improvement in computer technology (hardware and software) and its widespread availability, molecular modeling has become a reliable and important tool in chemical research. Consequently, experimentalists have incorporated molecular modeling techniques in their research, and partnerships with computational chemists have become common. This is a wellorganized and thorough monograph that devotes its attention to one type of molecular modeling, molecular mechanics, and one molecular modeling software package, PCMODEL. Schlecht targets two reader-user groups, the novice and the journeyman modeler, and articulates three goals. He wants to provide the novice with an introduction to molecular mechanics, and after that with some practical examples of the use of empirical force field calculations. His third goal is to provide the journeyman modeler with a reference work that will aid "further study and practice". These are potentially conflicting goals, but Schlecht is, in my opinion, successful because of the way his book is organized. A comprehensive treatment such as this one is not meant to be read from cover to cover, because it is both an exposition of basic principles and a user's manual. Therefore, the novice and the experienced modeler will undoubtedly use this book in different ways. For example, a novice modeler might be advised to read the Preface and Chapter 1, which together provide a broad introduction to the historical development and goals of molecular mechanics. From there the novice could go to Chapter 5 and read section 5.1 on the components of the molecular mechanics force field, which is presented in 22 pages with plenty of graphical support. The reader is now ready to move to Chapter 6 on applications and work through the 32 exercises (Chapters 3 and 4 have an additional 11 exercises) designed to illustrate the current uses of molecular modeling in academic and industrial research. Chapter 3 (Input and Output), Chapter 4 (File Formats), and the balance of Chapter 5 can be consulted as needed. For example, Chapter 5 contains 160 pages on the evolution of the various empirical force fields in use today and important information in each case on parameterization and implementation. Besides finding a clearly written, wellorganized, thorough presentation, the reader will appreciate a number of other important features. There are numerous references (993) to the primary literature covering the field of molecular mechanics from its beginnings to mid1997, when the book went to press. There is a complete glossary of PCMODEL commands, and a comprehensive and valuable glossary (77 pages) of frequently used computer terms. There are 392 figures (many of them screen captures) providing illustrations of the PCMODEL interface in use and examples of input and output files. To aid the reader/user in obtaining expertise as a modeler, a diskette containing all the structure files for all the exercises accompanies the text. In addition, the author provides, on the same diskette, a browserreadable HTML file that contains links to a large number of pertinent resources on the World Wide Web. In summary, Molecular Modeling on the PC, by Matthew Schlecht, is a very impressive contribution to the molecular modeling literature. Schlecht's book should be in every college and university library and in the personal libraries of those who want to learn more about molecular mechanics or who anticipate its use in their teaching or research.

Optimization of a polymer composite employing molecular mechanic simulations and artificial neural networks for a novel intravaginal bioadhesive drug delivery device.

PubMed

Ndesendo, Valence M K; Pillay, Viness; Choonara, Yahya E; du Toit, Lisa C; Kumar, Pradeep; Buchmann, Eckhart; Meyer, Leith C R; Khan, Riaz A

2012-01-01

This study aimed at elucidating an optimal synergistic polymer composite for achieving a desirable molecular bioadhesivity and Matrix Erosion of a bioactive-loaded Intravaginal Bioadhesive Polymeric Device (IBPD) employing Molecular Mechanic Simulations and Artificial Neural Networks (ANN). Fifteen lead caplet-shaped devices were formulated by direct compression with the model bioactives zidovudine and polystyrene sulfonate. The Matrix Erosion was analyzed in simulated vaginal fluid to assess the critical integrity. Blueprinting the molecular mechanics of bioadhesion between vaginal epithelial glycoprotein (EGP), mucin (MUC) and the IBPD were performed on HyperChem 8.0.8 software (MM+ and AMBER force fields) for the quantification and characterization of correlative molecular interactions during molecular bioadhesion. Results proved that the IBPD bioadhesivity was pivoted on the conformation, orientation, and poly(acrylic acid) (PAA) composition that interacted with EGP and MUC present on the vaginal epithelium due to heterogeneous surface residue distributions (free energy= -46.33 kcalmol(-1)). ANN sensitivity testing as a connectionist model enabled strategic polymer selection for developing an IBPD with an optimally prolonged Matrix Erosion and superior molecular bioadhesivity (ME = 1.21-7.68%; BHN = 2.687-4.981 N/mm(2)). Molecular modeling aptly supported the EGP-MUC-PAA molecular interaction at the vaginal epithelium confirming the role of PAA in bioadhesion of the IBPD once inserted into the posterior fornix of the vagina.

Computer Simulations of Epoxy Adhesive Monomer Interactions with Alumina Surfaces

DTIC Science & Technology

1992-08-01

using Sybyl"’ molecular modeling software 9 on a Digital Equipment Corporation microVAXw cluster. The Tripos force field was employed in the...Ave, N, Ft Leonard Wood, MO 65473-5000 1 ATM- Libary Commander, US. Army Enginer Waterways Expenment Station, P.O. Box 631, Vicksburg, MS 39180 1 ATTN

Using Computer Visualization Models in High School Chemistry: The Role of Teacher Beliefs.

ERIC Educational Resources Information Center

Robblee, Karen M.; Garik, Peter; Abegg, Gerald L.; Faux, Russell; Horwitz, Paul

This paper discusses the role of high school chemistry teachers' beliefs in implementing computer visualization software to teach atomic and molecular structure from a quantum mechanical perspective. The informants in this study were four high school chemistry teachers with comparable academic and professional backgrounds. These teachers received…

Dopamine Receptor DOP-4 Modulates Habituation to Repetitive Photoactivation of a "C. elegans" Polymodal Nociceptor

ERIC Educational Resources Information Center

Ardiel, Evan L.; Giles, Andrew C.; Yu, Alex J.; Lindsay, Theodore H.; Lockery, Shawn R.; Rankin, Catharine H.

2016-01-01

Habituation is a highly conserved phenomenon that remains poorly understood at the molecular level. Invertebrate model systems, like "Caenorhabditis elegans," can be a powerful tool for investigating this fundamental process. Here we established a high-throughput learning assay that used real-time computer vision software for behavioral…

A New Exploration of the Torsional Energy Surface of N-Pentane Using Molecular Modeling Software

ERIC Educational Resources Information Center

Galembeck, Sergio E.; Caramori, Giovanni F.; Romero, Jose Ricardo

2005-01-01

The torsional potential energy surface of a chemical compounds, the accessible conformations at a specified temperature and the transition states that connect these confirmations establishes many chemical properties such as dynamic behavior, reactivity and biological activity. A conformational search of n-pentane is presented using computational…

Fullrmc, a rigid body Reverse Monte Carlo modeling package enabled with machine learning and artificial intelligence.

PubMed

Aoun, Bachir

2016-05-05

A new Reverse Monte Carlo (RMC) package "fullrmc" for atomic or rigid body and molecular, amorphous, or crystalline materials is presented. fullrmc main purpose is to provide a fully modular, fast and flexible software, thoroughly documented, complex molecules enabled, written in a modern programming language (python, cython, C and C++ when performance is needed) and complying to modern programming practices. fullrmc approach in solving an atomic or molecular structure is different from existing RMC algorithms and software. In a nutshell, traditional RMC methods and software randomly adjust atom positions until the whole system has the greatest consistency with a set of experimental data. In contrast, fullrmc applies smart moves endorsed with reinforcement machine learning to groups of atoms. While fullrmc allows running traditional RMC modeling, the uniqueness of this approach resides in its ability to customize grouping atoms in any convenient way with no additional programming efforts and to apply smart and more physically meaningful moves to the defined groups of atoms. In addition, fullrmc provides a unique way with almost no additional computational cost to recur a group's selection, allowing the system to go out of local minimas by refining a group's position or exploring through and beyond not allowed positions and energy barriers the unrestricted three dimensional space around a group. © 2016 Wiley Periodicals, Inc.

Fullrmc, a rigid body reverse monte carlo modeling package enabled with machine learning and artificial intelligence

DOE PAGES

Aoun, Bachir

2016-01-22

Here, a new Reverse Monte Carlo (RMC) package ‘fullrmc’ for atomic or rigid body and molecular, amorphous or crystalline materials is presented. fullrmc main purpose is to provide a fully modular, fast and flexible software, thoroughly documented, complex molecules enabled, written in a modern programming language (python, cython ,C and C++ when performance is needed) and complying to modern programming practices. fullrmc approach in solving an atomic or molecular structure is different from existing RMC algorithms and software. In a nutshell, traditional RMC methods and software randomly adjust atom positions until the whole system has the greatest consistency with amore » set of experimental data. In contrast, fullrmc applies smart moves endorsed with reinforcement machine learning to groups of atoms. While fullrmc allows running traditional RMC modelling, the uniqueness of this approach resides in its ability to customize grouping atoms in any convenient way with no additional programming efforts and to apply smart and more physically meaningful moves to the defined groups of atoms. Also fullrmc provides a unique way with almost no additional computational cost to recur a group’s selection, allowing the system to go out of local minimas by refining a group’s position or exploring through and beyond not allowed positions and energy barriers the unrestricted three dimensional space around a group.« less

Fullrmc, a rigid body reverse monte carlo modeling package enabled with machine learning and artificial intelligence

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aoun, Bachir

Here, a new Reverse Monte Carlo (RMC) package ‘fullrmc’ for atomic or rigid body and molecular, amorphous or crystalline materials is presented. fullrmc main purpose is to provide a fully modular, fast and flexible software, thoroughly documented, complex molecules enabled, written in a modern programming language (python, cython ,C and C++ when performance is needed) and complying to modern programming practices. fullrmc approach in solving an atomic or molecular structure is different from existing RMC algorithms and software. In a nutshell, traditional RMC methods and software randomly adjust atom positions until the whole system has the greatest consistency with amore » set of experimental data. In contrast, fullrmc applies smart moves endorsed with reinforcement machine learning to groups of atoms. While fullrmc allows running traditional RMC modelling, the uniqueness of this approach resides in its ability to customize grouping atoms in any convenient way with no additional programming efforts and to apply smart and more physically meaningful moves to the defined groups of atoms. Also fullrmc provides a unique way with almost no additional computational cost to recur a group’s selection, allowing the system to go out of local minimas by refining a group’s position or exploring through and beyond not allowed positions and energy barriers the unrestricted three dimensional space around a group.« less

DMG-α--a computational geometry library for multimolecular systems.

PubMed

Szczelina, Robert; Murzyn, Krzysztof

2014-11-24

The DMG-α library grants researchers in the field of computational biology, chemistry, and biophysics access to an open-sourced, easy to use, and intuitive software for performing fine-grained geometric analysis of molecular systems. The library is capable of computing power diagrams (weighted Voronoi diagrams) in three dimensions with 3D periodic boundary conditions, computing approximate projective 2D Voronoi diagrams on arbitrarily defined surfaces, performing shape properties recognition using α-shape theory and can do exact Solvent Accessible Surface Area (SASA) computation. The software is written mainly as a template-based C++ library for greater performance, but a rich Python interface (pydmga) is provided as a convenient way to manipulate the DMG-α routines. To illustrate possible applications of the DMG-α library, we present results of sample analyses which allowed to determine nontrivial geometric properties of two Escherichia coli-specific lipids as emerging from molecular dynamics simulations of relevant model bilayers.

High-Resolution Spectroscopic Database for the NASA Earth Observing System Program

NASA Technical Reports Server (NTRS)

Rothman, Laurence

2003-01-01

The purpose of this project is to develop and enhance the HITRAN molecular spectroscopic database and associated software to support the observational programs of the Earth Observing System (EOS). In particular, the focus is on the EOS projects: the Atmospheric Infrared Sounder (AIRS), the High-Resolution Dynamics Limb Sounder (HIRDLS), Measurements of Pollution in the Troposphere (MOPITT), the Tropospheric Emission Spectrometer (TES), and the Stratospheric Aerosol and Gas Experiment (SAGE III). The HITRAN program is also involved in the Ozone Monitoring Experiment (OMI). The data requirements of these programs in terms of spectroscopy are varied with respect to constituents being observed, required remote-sensing parameters, and spectral coverage. A general requisite is for additional spectral parameters and improvements to existing molecular bands sufficient for the simulation of the observations leading to retrieval of the atmospheric state. In addition, cross-section data for heavier molecular species must be expanded and made amenable to modeling in remote sensing. The effort in the project also includes developing software and distribution to make access, manipulation, and use of HITRAN functional to the EOS program.

High Resolution Spectroscopic Database for the NASA Earth Observing System Program

NASA Technical Reports Server (NTRS)

Rothman, Laurence

2004-01-01

The purpose of this project has been to develop and enhance the HITRAN molecular spectroscopic database and associated software to support the observational programs of the Earth Observing System (EOS). Emphasis has been on the EOS projects: the Atmospheric Infrared Sounder (AIRS), the High-Resolution Dynamics Limb Sounder (HIRDLS), Measurements of Pollution in the Troposphere (MOPITT), the Tropospheric Emission Spectrometer (TES), and the Stratospheric Aerosol and Gas Experiment (SAGE III). The HITRAN program is also involved in the Ozone Monitoring Experiment (OMI). The data requirements of these programs in terms of spectroscopy are varied with respect to constituents being observed, required remote-sensing parameters, and spectral coverage. A general requisite is for additional spectral parameters and improvements to existing molecular bands sufficient for the simulation of the observations leading to retrieval of the atmospheric state. In addition, cross-section data for heavier molecular species must be expanded and made amenable to modeling in remote sensing. The effort in the project also includes developing software and distribution to make access, manipulation, and use of HITRAN functional to the EOS program.

High-Resolution Spectroscopic Database for the NASA Earth Observing System Program

NASA Technical Reports Server (NTRS)

Rothman, Laurence S.

2004-01-01

The purpose of this project is to develop and enhance the HITRAN molecular spectroscopic database and associated - software to support the observational programs of the Earth observing System (EOS). In particular, the focus is on the EOS projects: the Atmospheric Infrared Sounder (AIRS), the High-Resolution Dynamics Limb Sounder (HIRDLS), Measurements of Pollution in the Troposphere (MOPITT), the Tropospheric Emission Spectrometer (TES), and the Stratospheric Aerosol and Gas Experiment (SAGE III). The HITRAN program is also involved in the Ozone Monitoring Experiment (OMI). The data requirements of these programs in terms of spectroscopy are varied with respect to constituents being observed, required remote-sensing parameters, and spectral coverage. A general requisite is for additional spectral parameters and improvements to existing molecular bands sufficient for the simulation of the observations leading to retrieval of the atmospheric state. In addition cross-section data for heavier molecular species must be expanded and made amenable to modeling in remote sensing. The effort in the project also includes developing software and distribution to make access, manipulation, and use HITRAN functional to the EOS program.

PyMOL mControl: Manipulating molecular visualization with mobile devices.

PubMed

Lam, Wendy W T; Siu, Shirley W I

2017-01-02

Viewing and manipulating three-dimensional (3D) structures in molecular graphics software are essential tasks for researchers and students to understand the functions of molecules. Currently, the way to manipulate a 3D molecular object is mainly based on mouse-and-keyboard control that is usually difficult and tedious to learn. While gesture-based and touch-based interactions are increasingly popular in interactive software systems, their suitability in handling molecular graphics has not yet been sufficiently explored. Here, we designed the gesture-based and touch-based interaction methods to manipulate virtual objects in PyMOL utilizing the motion and touch sensors in a mobile device. Three fundamental viewing controls-zooming, translation and rotation-and frequently used functions were implemented. Results from a pilot user study reveal that task performances on viewing controls using a mobile device are slightly reduced as compared to mouse-and-keyboard method. However, it is considered to be more suitable for oral presentations and equally suitable for education scenarios such as school classes. Overall, PyMOL mControl provides an alternative way to manipulate objects in molecular graphic software with new user experiences. The software is freely available at http://cbbio.cis.umac.mo/mcontrol.html. © 2016 by The International Union of Biochemistry and Molecular Biology, 45(1):76-83, 2017. © 2016 The International Union of Biochemistry and Molecular Biology.

GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations.

PubMed

Jung, Jaewoon; Mori, Takaharu; Kobayashi, Chigusa; Matsunaga, Yasuhiro; Yoda, Takao; Feig, Michael; Sugita, Yuji

2015-07-01

GENESIS (Generalized-Ensemble Simulation System) is a new software package for molecular dynamics (MD) simulations of macromolecules. It has two MD simulators, called ATDYN and SPDYN. ATDYN is parallelized based on an atomic decomposition algorithm for the simulations of all-atom force-field models as well as coarse-grained Go-like models. SPDYN is highly parallelized based on a domain decomposition scheme, allowing large-scale MD simulations on supercomputers. Hybrid schemes combining OpenMP and MPI are used in both simulators to target modern multicore computer architectures. Key advantages of GENESIS are (1) the highly parallel performance of SPDYN for very large biological systems consisting of more than one million atoms and (2) the availability of various REMD algorithms (T-REMD, REUS, multi-dimensional REMD for both all-atom and Go-like models under the NVT, NPT, NPAT, and NPγT ensembles). The former is achieved by a combination of the midpoint cell method and the efficient three-dimensional Fast Fourier Transform algorithm, where the domain decomposition space is shared in real-space and reciprocal-space calculations. Other features in SPDYN, such as avoiding concurrent memory access, reducing communication times, and usage of parallel input/output files, also contribute to the performance. We show the REMD simulation results of a mixed (POPC/DMPC) lipid bilayer as a real application using GENESIS. GENESIS is released as free software under the GPLv2 licence and can be easily modified for the development of new algorithms and molecular models. WIREs Comput Mol Sci 2015, 5:310-323. doi: 10.1002/wcms.1220.

Bayesian random local clocks, or one rate to rule them all

PubMed Central

2010-01-01

Background Relaxed molecular clock models allow divergence time dating and "relaxed phylogenetic" inference, in which a time tree is estimated in the face of unequal rates across lineages. We present a new method for relaxing the assumption of a strict molecular clock using Markov chain Monte Carlo to implement Bayesian modeling averaging over random local molecular clocks. The new method approaches the problem of rate variation among lineages by proposing a series of local molecular clocks, each extending over a subregion of the full phylogeny. Each branch in a phylogeny (subtending a clade) is a possible location for a change of rate from one local clock to a new one. Thus, including both the global molecular clock and the unconstrained model results, there are a total of 22n-2 possible rate models available for averaging with 1, 2, ..., 2n - 2 different rate categories. Results We propose an efficient method to sample this model space while simultaneously estimating the phylogeny. The new method conveniently allows a direct test of the strict molecular clock, in which one rate rules them all, against a large array of alternative local molecular clock models. We illustrate the method's utility on three example data sets involving mammal, primate and influenza evolution. Finally, we explore methods to visualize the complex posterior distribution that results from inference under such models. Conclusions The examples suggest that large sequence datasets may only require a small number of local molecular clocks to reconcile their branch lengths with a time scale. All of the analyses described here are implemented in the open access software package BEAST 1.5.4 (http://beast-mcmc.googlecode.com/). PMID:20807414

Automated measurement of zebrafish larval movement

PubMed Central

Cario, Clinton L; Farrell, Thomas C; Milanese, Chiara; Burton, Edward A

2011-01-01

Abstract The zebrafish is a powerful vertebrate model that is readily amenable to genetic, pharmacological and environmental manipulations to elucidate the molecular and cellular basis of movement and behaviour. We report software enabling automated analysis of zebrafish movement from video recordings captured with cameras ranging from a basic camcorder to more specialized equipment. The software, which is provided as open-source MATLAB functions, can be freely modified and distributed, and is compatible with multiwell plates under a wide range of experimental conditions. Automated measurement of zebrafish movement using this technique will be useful for multiple applications in neuroscience, pharmacology and neuropsychiatry. PMID:21646414

Automated measurement of zebrafish larval movement.

PubMed

Cario, Clinton L; Farrell, Thomas C; Milanese, Chiara; Burton, Edward A

2011-08-01

The zebrafish is a powerful vertebrate model that is readily amenable to genetic, pharmacological and environmental manipulations to elucidate the molecular and cellular basis of movement and behaviour. We report software enabling automated analysis of zebrafish movement from video recordings captured with cameras ranging from a basic camcorder to more specialized equipment. The software, which is provided as open-source MATLAB functions, can be freely modified and distributed, and is compatible with multiwell plates under a wide range of experimental conditions. Automated measurement of zebrafish movement using this technique will be useful for multiple applications in neuroscience, pharmacology and neuropsychiatry.

MIiSR: Molecular Interactions in Super-Resolution Imaging Enables the Analysis of Protein Interactions, Dynamics and Formation of Multi-protein Structures.

PubMed

Caetano, Fabiana A; Dirk, Brennan S; Tam, Joshua H K; Cavanagh, P Craig; Goiko, Maria; Ferguson, Stephen S G; Pasternak, Stephen H; Dikeakos, Jimmy D; de Bruyn, John R; Heit, Bryan

2015-12-01

Our current understanding of the molecular mechanisms which regulate cellular processes such as vesicular trafficking has been enabled by conventional biochemical and microscopy techniques. However, these methods often obscure the heterogeneity of the cellular environment, thus precluding a quantitative assessment of the molecular interactions regulating these processes. Herein, we present Molecular Interactions in Super Resolution (MIiSR) software which provides quantitative analysis tools for use with super-resolution images. MIiSR combines multiple tools for analyzing intermolecular interactions, molecular clustering and image segmentation. These tools enable quantification, in the native environment of the cell, of molecular interactions and the formation of higher-order molecular complexes. The capabilities and limitations of these analytical tools are demonstrated using both modeled data and examples derived from the vesicular trafficking system, thereby providing an established and validated experimental workflow capable of quantitatively assessing molecular interactions and molecular complex formation within the heterogeneous environment of the cell.

Toward a reaction rate model of condensed-phase RDX decomposition under high temperatures

NASA Astrophysics Data System (ADS)

Schweigert, Igor

2014-03-01

Shock ignition of energetic molecular solids is driven by microstructural heterogeneities, at which even moderate stresses can result in sufficiently high temperatures to initiate material decomposition and the release of the chemical energy. Mesoscale modeling of these ``hot spots'' requires a chemical reaction rate model that describes the energy release with a sub-microsecond resolution and under a wide range of temperatures. No such model is available even for well-studied energetic materials such as RDX. In this presentation, I will describe an ongoing effort to develop a reaction rate model of condensed-phase RDX decomposition under high temperatures using first-principles molecular dynamics, transition-state theory, and reaction network analysis. This work was supported by the Naval Research Laboratory, by the Office of Naval Research, and by the DOD High Performance Computing Modernization Program Software Application Institute for Multiscale Reactive Modeling of Insensitive Munitions.

Toward a reaction rate model of condensed-phase RDX decomposition under high temperatures

NASA Astrophysics Data System (ADS)

Schweigert, Igor

2015-06-01

Shock ignition of energetic molecular solids is driven by microstructural heterogeneities, at which even moderate stresses can result in sufficiently high temperatures to initiate material decomposition and chemical energy release. Mesoscale modeling of these ``hot spots'' requires a reaction rate model that describes the energy release with a sub-microsecond resolution and under a wide range of temperatures. No such model is available even for well-studied energetic materials such as RDX. In this presentation, I will describe an ongoing effort to develop a reaction rate model of condensed-phase RDX decomposition under high temperatures using first-principles molecular dynamics, transition-state theory, and reaction network analysis. This work was supported by the Naval Research Laboratory, by the Office of Naval Research, and by the DoD High Performance Computing Modernization Program Software Application Institute for Multiscale Reactive Modeling of Insensitive Munitions.

Molecular Modeling, Docking, Dynamics and simulation of Gefitinib and its derivatives with EGFR in Non-Small Cell Lung Cancer.

PubMed

Reddy, Pulakuntla Swetha; Lokhande, Kiran Bharat; Nagar, Shuchi; Reddy, Vaddi Damodara; Murthy, P Sushma; Swamy, K Venkateswara

2018-02-27

Gefitinib (lressa) is the most prescribed drug, highly effective to treat of non-small cell lung cancer; primarily it was considered targeted therapy is a kinase inhibitor. The non-small cell lung cancer caused by the mutation in the Epithelial Growth Factor Receptor (EGFR) gene, Iressa works by blocking the EGFR protein that helps the cancer cell growth. EGFR protein has lead to the development of anticancer therapeutics directed against EGFR inhibitor including Gefitinib for non-small cell lung cancer. To explore research on Gefitinib and its derivatives interaction with crystal structure EGFR to understand the better molecular insights interaction strategies. Molecular modeling of ligands (Gefitinib and its derivatives) was carried out by Avogadro software till atomic angle stable confirmation obtained. The partial charges for the ligands were assigned as per standard protocol for molecular docking. All docking simulations were performed with AutoDockVina. Virtual screening carried out based on binding energy and hydrogen bonding affinity. Molecular dynamics (MD) and Simulation EGFR was done using GROMACS 5.1.1 software to explore the interaction stability in a cell. The stable conformation for EGFR protein trajectories were captured at various time intervals 0-20ns. Few compounds screen based on high affinity as the inhibitor for EGFR may inhibit the cell cycle signalling in non-small cell lung cancer. These result suggested that a computer aided screening approach of a Gefitinib derivatives compounds with regard to their binding to EGFR for identifying novel drugs for the treatment of non-small cell lung cancer. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Integrating open-source software applications to build molecular dynamics systems.

PubMed

Allen, Bruce M; Predecki, Paul K; Kumosa, Maciej

2014-04-05

Three open-source applications, NanoEngineer-1, packmol, and mis2lmp are integrated using an open-source file format to quickly create molecular dynamics (MD) cells for simulation. The three software applications collectively make up the open-source software (OSS) suite known as MD Studio (MDS). The software is validated through software engineering practices and is verified through simulation of the diglycidyl ether of bisphenol-a and isophorone diamine (DGEBA/IPD) system. Multiple simulations are run using the MDS software to create MD cells, and the data generated are used to calculate density, bulk modulus, and glass transition temperature of the DGEBA/IPD system. Simulation results compare well with published experimental and numerical results. The MDS software prototype confirms that OSS applications can be analyzed against real-world research requirements and integrated to create a new capability. Copyright © 2014 Wiley Periodicals, Inc.

QuBiLS-MIDAS: a parallel free-software for molecular descriptors computation based on multilinear algebraic maps.

PubMed

García-Jacas, César R; Marrero-Ponce, Yovani; Acevedo-Martínez, Liesner; Barigye, Stephen J; Valdés-Martiní, José R; Contreras-Torres, Ernesto

2014-07-05

The present report introduces the QuBiLS-MIDAS software belonging to the ToMoCoMD-CARDD suite for the calculation of three-dimensional molecular descriptors (MDs) based on the two-linear (bilinear), three-linear, and four-linear (multilinear or N-linear) algebraic forms. Thus, it is unique software that computes these tensor-based indices. These descriptors, establish relations for two, three, and four atoms by using several (dis-)similarity metrics or multimetrics, matrix transformations, cutoffs, local calculations and aggregation operators. The theoretical background of these N-linear indices is also presented. The QuBiLS-MIDAS software was developed in the Java programming language and employs the Chemical Development Kit library for the manipulation of the chemical structures and the calculation of the atomic properties. This software is composed by a desktop user-friendly interface and an Abstract Programming Interface library. The former was created to simplify the configuration of the different options of the MDs, whereas the library was designed to allow its easy integration to other software for chemoinformatics applications. This program provides functionalities for data cleaning tasks and for batch processing of the molecular indices. In addition, it offers parallel calculation of the MDs through the use of all available processors in current computers. The studies of complexity of the main algorithms demonstrate that these were efficiently implemented with respect to their trivial implementation. Lastly, the performance tests reveal that this software has a suitable behavior when the amount of processors is increased. Therefore, the QuBiLS-MIDAS software constitutes a useful application for the computation of the molecular indices based on N-linear algebraic maps and it can be used freely to perform chemoinformatics studies. Copyright © 2014 Wiley Periodicals, Inc.

pysimm: A Python Package for Simulation of Molecular Systems

NASA Astrophysics Data System (ADS)

Fortunato, Michael; Colina, Coray

pysimm, short for python simulation interface for molecular modeling, is a python package designed to facilitate the structure generation and simulation of molecular systems through convenient and programmatic access to object-oriented representations of molecular system data. This poster presents core features of pysimm and design philosophies that highlight a generalized methodology for incorporation of third-party software packages through API interfaces. The integration with the LAMMPS simulation package is explained to demonstrate this methodology. pysimm began as a back-end python library that powered a cloud-based application on nanohub.org for amorphous polymer simulation. The extension from a specific application library to general purpose simulation interface is explained. Additionally, this poster highlights the rapid development of new applications to construct polymer chains capable of controlling chain morphology such as molecular weight distribution and monomer composition.

Application of the Monte Carlo method for building up models for octanol-water partition coefficient of platinum complexes

NASA Astrophysics Data System (ADS)

Toropov, Andrey A.; Toropova, Alla P.

2018-06-01

Predictive model of logP for Pt(II) and Pt(IV) complexes built up with the Monte Carlo method using the CORAL software has been validated with six different splits into the training and validation sets. The improving of the predictive potential of models for six different splits has been obtained using so-called index of ideality of correlation. The suggested models give possibility to extract molecular features, which cause the increase or vice versa decrease of the logP.

Molecular Genetics Information System (MOLGENIS): alternatives in developing local experimental genomics databases.

PubMed

Swertz, Morris A; De Brock, E O; Van Hijum, Sacha A F T; De Jong, Anne; Buist, Girbe; Baerends, Richard J S; Kok, Jan; Kuipers, Oscar P; Jansen, Ritsert C

2004-09-01

Genomic research laboratories need adequate infrastructure to support management of their data production and research workflow. But what makes infrastructure adequate? A lack of appropriate criteria makes any decision on buying or developing a system difficult. Here, we report on the decision process for the case of a molecular genetics group establishing a microarray laboratory. Five typical requirements for experimental genomics database systems were identified: (i) evolution ability to keep up with the fast developing genomics field; (ii) a suitable data model to deal with local diversity; (iii) suitable storage of data files in the system; (iv) easy exchange with other software; and (v) low maintenance costs. The computer scientists and the researchers of the local microarray laboratory considered alternative solutions for these five requirements and chose the following options: (i) use of automatic code generation; (ii) a customized data model based on standards; (iii) storage of datasets as black boxes instead of decomposing them in database tables; (iv) loosely linking to other programs for improved flexibility; and (v) a low-maintenance web-based user interface. Our team evaluated existing microarray databases and then decided to build a new system, Molecular Genetics Information System (MOLGENIS), implemented using code generation in a period of three months. This case can provide valuable insights and lessons to both software developers and a user community embarking on large-scale genomic projects. http://www.molgenis.nl

Computer-Based Semantic Network in Molecular Biology: A Demonstration.

ERIC Educational Resources Information Center

Callman, Joshua L.; And Others

This paper analyzes the hardware and software features that would be desirable in a computer-based semantic network system for representing biology knowledge. It then describes in detail a prototype network of molecular biology knowledge that has been developed using Filevision software and a Macintosh computer. The prototype contains about 100…

Optimizing legacy molecular dynamics software with directive-based offload

NASA Astrophysics Data System (ADS)

Michael Brown, W.; Carrillo, Jan-Michael Y.; Gavhane, Nitin; Thakkar, Foram M.; Plimpton, Steven J.

2015-10-01

Directive-based programming models are one solution for exploiting many-core coprocessors to increase simulation rates in molecular dynamics. They offer the potential to reduce code complexity with offload models that can selectively target computations to run on the CPU, the coprocessor, or both. In this paper, we describe modifications to the LAMMPS molecular dynamics code to enable concurrent calculations on a CPU and coprocessor. We demonstrate that standard molecular dynamics algorithms can run efficiently on both the CPU and an x86-based coprocessor using the same subroutines. As a consequence, we demonstrate that code optimizations for the coprocessor also result in speedups on the CPU; in extreme cases up to 4.7X. We provide results for LAMMPS benchmarks and for production molecular dynamics simulations using the Stampede hybrid supercomputer with both Intel® Xeon Phi™ coprocessors and NVIDIA GPUs. The optimizations presented have increased simulation rates by over 2X for organic molecules and over 7X for liquid crystals on Stampede. The optimizations are available as part of the "Intel package" supplied with LAMMPS.

BioMOL: a computer-assisted biological modeling tool for complex chemical mixtures and biological processes at the molecular level.

PubMed Central

Klein, Michael T; Hou, Gang; Quann, Richard J; Wei, Wei; Liao, Kai H; Yang, Raymond S H; Campain, Julie A; Mazurek, Monica A; Broadbelt, Linda J

2002-01-01

A chemical engineering approach for the rigorous construction, solution, and optimization of detailed kinetic models for biological processes is described. This modeling capability addresses the required technical components of detailed kinetic modeling, namely, the modeling of reactant structure and composition, the building of the reaction network, the organization of model parameters, the solution of the kinetic model, and the optimization of the model. Even though this modeling approach has enjoyed successful application in the petroleum industry, its application to biomedical research has just begun. We propose to expand the horizons on classic pharmacokinetics and physiologically based pharmacokinetics (PBPK), where human or animal bodies were often described by a few compartments, by integrating PBPK with reaction network modeling described in this article. If one draws a parallel between an oil refinery, where the application of this modeling approach has been very successful, and a human body, the individual processing units in the oil refinery may be considered equivalent to the vital organs of the human body. Even though the cell or organ may be much more complicated, the complex biochemical reaction networks in each organ may be similarly modeled and linked in much the same way as the modeling of the entire oil refinery through linkage of the individual processing units. The integrated chemical engineering software package described in this article, BioMOL, denotes the biological application of molecular-oriented lumping. BioMOL can build a detailed model in 1-1,000 CPU sec using standard desktop hardware. The models solve and optimize using standard and widely available hardware and software and can be presented in the context of a user-friendly interface. We believe this is an engineering tool with great promise in its application to complex biological reaction networks. PMID:12634134

Discovery of novel inhibitors of Mycobacterium tuberculosis MurG: homology modelling, structure based pharmacophore, molecular docking, and molecular dynamics simulations.

PubMed

Saxena, Shalini; Abdullah, Maaged; Sriram, Dharmarajan; Guruprasad, Lalitha

2017-10-17

MurG (Rv2153c) is a key player in the biosynthesis of the peptidoglycan layer in Mycobacterium tuberculosis (Mtb). This work is an attempt to highlight the structural and functional relationship of Mtb MurG, the three-dimensional (3D) structure of protein was constructed by homology modelling using Discovery Studio 3.5 software. The quality and consistency of generated model was assessed by PROCHECK, ProSA and ERRAT. Later, the model was optimized by molecular dynamics (MD) simulations and the optimized model complex with substrate Uridine-diphosphate-N-acetylglucosamine (UD1) facilitated us to employ structure-based virtual screening approach to obtain new hits from Asinex database using energy-optimized pharmacophore modelling (e-pharmacophore). The pharmacophore model was validated using enrichment calculations, and finally, validated model was employed for high-throughput virtual screening and molecular docking to identify novel Mtb MurG inhibitors. This study led to the identification of 10 potential compounds with good fitness, docking score, which make important interactions with the protein active site. The 25 ns MD simulations of three potential lead compounds with protein confirmed that the structure was stable and make several non-bonding interactions with amino acids, such as Leu290, Met310 and Asn167. Hence, we concluded that the identified compounds may act as new leads for the design of Mtb MurG inhibitors.

GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations

PubMed Central

Jung, Jaewoon; Mori, Takaharu; Kobayashi, Chigusa; Matsunaga, Yasuhiro; Yoda, Takao; Feig, Michael; Sugita, Yuji

2015-01-01

GENESIS (Generalized-Ensemble Simulation System) is a new software package for molecular dynamics (MD) simulations of macromolecules. It has two MD simulators, called ATDYN and SPDYN. ATDYN is parallelized based on an atomic decomposition algorithm for the simulations of all-atom force-field models as well as coarse-grained Go-like models. SPDYN is highly parallelized based on a domain decomposition scheme, allowing large-scale MD simulations on supercomputers. Hybrid schemes combining OpenMP and MPI are used in both simulators to target modern multicore computer architectures. Key advantages of GENESIS are (1) the highly parallel performance of SPDYN for very large biological systems consisting of more than one million atoms and (2) the availability of various REMD algorithms (T-REMD, REUS, multi-dimensional REMD for both all-atom and Go-like models under the NVT, NPT, NPAT, and NPγT ensembles). The former is achieved by a combination of the midpoint cell method and the efficient three-dimensional Fast Fourier Transform algorithm, where the domain decomposition space is shared in real-space and reciprocal-space calculations. Other features in SPDYN, such as avoiding concurrent memory access, reducing communication times, and usage of parallel input/output files, also contribute to the performance. We show the REMD simulation results of a mixed (POPC/DMPC) lipid bilayer as a real application using GENESIS. GENESIS is released as free software under the GPLv2 licence and can be easily modified for the development of new algorithms and molecular models. WIREs Comput Mol Sci 2015, 5:310–323. doi: 10.1002/wcms.1220 PMID:26753008

skelesim: an extensible, general framework for population genetic simulation in R.

PubMed

Parobek, Christian M; Archer, Frederick I; DePrenger-Levin, Michelle E; Hoban, Sean M; Liggins, Libby; Strand, Allan E

2017-01-01

Simulations are a key tool in molecular ecology for inference and forecasting, as well as for evaluating new methods. Due to growing computational power and a diversity of software with different capabilities, simulations are becoming increasingly powerful and useful. However, the widespread use of simulations by geneticists and ecologists is hindered by difficulties in understanding these softwares' complex capabilities, composing code and input files, a daunting bioinformatics barrier and a steep conceptual learning curve. skelesim (an R package) guides users in choosing appropriate simulations, setting parameters, calculating genetic summary statistics and organizing data output, in a reproducible pipeline within the R environment. skelesim is designed to be an extensible framework that can 'wrap' around any simulation software (inside or outside the R environment) and be extended to calculate and graph any genetic summary statistics. Currently, skelesim implements coalescent and forward-time models available in the fastsimcoal2 and rmetasim simulation engines to produce null distributions for multiple population genetic statistics and marker types, under a variety of demographic conditions. skelesim is intended to make simulations easier while still allowing full model complexity to ensure that simulations play a fundamental role in molecular ecology investigations. skelesim can also serve as a teaching tool: demonstrating the outcomes of stochastic population genetic processes; teaching general concepts of simulations; and providing an introduction to the R environment with a user-friendly graphical user interface (using shiny). © 2016 John Wiley & Sons Ltd.

[Quantitative relationship between gas chromatographic retention time and structural parameters of alkylphenols].

PubMed

Ruan, Xiaofang; Zhang, Ruisheng; Yao, Xiaojun; Liu, Mancang; Fan, Botao

2007-03-01

Alkylphenols are a group of permanent pollutants in the environment and could adversely disturb the human endocrine system. It is therefore important to effectively separate and measure the alkylphenols. To guide the chromatographic analysis of these compounds in practice, the development of quantitative relationship between the molecular structure and the retention time of alkylphenols becomes necessary. In this study, topological, constitutional, geometrical, electrostatic and quantum-chemical descriptors of 44 alkylphenols were calculated using a software, CODESSA, and these descriptors were pre-selected using the heuristic method. As a result, three-descriptor linear model (LM) was developed to describe the relationship between the molecular structure and the retention time of alkylphenols. Meanwhile, the non-linear regression model was also developed based on support vector machine (SVM) using the same three descriptors. The correlation coefficient (R(2)) for the LM and SVM was 0.98 and 0. 92, and the corresponding root-mean-square error was 0. 99 and 2. 77, respectively. By comparing the stability and prediction ability of the two models, it was found that the linear model was a better method for describing the quantitative relationship between the retention time of alkylphenols and the molecular structure. The results obtained suggested that the linear model could be applied for the chromatographic analysis of alkylphenols with known molecular structural parameters.

Visually impaired researchers get their hands on quantum chemistry: application to a computational study on the isomerization of a sterol.

PubMed

Lounnas, Valère; Wedler, Henry B; Newman, Timothy; Schaftenaar, Gijs; Harrison, Jason G; Nepomuceno, Gabriella; Pemberton, Ryan; Tantillo, Dean J; Vriend, Gert

2014-11-01

In molecular sciences, articles tend to revolve around 2D representations of 3D molecules, and sighted scientists often resort to 3D virtual reality software to study these molecules in detail. Blind and visually impaired (BVI) molecular scientists have access to a series of audio devices that can help them read the text in articles and work with computers. Reading articles published in this journal, though, is nearly impossible for them because they need to generate mental 3D images of molecules, but the article-reading software cannot do that for them. We have previously designed AsteriX, a web server that fully automatically decomposes articles, detects 2D plots of low molecular weight molecules, removes meta data and annotations from these plots, and converts them into 3D atomic coordinates. AsteriX-BVI goes one step further and converts the 3D representation into a 3D printable, haptic-enhanced format that includes Braille annotations. These Braille-annotated physical 3D models allow BVI scientists to generate a complete mental model of the molecule. AsteriX-BVI uses Molden to convert the meta data of quantum chemistry experiments into BVI friendly formats so that the entire line of scientific information that sighted people take for granted-from published articles, via printed results of computational chemistry experiments, to 3D models-is now available to BVI scientists too. The possibilities offered by AsteriX-BVI are illustrated by a project on the isomerization of a sterol, executed by the blind co-author of this article (HBW).

Asymmetric Epoxidation: A Twinned Laboratory and Molecular Modeling Experiment for Upper-Level Organic Chemistry Students

ERIC Educational Resources Information Center

Hii, King Kuok; Rzepa, Henry S.; Smith, Edward H.

2015-01-01

The coupling of a student experiment involving the preparation and use of a catalyst for the asymmetric epoxidation of an alkene with computational simulations of various properties of the resulting epoxide is set out in the form of a software toolbox from which students select appropriate components. At the core of these are the computational…

Development of monograph titled "augmented chemistry aldehida & keton" with 3 dimensional (3D) illustration as a supplement book on chemistry learning

NASA Astrophysics Data System (ADS)

Damayanti, Latifah Adelina; Ikhsan, Jaslin

2017-05-01

Integration of information technology in education more rapidly performed in a medium of learning. Three-dimensional (3D) molecular modeling was performed in Augmented Reality as a tangible manifestation of increasingly modern technology utilization. Based on augmented reality, three-dimensional virtual object is projected in real time and the exact environment. This paper reviewed the uses of chemical learning supplement book of aldehydes and ketones which are equipped with three-dimensional molecular modeling by which students can inspect molecules from various viewpoints. To plays the 3D illustration printed on the book, smartphones with the open-source software of the technology based integrated Augmented Reality can be used. The aims of this research were to develop the monograph of aldehydes and ketones with 3 dimensional (3D) illustrations, to determine the specification of the monograph, and to determine the quality of the monograph. The quality of the monograph is evaluated by experiencing chemistry teachers on the five aspects of contents/materials, presentations, language and images, graphs, and software engineering, resulted in the result that the book has a very good quality to be used as a chemistry learning supplement book.

Environmental and Molecular Science Laboratory Arrow

DOE Office of Scientific and Technical Information (OSTI.GOV)

2016-06-24

Arrows is a software package that combines NWChem, SQL and NOSQL databases, email, and social networks (e.g. Twitter, Tumblr) that simplifies molecular and materials modeling and makes these modeling capabilities accessible to all scientists and engineers. EMSL Arrows is very simple to use. The user just emails chemical reactions to arrows@emsl.pnnl.gov and then an email is sent back with thermodynamic, reaction pathway (kinetic), spectroscopy, and other results. EMSL Arrows parses the email and then searches the database for the compounds in the reactions. If a compound isn't there, an NWChem calculation is setup and submitted to calculate it. Once themore » calculation is finished the results are entered into the database and then results are emailed back.« less

The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button

PubMed Central

2010-01-01

Background There is a huge demand on bioinformaticians to provide their biologists with user friendly and scalable software infrastructures to capture, exchange, and exploit the unprecedented amounts of new *omics data. We here present MOLGENIS, a generic, open source, software toolkit to quickly produce the bespoke MOLecular GENetics Information Systems needed. Methods The MOLGENIS toolkit provides bioinformaticians with a simple language to model biological data structures and user interfaces. At the push of a button, MOLGENIS’ generator suite automatically translates these models into a feature-rich, ready-to-use web application including database, user interfaces, exchange formats, and scriptable interfaces. Each generator is a template of SQL, JAVA, R, or HTML code that would require much effort to write by hand. This ‘model-driven’ method ensures reuse of best practices and improves quality because the modeling language and generators are shared between all MOLGENIS applications, so that errors are found quickly and improvements are shared easily by a re-generation. A plug-in mechanism ensures that both the generator suite and generated product can be customized just as much as hand-written software. Results In recent years we have successfully evaluated the MOLGENIS toolkit for the rapid prototyping of many types of biomedical applications, including next-generation sequencing, GWAS, QTL, proteomics and biobanking. Writing 500 lines of model XML typically replaces 15,000 lines of hand-written programming code, which allows for quick adaptation if the information system is not yet to the biologist’s satisfaction. Each application generated with MOLGENIS comes with an optimized database back-end, user interfaces for biologists to manage and exploit their data, programming interfaces for bioinformaticians to script analysis tools in R, Java, SOAP, REST/JSON and RDF, a tab-delimited file format to ease upload and exchange of data, and detailed technical documentation. Existing databases can be quickly enhanced with MOLGENIS generated interfaces using the ‘ExtractModel’ procedure. Conclusions The MOLGENIS toolkit provides bioinformaticians with a simple model to quickly generate flexible web platforms for all possible genomic, molecular and phenotypic experiments with a richness of interfaces not provided by other tools. All the software and manuals are available free as LGPLv3 open source at http://www.molgenis.org. PMID:21210979

A COMPUTER MODELING STUDY OF BINDING PROPERTIES OF CHIRAL NUCLEOPEPTIDE FOR BIOMEDICAL APPLICATIONS.

PubMed

Pirtskhalava, M; Egoyan, A; Mirtskhulava, M; Roviello, G

2017-12-01

Nucleopeptides often show interesting properties of molecular binding that render them good candidates for development of innovative drugs for anticancer and antiviral therapies. In this work we present results of computer modeling of interactions between the molecules of hexathymine nucleopeptide (T6) and poly rA RNA (A18). The results of geometry optimization calculated using Hyperchem software and our own computer program for molecular docking show that molecules establish stable complexes due to the complementary-nucleobase interaction and the electrostatic interaction between the negative phosphate group of poly rA and the positively-charged residues present in the cationic nucleopeptide structure. Computer modeling makes it possible to find the optimal binding configuration of the molecules of a nucleopeptide and poly rA RNA and to estimate the binding energy between the molecules.

Hierarchical Petascale Simulation Framework For Stress Corrosion Cracking

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grama, Ananth

2013-12-18

A number of major accomplishments resulted from the project. These include: • Data Structures, Algorithms, and Numerical Methods for Reactive Molecular Dynamics. We have developed a range of novel data structures, algorithms, and solvers (amortized ILU, Spike) for use with ReaxFF and charge equilibration. • Parallel Formulations of ReactiveMD (Purdue ReactiveMolecular Dynamics Package, PuReMD, PuReMD-GPU, and PG-PuReMD) for Messaging, GPU, and GPU Cluster Platforms. We have developed efficient serial, parallel (MPI), GPU (Cuda), and GPU Cluster (MPI/Cuda) implementations. Our implementations have been demonstrated to be significantly better than the state of the art, both in terms of performance and scalability.more » • Comprehensive Validation in the Context of Diverse Applications. We have demonstrated the use of our software in diverse systems, including silica-water, silicon-germanium nanorods, and as part of other projects, extended it to applications ranging from explosives (RDX) to lipid bilayers (biomembranes under oxidative stress). • Open Source Software Packages for Reactive Molecular Dynamics. All versions of our soft- ware have been released over the public domain. There are over 100 major research groups worldwide using our software. • Implementation into the Department of Energy LAMMPS Software Package. We have also integrated our software into the Department of Energy LAMMPS software package.« less

MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis.

PubMed

Kumar, Sudhir; Stecher, Glen; Peterson, Daniel; Tamura, Koichiro

2012-10-15

There is a growing need in the research community to apply the molecular evolutionary genetics analysis (MEGA) software tool for batch processing a large number of datasets and to integrate it into analysis workflows. Therefore, we now make available the computing core of the MEGA software as a stand-alone executable (MEGA-CC), along with an analysis prototyper (MEGA-Proto). MEGA-CC provides users with access to all the computational analyses available through MEGA's graphical user interface version. This includes methods for multiple sequence alignment, substitution model selection, evolutionary distance estimation, phylogeny inference, substitution rate and pattern estimation, tests of natural selection and ancestral sequence inference. Additionally, we have upgraded the source code for phylogenetic analysis using the maximum likelihood methods for parallel execution on multiple processors and cores. Here, we describe MEGA-CC and outline the steps for using MEGA-CC in tandem with MEGA-Proto for iterative and automated data analysis. http://www.megasoftware.net/.

Application of computer-assisted molecular modeling for immunoassay of low molecular weight food contaminants: A review.

PubMed

Xu, Zhen-Lin; Shen, Yu-Dong; Beier, Ross C; Yang, Jin-Yi; Lei, Hong-Tao; Wang, Hong; Sun, Yuan-Ming

2009-08-11

Immunoassay for low molecular weight food contaminants, such as pesticides, veterinary drugs, and mycotoxins is now a well-established technique which meets the demand for a rapid, reliable, and cost-effective analytical method. However, due to limited understanding of the molecular structure of antibody binding sites and antigenic epitopes, as well as the intermolecular binding forces that come into play, the traditional 'trial and error' method used to develop antibodies still remains the method of choice. Therefore, development of enhanced immunochemical techniques for specific- and generic-assays, requires new approaches for antibody design that will improve affinity and specificity of the antibody in a more rapid and economic manner. Computer-assisted molecular modeling (CAMM) has been demonstrated to be a useful tool to help the immunochemist develop immunoassays. CAMM methods can be used to help direct improvements to important antibody features, and can provide insights into the effects of molecular structure on biological activity that are difficult or impossible to obtain in any other way. In this review, we briefly summarize applications of CAMM in immunoassay development, including assisting in hapten design, explaining cross-reactivity, modeling antibody-antigen interactions, and providing insights into the effects of the mouse body temperature on the three-dimensional conformation of a hapten during antibody production. The fundamentals and theory, programs and software, limitations, and prospects of CAMM in immunoassay development were also discussed.

A topological substructural molecular design approach for predicting mutagenesis end-points of alpha, beta-unsaturated carbonyl compounds.

PubMed

Pérez-Garrido, Alfonso; Helguera, Aliuska Morales; López, Gabriel Caravaca; Cordeiro, M Natália D S; Escudero, Amalio Garrido

2010-01-31

Chemically reactive, alpha, beta-unsaturated carbonyl compounds are common environmental pollutants able to produce a wide range of adverse effects, including, e.g. mutagenicity. This toxic property can often be related to chemical structure, in particular to specific molecular substructures or fragments (alerts), which can then be used in specialized software or expert systems for predictive purposes. In the past, there have been many attempts to predict the mutagenicity of alpha, beta-unsaturated carbonyl compounds through quantitative structure activity relationships (QSAR) but considering only one exclusive endpoint: the Ames test. Besides, even though those studies give a comprehensive understanding of the phenomenon, they do not provide substructural information that could be useful forward improving expert systems based on structural alerts (SAs). This work reports an evaluation of classification models to probe the mutagenic activity of alpha, beta-unsaturated carbonyl compounds over two endpoints--the Ames and mammalian cell gene mutation tests--based on linear discriminant analysis along with the topological Substructure molecular design (TOPS-MODE) approach. The obtained results showed the better ability of the TOPS-MODE approach in flagging structural alerts for the mutagenicity of these compounds compared to the expert system TOXTREE. Thus, the application of the present QSAR models can aid toxicologists in risk assessment and in prioritizing testing, as well as in the improvement of expert systems, such as the TOXTREE software, where SAs are implemented. 2009 Elsevier Ireland Ltd. All rights reserved.

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

PubMed

Kumar, Sudhir; Stecher, Glen; Li, Michael; Knyaz, Christina; Tamura, Koichiro

2018-06-01

The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.

Three Dimensional (3D) Printing: A Straightforward, User-Friendly Protocol to Convert Virtual Chemical Models to Real-Life Objects

ERIC Educational Resources Information Center

Rossi, Sergio; Benaglia, Maurizio; Brenna, Davide; Porta, Riccardo; Orlandi, Manuel

2015-01-01

A simple procedure to convert protein data bank files (.pdb) into a stereolithography file (.stl) using VMD software (Virtual Molecular Dynamic) is reported. This tutorial allows generating, with a very simple protocol, three-dimensional customized structures that can be printed by a low-cost 3D-printer, and used for teaching chemical education…

Advanced Shutter Control for a Molecular Beam Epitaxy Reactor

DTIC Science & Technology

An open-source hardware and software-based shutter controller solution was developed that communicates over Ethernet with our original equipment...manufacturer (OEM) molecular beam epitaxy (MBE) reactor control software. An Arduino Mega microcontroller is the used for the brain of the shutter... controller , while a custom-designed circuit board distributes 24-V power to each of the 16 shutter solenoids available on the MBE. Using Ethernet

Inside a VAMDC data node—putting standards into practical software

NASA Astrophysics Data System (ADS)

Regandell, Samuel; Marquart, Thomas; Piskunov, Nikolai

2018-03-01

Access to molecular and atomic data is critical for many forms of remote sensing analysis across different fields. Many atomic and molecular databases are however highly specialised for their intended application, complicating querying and combination data between sources. The Virtual Atomic and Molecular Data Centre, VAMDC, is an electronic infrastructure that allows each database to register as a ‘node’. Through services such as VAMDC’s portal website, users can then access and query all nodes in a homogenised way. Today all major Atomic and Molecular databases are attached to VAMDC This article describes the software tools we developed to help data providers create and manage a VAMDC node. It gives an overview of the VAMDC infrastructure and of the various standards it uses. The article then discusses the development choices made and how the standards are implemented in practice. It concludes with a full example of implementing a VAMDC node using a real-life case as well as future plans for the node software.

Optimizing legacy molecular dynamics software with directive-based offload

DOE PAGES

Michael Brown, W.; Carrillo, Jan-Michael Y.; Gavhane, Nitin; ...

2015-05-14

The directive-based programming models are one solution for exploiting many-core coprocessors to increase simulation rates in molecular dynamics. They offer the potential to reduce code complexity with offload models that can selectively target computations to run on the CPU, the coprocessor, or both. In our paper, we describe modifications to the LAMMPS molecular dynamics code to enable concurrent calculations on a CPU and coprocessor. We also demonstrate that standard molecular dynamics algorithms can run efficiently on both the CPU and an x86-based coprocessor using the same subroutines. As a consequence, we demonstrate that code optimizations for the coprocessor also resultmore » in speedups on the CPU; in extreme cases up to 4.7X. We provide results for LAMMAS benchmarks and for production molecular dynamics simulations using the Stampede hybrid supercomputer with both Intel (R) Xeon Phi (TM) coprocessors and NVIDIA GPUs: The optimizations presented have increased simulation rates by over 2X for organic molecules and over 7X for liquid crystals on Stampede. The optimizations are available as part of the "Intel package" supplied with LAMMPS. (C) 2015 Elsevier B.V. All rights reserved.« less

Characteristics and evolution of the ecosystem of software tools supporting research in molecular biology.

PubMed

Pazos, Florencio; Chagoyen, Monica

2018-01-16

Daily work in molecular biology presently depends on a large number of computational tools. An in-depth, large-scale study of that 'ecosystem' of Web tools, its characteristics, interconnectivity, patterns of usage/citation, temporal evolution and rate of decay is crucial for understanding the forces that shape it and for informing initiatives aimed at its funding, long-term maintenance and improvement. In particular, the long-term maintenance of these tools is compromised because of their specific development model. Hundreds of published studies become irreproducible de facto, as the software tools used to conduct them become unavailable. In this study, we present a large-scale survey of >5400 publications describing Web servers within the two main bibliographic resources for disseminating new software developments in molecular biology. For all these servers, we studied their citation patterns, the subjects they address, their citation networks and the temporal evolution of these factors. We also analysed how these factors affect the availability of these servers (whether they are alive). Our results show that this ecosystem of tools is highly interconnected and adapts to the 'trendy' subjects in every moment. The servers present characteristic temporal patterns of citation/usage, and there is a worrying rate of server 'death', which is influenced by factors such as the server popularity and the institutions that hosts it. These results can inform initiatives aimed at the long-term maintenance of these resources. © The Author(s) 2018. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, Hong, E-mail: h-yu@seu.edu.cn; Chen, Hong-Bo

In this article, a new semi-continuum model is built to describe the fundamental vibration frequency of the silicon nanowires in <111> orientation. The Keating potential model and the discrete nature in the width and the thickness direction of the silicon nanowires in <111> orientation are applied in the new semi-continuum model. Based on the Keating model and the principle of conservation of energy, the vibration frequency of the silicon nanowires with the triangle, the rhombus, and the hexagon cross sections are derived. It is indicated that the calculation results based on this new model are accordant with the simulation resultsmore » of the software based on molecular dynamics (MD).« less

Using open source computational tools for predicting human metabolic stability and additional absorption, distribution, metabolism, excretion, and toxicity properties.

PubMed

Gupta, Rishi R; Gifford, Eric M; Liston, Ted; Waller, Chris L; Hohman, Moses; Bunin, Barry A; Ekins, Sean

2010-11-01

Ligand-based computational models could be more readily shared between researchers and organizations if they were generated with open source molecular descriptors [e.g., chemistry development kit (CDK)] and modeling algorithms, because this would negate the requirement for proprietary commercial software. We initially evaluated open source descriptors and model building algorithms using a training set of approximately 50,000 molecules and a test set of approximately 25,000 molecules with human liver microsomal metabolic stability data. A C5.0 decision tree model demonstrated that CDK descriptors together with a set of Smiles Arbitrary Target Specification (SMARTS) keys had good statistics [κ = 0.43, sensitivity = 0.57, specificity = 0.91, and positive predicted value (PPV) = 0.64], equivalent to those of models built with commercial Molecular Operating Environment 2D (MOE2D) and the same set of SMARTS keys (κ = 0.43, sensitivity = 0.58, specificity = 0.91, and PPV = 0.63). Extending the dataset to ∼193,000 molecules and generating a continuous model using Cubist with a combination of CDK and SMARTS keys or MOE2D and SMARTS keys confirmed this observation. When the continuous predictions and actual values were binned to get a categorical score we observed a similar κ statistic (0.42). The same combination of descriptor set and modeling method was applied to passive permeability and P-glycoprotein efflux data with similar model testing statistics. In summary, open source tools demonstrated predictive results comparable to those of commercial software with attendant cost savings. We discuss the advantages and disadvantages of open source descriptors and the opportunity for their use as a tool for organizations to share data precompetitively, avoiding repetition and assisting drug discovery.

BioRuby: bioinformatics software for the Ruby programming language.

PubMed

Goto, Naohisa; Prins, Pjotr; Nakao, Mitsuteru; Bonnal, Raoul; Aerts, Jan; Katayama, Toshiaki

2010-10-15

The BioRuby software toolkit contains a comprehensive set of free development tools and libraries for bioinformatics and molecular biology, written in the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO. BioRuby comes with a tutorial, documentation and an interactive environment, which can be used in the shell, and in the web browser. BioRuby is free and open source software, made available under the Ruby license. BioRuby runs on all platforms that support Ruby, including Linux, Mac OS X and Windows. And, with JRuby, BioRuby runs on the Java Virtual Machine. The source code is available from http://www.bioruby.org/. katayama@bioruby.org

Simulation of meso-damage of refractory based on cohesion model and molecular dynamics method

NASA Astrophysics Data System (ADS)

Zhao, Jiuling; Shang, Hehao; Zhu, Zhaojun; Zhang, Guoxing; Duan, Leiguang; Sun, Xinya

2018-06-01

In order to describe the meso-damage of the refractories more accurately, and to study of the relationship between the mesostructured of the refractories and the macro-mechanics, this paper takes the magnesia-carbon refractories as the research object and uses the molecular dynamics method to instead the traditional sequential algorithm to establish the meso-particles filling model including small and large particles. Finally, the finite element software-ABAQUS is used to conducts numerical simulation on the meso-damage evolution process of refractory materials. From the results, the process of initiation and propagation of microscopic interface cracks can be observed intuitively, and the macroscopic stress-strain curve of the refractory material is obtained. The results show that the combination of molecular dynamics modeling and the use of Python in the interface to insert the cohesive element numerical simulation, obtaining of more accurate interface parameters through parameter inversion, can be more accurate to observe the interface of the meso-damage evolution process and effective to consider the effect of the mesostructured of the refractory material on its macroscopic mechanical properties.

Thermalized Drude Oscillators with the LAMMPS Molecular Dynamics Simulator.

PubMed

Dequidt, Alain; Devémy, Julien; Pádua, Agílio A H

2016-01-25

LAMMPS is a very customizable molecular dynamics simulation software, which can be used to simulate a large diversity of systems. We introduce a new package for simulation of polarizable systems with LAMMPS using thermalized Drude oscillators. The implemented functionalities are described and are illustrated by examples. The implementation was validated by comparing simulation results with published data and using a reference software. Computational performance is also analyzed.

Advances in molecular labeling, high throughput imaging and machine intelligence portend powerful functional cellular biochemistry tools.

PubMed

Price, Jeffrey H; Goodacre, Angela; Hahn, Klaus; Hodgson, Louis; Hunter, Edward A; Krajewski, Stanislaw; Murphy, Robert F; Rabinovich, Andrew; Reed, John C; Heynen, Susanne

2002-01-01

Cellular behavior is complex. Successfully understanding systems at ever-increasing complexity is fundamental to advances in modern science and unraveling the functional details of cellular behavior is no exception. We present a collection of prospectives to provide a glimpse of the techniques that will aid in collecting, managing and utilizing information on complex cellular processes via molecular imaging tools. These include: 1) visualizing intracellular protein activity with fluorescent markers, 2) high throughput (and automated) imaging of multilabeled cells in statistically significant numbers, and 3) machine intelligence to analyze subcellular image localization and pattern. Although not addressed here, the importance of combining cell-image-based information with detailed molecular structure and ligand-receptor binding models cannot be overlooked. Advanced molecular imaging techniques have the potential to impact cellular diagnostics for cancer screening, clinical correlations of tissue molecular patterns for cancer biology, and cellular molecular interactions for accelerating drug discovery. The goal of finally understanding all cellular components and behaviors will be achieved by advances in both instrumentation engineering (software and hardware) and molecular biochemistry. Copyright 2002 Wiley-Liss, Inc.

Molecular modeling of the process of reversible dissolution of the collagen protein under the action of tissue-clearing agents

NASA Astrophysics Data System (ADS)

Dvoretsky, K. N.; Berezin, K. V.; Chernavina, M. L.; Likhter, A. M.; Shagautdinova, I. T.; Antonova, E. M.; Rybakov, A. V.; Grechukhina, O. N.; Tuchin, V. V.

2018-04-01

The interaction of glycerol immersion agent with collagen mimetic peptide ((GPH)9)3 and a fragment of the microfibril 5((GPH)12)3 was studied by the classical molecular dynamics method using the GROMACS software. The change in geometric parameters of collagen α-chains at various concentrations of an aqueous solution of glycerol is analyzed. It is shown that these changes nonlinearly depend on the concentration and are limited to a certain level, which correlates with the experimental data on optical clearing efficiency of human skin. A hypothesis on the cause of the decreased efficiency of optical skin clearing at high immersion agent concentrations is put forward. The molecular mechanism of immersion optical clearing of biological tissues is discussed.

Protein Simulation Data in the Relational Model.

PubMed

Simms, Andrew M; Daggett, Valerie

2012-10-01

High performance computing is leading to unprecedented volumes of data. Relational databases offer a robust and scalable model for storing and analyzing scientific data. However, these features do not come without a cost-significant design effort is required to build a functional and efficient repository. Modeling protein simulation data in a relational database presents several challenges: the data captured from individual simulations are large, multi-dimensional, and must integrate with both simulation software and external data sites. Here we present the dimensional design and relational implementation of a comprehensive data warehouse for storing and analyzing molecular dynamics simulations using SQL Server.

Protein Simulation Data in the Relational Model

PubMed Central

Simms, Andrew M.; Daggett, Valerie

2011-01-01

High performance computing is leading to unprecedented volumes of data. Relational databases offer a robust and scalable model for storing and analyzing scientific data. However, these features do not come without a cost—significant design effort is required to build a functional and efficient repository. Modeling protein simulation data in a relational database presents several challenges: the data captured from individual simulations are large, multi-dimensional, and must integrate with both simulation software and external data sites. Here we present the dimensional design and relational implementation of a comprehensive data warehouse for storing and analyzing molecular dynamics simulations using SQL Server. PMID:23204646

A Simplified Model of Local Structure in Aqueous Proline Amino Acid Revealed by First-Principles Molecular Dynamics Simulations

PubMed Central

Troitzsch, Raphael Z.; Tulip, Paul R.; Crain, Jason; Martyna, Glenn J.

2008-01-01

Aqueous proline solutions are deceptively simple as they can take on complex roles such as protein chaperones, cryoprotectants, and hydrotropic agents in biological processes. Here, a molecular level picture of proline/water mixtures is developed. Car-Parrinello ab initio molecular dynamics (CPAIMD) simulations of aqueous proline amino acid at the B-LYP level of theory, performed using IBM's Blue Gene/L supercomputer and massively parallel software, reveal hydrogen-bonding propensities that are at odds with the predictions of the CHARMM22 empirical force field but are in better agreement with results of recent neutron diffraction experiments. In general, the CPAIMD (B-LYP) simulations predict a simplified structural model of proline/water mixtures consisting of fewer distinct local motifs. Comparisons of simulation results to experiment are made by direct evaluation of the neutron static structure factor S(Q) from CPAIMD (B-LYP) trajectories as well as to the results of the empirical potential structure refinement reverse Monte Carlo procedure applied to the neutron data. PMID:18790850

A simplified model of local structure in aqueous proline amino acid revealed by first-principles molecular dynamics simulations.

PubMed

Troitzsch, Raphael Z; Tulip, Paul R; Crain, Jason; Martyna, Glenn J

2008-12-01

Aqueous proline solutions are deceptively simple as they can take on complex roles such as protein chaperones, cryoprotectants, and hydrotropic agents in biological processes. Here, a molecular level picture of proline/water mixtures is developed. Car-Parrinello ab initio molecular dynamics (CPAIMD) simulations of aqueous proline amino acid at the B-LYP level of theory, performed using IBM's Blue Gene/L supercomputer and massively parallel software, reveal hydrogen-bonding propensities that are at odds with the predictions of the CHARMM22 empirical force field but are in better agreement with results of recent neutron diffraction experiments. In general, the CPAIMD (B-LYP) simulations predict a simplified structural model of proline/water mixtures consisting of fewer distinct local motifs. Comparisons of simulation results to experiment are made by direct evaluation of the neutron static structure factor S(Q) from CPAIMD (B-LYP) trajectories as well as to the results of the empirical potential structure refinement reverse Monte Carlo procedure applied to the neutron data.

Software for Demonstration of Features of Chain Polymerization Processes

ERIC Educational Resources Information Center

Sosnowski, Stanislaw

2013-01-01

Free software for the demonstration of the features of homo- and copolymerization processes (free radical, controlled radical, and living) is described. The software is based on the Monte Carlo algorithms and offers insight into the kinetics, molecular weight distribution, and microstructure of the macromolecules formed in those processes. It also…

STSE: Spatio-Temporal Simulation Environment Dedicated to Biology.

PubMed

Stoma, Szymon; Fröhlich, Martina; Gerber, Susanne; Klipp, Edda

2011-04-28

Recently, the availability of high-resolution microscopy together with the advancements in the development of biomarkers as reporters of biomolecular interactions increased the importance of imaging methods in molecular cell biology. These techniques enable the investigation of cellular characteristics like volume, size and geometry as well as volume and geometry of intracellular compartments, and the amount of existing proteins in a spatially resolved manner. Such detailed investigations opened up many new areas of research in the study of spatial, complex and dynamic cellular systems. One of the crucial challenges for the study of such systems is the design of a well stuctured and optimized workflow to provide a systematic and efficient hypothesis verification. Computer Science can efficiently address this task by providing software that facilitates handling, analysis, and evaluation of biological data to the benefit of experimenters and modelers. The Spatio-Temporal Simulation Environment (STSE) is a set of open-source tools provided to conduct spatio-temporal simulations in discrete structures based on microscopy images. The framework contains modules to digitize, represent, analyze, and mathematically model spatial distributions of biochemical species. Graphical user interface (GUI) tools provided with the software enable meshing of the simulation space based on the Voronoi concept. In addition, it supports to automatically acquire spatial information to the mesh from the images based on pixel luminosity (e.g. corresponding to molecular levels from microscopy images). STSE is freely available either as a stand-alone version or included in the linux live distribution Systems Biology Operational Software (SB.OS) and can be downloaded from http://www.stse-software.org/. The Python source code as well as a comprehensive user manual and video tutorials are also offered to the research community. We discuss main concepts of the STSE design and workflow. We demonstrate it's usefulness using the example of a signaling cascade leading to formation of a morphological gradient of Fus3 within the cytoplasm of the mating yeast cell Saccharomyces cerevisiae. STSE is an efficient and powerful novel platform, designed for computational handling and evaluation of microscopic images. It allows for an uninterrupted workflow including digitization, representation, analysis, and mathematical modeling. By providing the means to relate the simulation to the image data it allows for systematic, image driven model validation or rejection. STSE can be scripted and extended using the Python language. STSE should be considered rather as an API together with workflow guidelines and a collection of GUI tools than a stand alone application. The priority of the project is to provide an easy and intuitive way of extending and customizing software using the Python language.

Modeling Nanocomposites for Molecular Dynamics (MD) Simulations

DTIC Science & Technology

2015-01-01

Parallel Simulator ( LAMMPS ) is used as the MD simulator [9], the coordinates must be formatted for use in LAMMPSs. VMD has a set of tools (TopoTools...that can be used to generate a LAMMPS -readable format [6]. 3 Figure 4. Ethylene Monomer Produced From Coordinates in PDB and Rendered Using...where, i and j are the atom subscripts. Simulations are performed using LAMMPS simulation software. Periodic boundary conditions are

Molecular Cloning Designer Simulator (MCDS): All-in-one molecular cloning and genetic engineering design, simulation and management software for complex synthetic biology and metabolic engineering projects.

PubMed

Shi, Zhenyu; Vickers, Claudia E

2016-12-01

Molecular Cloning Designer Simulator (MCDS) is a powerful new all-in-one cloning and genetic engineering design, simulation and management software platform developed for complex synthetic biology and metabolic engineering projects. In addition to standard functions, it has a number of features that are either unique, or are not found in combination in any one software package: (1) it has a novel interactive flow-chart user interface for complex multi-step processes, allowing an integrated overview of the whole project; (2) it can perform a user-defined workflow of cloning steps in a single execution of the software; (3) it can handle multiple types of genetic recombineering, a technique that is rapidly replacing classical cloning for many applications; (4) it includes experimental information to conveniently guide wet lab work; and (5) it can store results and comments to allow the tracking and management of the whole project in one platform. MCDS is freely available from https://mcds.codeplex.com.

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

PubMed Central

Tamura, Koichiro; Peterson, Daniel; Peterson, Nicholas; Stecher, Glen; Nei, Masatoshi; Kumar, Sudhir

2011-01-01

Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which is a user-friendly software for mining online databases, building sequence alignments and phylogenetic trees, and using methods of evolutionary bioinformatics in basic biology, biomedicine, and evolution. The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models (nucleotide or amino acid), inferring ancestral states and sequences (along with probabilities), and estimating evolutionary rates site-by-site. In computer simulation analyses, ML tree inference algorithms in MEGA5 compared favorably with other software packages in terms of computational efficiency and the accuracy of the estimates of phylogenetic trees, substitution parameters, and rate variation among sites. The MEGA user interface has now been enhanced to be activity driven to make it easier for the use of both beginners and experienced scientists. This version of MEGA is intended for the Windows platform, and it has been configured for effective use on Mac OS X and Linux desktops. It is available free of charge from http://www.megasoftware.net. PMID:21546353

Updates to the Virtual Atomic and Molecular Data Centre

NASA Astrophysics Data System (ADS)

Hill, Christian; Tennyson, Jonathan; Gordon, Iouli E.; Rothman, Laurence S.; Dubernet, Marie-Lise

2014-06-01

The Virtual Atomic and Molecular Data Centre (VAMDC) has established a set of standards for the storage and transmission of atomic and molecular data and an SQL-based query language (VSS2) for searching online databases, known as nodes. The project has also created an online service, the VAMDC Portal, through which all of these databases may be searched and their results compared and aggregated. Since its inception four years ago, the VAMDC e-infrastructure has grown to encompass over 40 databases, including HITRAN, in more than 20 countries and engages actively with scientists in six continents. Associated with the portal are a growing suite of software tools for the transformation of data from its native, XML-based, XSAMS format, to a range of more convenient human-readable (such as HTML) and machinereadable (such as CSV) formats. The relational database for HITRAN1, created as part of the VAMDC project is a flexible and extensible data model which is able to represent a wider range of parameters than the current fixed-format text-based one. Over the next year, a new online interface to this database will be tested, released and fully documented - this web application, HITRANonline2, will fully replace the ageing and incomplete JavaHAWKS software suite.

Molecular simulations of self-assembly processes of amphiphiles in dilute solutions: the challenge for quantitative modelling

NASA Astrophysics Data System (ADS)

Jusufi, Arben

2013-11-01

We report on two recent developments in molecular simulations of self-assembly processes of amphiphilic solutions. We focus on the determination of micelle formation of ionic surfactants which exhibit the archetype of self-assembling compounds in solution. The first approach is centred on the challenge in predicting micellisation properties through explicit solvent molecular dynamics simulations. Even with a coarse-grained (CG) approach and the use of highly optimised software packages run on graphics processing unit hardware, it remains in many cases computationally infeasible to directly extract the critical micelle concentration (cmc). However, combined with a recently presented theoretical mean-field model this task becomes resolved. An alternative approach to study self-assembly is through implicit solvent modelling of the surfactants. Here we review some latest results and present new ones regarding capabilities of such a modelling approach in determining the cmc, and the aggregate structures in the dilute regime, that is currently not accessible through explicit solvent simulations, neither through atomistic nor through CG approaches. A special focus is put on surfactant concentration effects and surfactant correlations quantified by scattering intensities that are compared to recently published small-angle X-ray scattering data.

QSPR using MOLGEN-QSPR: the challenge of fluoroalkane boiling points.

PubMed

Rücker, Christoph; Meringer, Markus; Kerber, Adalbert

2005-01-01

By means of the new software MOLGEN-QSPR, a multilinear regression model for the boiling points of lower fluoroalkanes is established. The model is based exclusively on simple descriptors derived directly from molecular structure and nevertheless describes a broader set of data more precisely than previous attempts that used either more demanding (quantum chemical) descriptors or more demanding (nonlinear) statistical methods such as neural networks. The model's internal consistency was confirmed by leave-one-out cross-validation. The model was used to predict all unknown boiling points of fluorobutanes, and the quality of predictions was estimated by means of comparison with boiling point predictions for fluoropentanes.

Parallel implementation of approximate atomistic models of the AMOEBA polarizable model

NASA Astrophysics Data System (ADS)

Demerdash, Omar; Head-Gordon, Teresa

2016-11-01

In this work we present a replicated data hybrid OpenMP/MPI implementation of a hierarchical progression of approximate classical polarizable models that yields speedups of up to ∼10 compared to the standard OpenMP implementation of the exact parent AMOEBA polarizable model. In addition, our parallel implementation exhibits reasonable weak and strong scaling. The resulting parallel software will prove useful for those who are interested in how molecular properties converge in the condensed phase with respect to the MBE, it provides a fruitful test bed for exploring different electrostatic embedding schemes, and offers an interesting possibility for future exascale computing paradigms.

Computationally Efficient Multiconfigurational Reactive Molecular Dynamics

PubMed Central

Yamashita, Takefumi; Peng, Yuxing; Knight, Chris; Voth, Gregory A.

2012-01-01

It is a computationally demanding task to explicitly simulate the electronic degrees of freedom in a system to observe the chemical transformations of interest, while at the same time sampling the time and length scales required to converge statistical properties and thus reduce artifacts due to initial conditions, finite-size effects, and limited sampling. One solution that significantly reduces the computational expense consists of molecular models in which effective interactions between particles govern the dynamics of the system. If the interaction potentials in these models are developed to reproduce calculated properties from electronic structure calculations and/or ab initio molecular dynamics simulations, then one can calculate accurate properties at a fraction of the computational cost. Multiconfigurational algorithms model the system as a linear combination of several chemical bonding topologies to simulate chemical reactions, also sometimes referred to as “multistate”. These algorithms typically utilize energy and force calculations already found in popular molecular dynamics software packages, thus facilitating their implementation without significant changes to the structure of the code. However, the evaluation of energies and forces for several bonding topologies per simulation step can lead to poor computational efficiency if redundancy is not efficiently removed, particularly with respect to the calculation of long-ranged Coulombic interactions. This paper presents accurate approximations (effective long-range interaction and resulting hybrid methods) and multiple-program parallelization strategies for the efficient calculation of electrostatic interactions in reactive molecular simulations. PMID:25100924

SHAPEMOL: Modelling molecular line emission in protoplanetary and planetary nebulae with SHAPE

NASA Astrophysics Data System (ADS)

Santander-García, M.; Bujarrabal, V.; Steffen, W.; Koning, N.

2014-04-01

Modern instrumentation in radioastronomy constitutes a valuable tool for studying the Universe: ALMA will reach unprecedented sensitivities and spatial resolution, while Herschel/HIFI has opened a new window for probing molecular warm gas (˜50-1000 K). On the other hand, the SHAPE software has emerged in the last few years as the standard tool for determining the morphology and velocity field of different kinds of gaseous emission nebulae via spatio-kinematical modelling. Standard SHAPE implements radiative transfer solving, but it is only available for atomic species and not for molecules. Being aware of the growing importance of the development of tools for easying the analyses of molecular data from new era observatories, we introduce the computer code shapemol, a plug-in for SHAPE v5.0 with which we intend to fill the so far empty molecular niche. Shapemol enables spatio-kinematic modeling with accurate non-LTE calculations of line excitation and radiative transfer in molecular species. This code has been succesfully tested in the study of the excitation conditions of the molecular envelope of the young planetary nebula NGC 7027 using data from Herschel/HIFI and IRAM 30m. Currently, it allows radiative transfer solving in the 12CO and 13CO J=1-0 to J=17-16 lines. Shapemol, used along SHAPE, allows to easily generate synthetic maps to test against interferometric observations, as well as synthetic line profiles to match single-dish observations.

Hybrid optimal descriptors as a tool to predict skin sensitization in accordance to OECD principles.

PubMed

Toropova, Alla P; Toropov, Andrey A

2017-06-05

Skin sensitization (allergic contact dermatitis) is a widespread problem arising from the contact of chemicals with the skin. The detection of molecular features with undesired effect for skin is complex task owing to unclear biochemical mechanisms and unclearness of conditions of action of chemicals to skin. The development of computational methods for estimation of this endpoint in order to reduce animal testing is recommended (Cosmetics Directive EC regulation 1907/2006; EU Regulation, Regulation, 1223/2009). The CORAL software (http://www.insilico.eu/coral) gives good predictive models for the skin sensitization. Simplified molecular input-line entry system (SMILES) together with molecular graph are used to represent the molecular structure for these models. So-called hybrid optimal descriptors are used to establish quantitative structure-activity relationships (QSARs). The aim of this study is the estimation of the predictive potential of the hybrid descriptors. Three different distributions into the training (≈70%), calibration (≈15%), and validation (≈15%) sets are studied. QSAR for these three distributions are built up with using the Monte Carlo technique. The statistical characteristics of these models for external validation set are used as a measure of predictive potential of these models. The best model, according to the above criterion, is characterized by n validation =29, r 2 validation =0.8596, RMSE validation =0.489. Mechanistic interpretation and domain of applicability for these models are defined. Copyright © 2017 Elsevier B.V. All rights reserved.

Software Reviews.

ERIC Educational Resources Information Center

Wulfson, Stephen, Ed.

1987-01-01

Reviews seven computer software programs that can be used in science education programs. Describes courseware which deals with muscles and bones, terminology, classifying animals without backbones, molecular structures, drugs, genetics, and shaping the earth's surface. (TW)

Crystal MD: The massively parallel molecular dynamics software for metal with BCC structure

NASA Astrophysics Data System (ADS)

Hu, Changjun; Bai, He; He, Xinfu; Zhang, Boyao; Nie, Ningming; Wang, Xianmeng; Ren, Yingwen

2017-02-01

Material irradiation effect is one of the most important keys to use nuclear power. However, the lack of high-throughput irradiation facility and knowledge of evolution process, lead to little understanding of the addressed issues. With the help of high-performance computing, we could make a further understanding of micro-level-material. In this paper, a new data structure is proposed for the massively parallel simulation of the evolution of metal materials under irradiation environment. Based on the proposed data structure, we developed the new molecular dynamics software named Crystal MD. The simulation with Crystal MD achieved over 90% parallel efficiency in test cases, and it takes more than 25% less memory on multi-core clusters than LAMMPS and IMD, which are two popular molecular dynamics simulation software. Using Crystal MD, a two trillion particles simulation has been performed on Tianhe-2 cluster.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Biyikli, Emre; To, Albert C., E-mail: albertto@pitt.edu

Atomistic/continuum coupling methods combine accurate atomistic methods and efficient continuum methods to simulate the behavior of highly ordered crystalline systems. Coupled methods utilize the advantages of both approaches to simulate systems at a lower computational cost, while retaining the accuracy associated with atomistic methods. Many concurrent atomistic/continuum coupling methods have been proposed in the past; however, their true computational efficiency has not been demonstrated. The present work presents an efficient implementation of a concurrent coupling method called the Multiresolution Molecular Mechanics (MMM) for serial, parallel, and adaptive analysis. First, we present the features of the software implemented along with themore » associated technologies. The scalability of the software implementation is demonstrated, and the competing effects of multiscale modeling and parallelization are discussed. Then, the algorithms contributing to the efficiency of the software are presented. These include algorithms for eliminating latent ghost atoms from calculations and measurement-based dynamic balancing of parallel workload. The efficiency improvements made by these algorithms are demonstrated by benchmark tests. The efficiency of the software is found to be on par with LAMMPS, a state-of-the-art Molecular Dynamics (MD) simulation code, when performing full atomistic simulations. Speed-up of the MMM method is shown to be directly proportional to the reduction of the number of the atoms visited in force computation. Finally, an adaptive MMM analysis on a nanoindentation problem, containing over a million atoms, is performed, yielding an improvement of 6.3–8.5 times in efficiency, over the full atomistic MD method. For the first time, the efficiency of a concurrent atomistic/continuum coupling method is comprehensively investigated and demonstrated.« less

Planform: an application and database of graph-encoded planarian regenerative experiments.

PubMed

Lobo, Daniel; Malone, Taylor J; Levin, Michael

2013-04-15

Understanding the mechanisms governing the regeneration capabilities of many organisms is a fundamental interest in biology and medicine. An ever-increasing number of manipulation and molecular experiments are attempting to discover a comprehensive model for regeneration, with the planarian flatworm being one of the most important model species. Despite much effort, no comprehensive, constructive, mechanistic models exist yet, and it is now clear that computational tools are needed to mine this huge dataset. However, until now, there is no database of regenerative experiments, and the current genotype-phenotype ontologies and databases are based on textual descriptions, which are not understandable by computers. To overcome these difficulties, we present here Planform (Planarian formalization), a manually curated database and software tool for planarian regenerative experiments, based on a mathematical graph formalism. The database contains more than a thousand experiments from the main publications in the planarian literature. The software tool provides the user with a graphical interface to easily interact with and mine the database. The presented system is a valuable resource for the regeneration community and, more importantly, will pave the way for the application of novel artificial intelligence tools to extract knowledge from this dataset. The database and software tool are freely available at http://planform.daniel-lobo.com.

Visually impaired researchers get their hands on quantum chemistry: application to a computational study on the isomerization of a sterol

NASA Astrophysics Data System (ADS)

Lounnas, Valère; Wedler, Henry B.; Newman, Timothy; Schaftenaar, Gijs; Harrison, Jason G.; Nepomuceno, Gabriella; Pemberton, Ryan; Tantillo, Dean J.; Vriend, Gert

2014-11-01

In molecular sciences, articles tend to revolve around 2D representations of 3D molecules, and sighted scientists often resort to 3D virtual reality software to study these molecules in detail. Blind and visually impaired (BVI) molecular scientists have access to a series of audio devices that can help them read the text in articles and work with computers. Reading articles published in this journal, though, is nearly impossible for them because they need to generate mental 3D images of molecules, but the article-reading software cannot do that for them. We have previously designed AsteriX, a web server that fully automatically decomposes articles, detects 2D plots of low molecular weight molecules, removes meta data and annotations from these plots, and converts them into 3D atomic coordinates. AsteriX-BVI goes one step further and converts the 3D representation into a 3D printable, haptic-enhanced format that includes Braille annotations. These Braille-annotated physical 3D models allow BVI scientists to generate a complete mental model of the molecule. AsteriX-BVI uses Molden to convert the meta data of quantum chemistry experiments into BVI friendly formats so that the entire line of scientific information that sighted people take for granted—from published articles, via printed results of computational chemistry experiments, to 3D models—is now available to BVI scientists too. The possibilities offered by AsteriX-BVI are illustrated by a project on the isomerization of a sterol, executed by the blind co-author of this article (HBW).

Shock Wave Propagation in Cementitious Materials at Micro/Meso Scales

NASA Astrophysics Data System (ADS)

Rajendran, Arunachalam

2015-06-01

The mechanical and constitutive response of materials like cement, and bio materials like fish scale and abalone shell is very complex due to heterogeneities that are inherently present in the nano and microstructures. The intrinsic constitutive behaviors are driven by the chemical composition and the molecular, micro, and meso structures. Therefore, it becomes important to identify the material genome as the building block for the material. For instance, in cementitious materials, the genome of C-S-H phase (the glue or the paste) that holds the various clinkers, such as the dicalcium silicate, tricalcium silicate, calcium ferroaluminates, and others is extremely complex. Often mechanical behaviors of C-S-H type materials are influenced by the chemistry and the structures at all nano to micro length scales. By explicitly modeling the molecular structures using appropriate potentials, it is then possible to compute the elastic tensor from molecular dynamics simulations using all atom method. The elastic tensors for the C-S-H gel and other clinkers are determined using the software suite ``Accelrys Materials Studio.'' A strain rate dependent, fracture mechanics based tensile damage model has been incorporated into ABAQUS finite element code to model spall evolution in the heterogeneous cementitious material with all constituents explicitly modeled through one micron element resolution. This paper presents results from nano/micro/meso scale analyses of shock wave propagation in a heterogeneous cementitious material using both molecular dynamic and finite element codes.

A multiscale simulation technique for molecular electronics: design of a directed self-assembled molecular n-bit shift register memory device.

PubMed

Lambropoulos, Nicholas A; Reimers, Jeffrey R; Crossley, Maxwell J; Hush, Noel S; Silverbrook, Kia

2013-12-20

A general method useful in molecular electronics design is developed that integrates modelling on the nano-scale (using quantum-chemical software) and on the micro-scale (using finite-element methods). It is applied to the design of an n-bit shift register memory that could conceivably be built using accessible technologies. To achieve this, the entire complex structure of the device would be built to atomic precision using feedback-controlled lithography to provide atomic-level control of silicon devices, controlled wet-chemical synthesis of molecular insulating pillars above the silicon, and controlled wet-chemical self-assembly of modular molecular devices to these pillars that connect to external metal electrodes (leads). The shift register consists of n connected cells that read data from an input electrode, pass it sequentially between the cells under the control of two external clock electrodes, and deliver it finally to an output device. The proposed cells are trimeric oligoporphyrin units whose internal states are manipulated to provide functionality, covalently connected to other cells via dipeptide linkages. Signals from the clock electrodes are conveyed by oligoporphyrin molecular wires, and μ-oxo porphyrin insulating columns are used as the supporting pillars. The developed multiscale modelling technique is applied to determine the characteristics of this molecular device, with in particular utilization of the inverted region for molecular electron-transfer processes shown to facilitate latching and control using exceptionally low energy costs per logic operation compared to standard CMOS shift register technology.

A multiscale simulation technique for molecular electronics: design of a directed self-assembled molecular n-bit shift register memory device

NASA Astrophysics Data System (ADS)

Lambropoulos, Nicholas A.; Reimers, Jeffrey R.; Crossley, Maxwell J.; Hush, Noel S.; Silverbrook, Kia

2013-12-01

A general method useful in molecular electronics design is developed that integrates modelling on the nano-scale (using quantum-chemical software) and on the micro-scale (using finite-element methods). It is applied to the design of an n-bit shift register memory that could conceivably be built using accessible technologies. To achieve this, the entire complex structure of the device would be built to atomic precision using feedback-controlled lithography to provide atomic-level control of silicon devices, controlled wet-chemical synthesis of molecular insulating pillars above the silicon, and controlled wet-chemical self-assembly of modular molecular devices to these pillars that connect to external metal electrodes (leads). The shift register consists of n connected cells that read data from an input electrode, pass it sequentially between the cells under the control of two external clock electrodes, and deliver it finally to an output device. The proposed cells are trimeric oligoporphyrin units whose internal states are manipulated to provide functionality, covalently connected to other cells via dipeptide linkages. Signals from the clock electrodes are conveyed by oligoporphyrin molecular wires, and μ-oxo porphyrin insulating columns are used as the supporting pillars. The developed multiscale modelling technique is applied to determine the characteristics of this molecular device, with in particular utilization of the inverted region for molecular electron-transfer processes shown to facilitate latching and control using exceptionally low energy costs per logic operation compared to standard CMOS shift register technology.

3D Printing of Biomolecular Models for Research and Pedagogy

PubMed Central

Da Veiga Beltrame, Eduardo; Tyrwhitt-Drake, James; Roy, Ian; Shalaby, Raed; Suckale, Jakob; Pomeranz Krummel, Daniel

2017-01-01

The construction of physical three-dimensional (3D) models of biomolecules can uniquely contribute to the study of the structure-function relationship. 3D structures are most often perceived using the two-dimensional and exclusively visual medium of the computer screen. Converting digital 3D molecular data into real objects enables information to be perceived through an expanded range of human senses, including direct stereoscopic vision, touch, and interaction. Such tangible models facilitate new insights, enable hypothesis testing, and serve as psychological or sensory anchors for conceptual information about the functions of biomolecules. Recent advances in consumer 3D printing technology enable, for the first time, the cost-effective fabrication of high-quality and scientifically accurate models of biomolecules in a variety of molecular representations. However, the optimization of the virtual model and its printing parameters is difficult and time consuming without detailed guidance. Here, we provide a guide on the digital design and physical fabrication of biomolecule models for research and pedagogy using open source or low-cost software and low-cost 3D printers that use fused filament fabrication technology. PMID:28362403

Gaussian Accelerated Molecular Dynamics: Theory, Implementation, and Applications

PubMed Central

Miao, Yinglong; McCammon, J. Andrew

2018-01-01

A novel Gaussian Accelerated Molecular Dynamics (GaMD) method has been developed for simultaneous unconstrained enhanced sampling and free energy calculation of biomolecules. Without the need to set predefined reaction coordinates, GaMD enables unconstrained enhanced sampling of the biomolecules. Furthermore, by constructing a boost potential that follows a Gaussian distribution, accurate reweighting of GaMD simulations is achieved via cumulant expansion to the second order. The free energy profiles obtained from GaMD simulations allow us to identify distinct low energy states of the biomolecules and characterize biomolecular structural dynamics quantitatively. In this chapter, we present the theory of GaMD, its implementation in the widely used molecular dynamics software packages (AMBER and NAMD), and applications to the alanine dipeptide biomolecular model system, protein folding, biomolecular large-scale conformational transitions and biomolecular recognition. PMID:29720925

Density functional theory molecular modeling, chemical synthesis, and antimicrobial behaviour of selected benzimidazole derivatives

NASA Astrophysics Data System (ADS)

Marinescu, Maria; Tudorache, Diana Gabriela; Marton, George Iuliu; Zalaru, Christina-Marie; Popa, Marcela; Chifiriuc, Mariana-Carmen; Stavarache, Cristina-Elena; Constantinescu, Catalin

2017-02-01

Eco-friendly, one-pot, solvent-free synthesis of biologically active 2-substituted benzimidazoles is presented and discussed herein. Novel N-Mannich bases are synthesized from benzimidazoles, secondary amines and formaldehyde, and their structures are confirmed by 1H nuclear magnetic resonance (NMR), Fourier transform infrared (FTIR), and elemental analysis. All benzimidazole derivatives are evaluated by qualitative and quantitative methods against 9 bacterial strains. The largest microbicide and anti-biofilm effect is observed for the 2-(1-hydroxyethyl)-compounds. Density functional theory (DFT) modeling of the molecular structure and frontier molecular orbitals, i.e. highest occupied molecular orbital and lowest unoccupied molecular orbital (HOMO/LUMO), is accomplished by using the GAMESS 2012 software. Antimicrobial activity is correlated with the electronic parameters (chemical hardness, electronic chemical potential, global electrophilicity index), Mullikan atomic charges and geometric parameters of the benzimidazole compounds. The planarity of the compound, symmetry of the molecule, and the presence of a nucleophilic group, are advantages for a high antimicrobial activity. Finally, we briefly show that further accurate processing of such compounds into thin films and hybrid structures, e.g. by laser ablation matrix-assisted pulsed laser evaporation and/or laser-induced forward transfer, may indeed provide simple and environmental friendly, state-of-the-art solutions for antimicrobial coatings.

Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale.

PubMed

Parton, Daniel L; Grinaway, Patrick B; Hanson, Sonya M; Beauchamp, Kyle A; Chodera, John D

2016-06-01

The rapidly expanding body of available genomic and protein structural data provides a rich resource for understanding protein dynamics with biomolecular simulation. While computational infrastructure has grown rapidly, simulations on an omics scale are not yet widespread, primarily because software infrastructure to enable simulations at this scale has not kept pace. It should now be possible to study protein dynamics across entire (super)families, exploiting both available structural biology data and conformational similarities across homologous proteins. Here, we present a new tool for enabling high-throughput simulation in the genomics era. Ensembler takes any set of sequences-from a single sequence to an entire superfamily-and shepherds them through various stages of modeling and refinement to produce simulation-ready structures. This includes comparative modeling to all relevant PDB structures (which may span multiple conformational states of interest), reconstruction of missing loops, addition of missing atoms, culling of nearly identical structures, assignment of appropriate protonation states, solvation in explicit solvent, and refinement and filtering with molecular simulation to ensure stable simulation. The output of this pipeline is an ensemble of structures ready for subsequent molecular simulations using computer clusters, supercomputers, or distributed computing projects like Folding@home. Ensembler thus automates much of the time-consuming process of preparing protein models suitable for simulation, while allowing scalability up to entire superfamilies. A particular advantage of this approach can be found in the construction of kinetic models of conformational dynamics-such as Markov state models (MSMs)-which benefit from a diverse array of initial configurations that span the accessible conformational states to aid sampling. We demonstrate the power of this approach by constructing models for all catalytic domains in the human tyrosine kinase family, using all available kinase catalytic domain structures from any organism as structural templates. Ensembler is free and open source software licensed under the GNU General Public License (GPL) v2. It is compatible with Linux and OS X. The latest release can be installed via the conda package manager, and the latest source can be downloaded from https://github.com/choderalab/ensembler.

A new approach to aid the characterisation and identification of metabolites of a model drug; partial isotope enrichment combined with novel formula elucidation software.

PubMed

Hobby, Kirsten; Gallagher, Richard T; Caldwell, Patrick; Wilson, Ian D

2009-01-01

This work describes the identification of 'isotopically enriched' metabolites of 4-cyanoaniline using the unique features of the software package 'Spectral Simplicity'. The software is capable of creating the theoretical mass spectra for partially isotope-enriched compounds, and subsequently performing an elemental composition analysis to give the elemental formula for the 'isotopically enriched' metabolite. A novel mass spectral correlation method, called 'FuzzyFit', was employed. 'FuzzyFit' utilises the expected experimental distribution of errors in both mass accuracy and isotope pattern and enables discrimination between statistically probable and improbable candidate formulae. The software correctly determined the molecular formulae of ten previously described metabolites of 4-cyanoaniline confirming the technique of partial isotope enrichment can produce results analogous to standard methodologies. Six previously unknown species were also identified, based on the presence of the unique 'designer' isotope ratio. Three of the unknowns were tentatively identified as N-acetylglutamine, O-methyl-N acetylglucuronide and a putative fatty acid conjugate. The discovery of a significant number of unknown species of a model drug with a comprehensive history of investigation highlights the potential for enhancement to the analytical process by the use of 'designer' isotope ratio compounds. The 'FuzzyFit' methodology significantly aided the elucidation of candidate formulae, by provision of a vastly simplified candidate formula data set. Copyright (c) 2008 John Wiley & Sons, Ltd.

Density functional theory molecular modeling and antimicrobial behaviour of selected 1,2,3,4,5,6,7,8-octahydroacridine-N(10)-oxides

NASA Astrophysics Data System (ADS)

Marinescu, Maria; Cinteza, Ludmila Otilia; Marton, George Iuliu; Marutescu, Luminita Gabriela; Chifiriuc, Mariana-Carmen; Constantinescu, Catalin

2017-09-01

A series of 9-substituted 1,2,3,4,5,6,7,8-octahydroacridine-N(10)-oxides is evaluated against 12 bacterial and fungal strains, for their microbicidal and anti-pathogenic features. The largest spectrum of the antibacterial activity is evidenced for the nitro- (2b) and hydroxy- (5b) N-oxides, followed by the amino-N-oxide (3b). Density functional theory (DFT) modeling of the molecular structure and frontier molecular orbitals, i.e. highest occupied/lowest unoccupied molecular orbital (HOMO/LUMO), is accomplished by using the GAMESS 2012 software at M11/ktzvp level of theory in order to find their structural and electronic parameters. We show that the planarity of the molecules and the presence of the electron withdrawing group are advantages for its antimicrobial activity. Finally, we briefly present and discuss results on the processing of such compounds into thin films and hybrid structures by laser-assisted techniques, i.e. matrix-assisted pulsed laser evaporation (MAPLE) or laser-induced forward transfer (LIFT), to provide simple and environmental friendly, state-of-the-art solutions for antimicrobial/medical coatings and devices.

Multi-scale modeling in cell biology

PubMed Central

Meier-Schellersheim, Martin; Fraser, Iain D. C.; Klauschen, Frederick

2009-01-01

Biomedical research frequently involves performing experiments and developing hypotheses that link different scales of biological systems such as, for instance, the scales of intracellular molecular interactions to the scale of cellular behavior and beyond to the behavior of cell populations. Computational modeling efforts that aim at exploring such multi-scale systems quantitatively with the help of simulations have to incorporate several different simulation techniques due to the different time and space scales involved. Here, we provide a non-technical overview of how different scales of experimental research can be combined with the appropriate computational modeling techniques. We also show that current modeling software permits building and simulating multi-scale models without having to become involved with the underlying technical details of computational modeling. PMID:20448808

Software Applications on the Peregrine System | High-Performance Computing

Science.gov Websites

programming and optimization. Gaussian Chemistry Program for calculating molecular electronic structure and Materials Science Open-source classical molecular dynamics program designed for massively parallel systems framework Q-Chem Chemistry ab initio quantum chemistry package for predictin molecular structures

Weighted Ensemble Simulation: Review of Methodology, Applications, and Software

PubMed Central

Zuckerman, Daniel M.; Chong, Lillian T.

2018-01-01

The weighted ensemble (WE) methodology orchestrates quasi-independent parallel simulations run with intermittent communication that can enhance sampling of rare events such as protein conformational changes, folding, and binding. The WE strategy can achieve superlinear scaling—the unbiased estimation of key observables such as rate constants and equilibrium state populations to greater precision than would be possible with ordinary parallel simulation. WE software can be used to control any dynamics engine, such as standard molecular dynamics and cell-modeling packages. This article reviews the theoretical basis of WE and goes on to describe successful applications to a number of complex biological processes—protein conformational transitions, (un)binding, and assembly processes, as well as cell-scale processes in systems biology. We furthermore discuss the challenges that need to be overcome in the next phase of WE methodological development. Overall, the combined advances in WE methodology and software have enabled the simulation of long-timescale processes that would otherwise not be practical on typical computing resources using standard simulation. PMID:28301772

Weighted Ensemble Simulation: Review of Methodology, Applications, and Software.

PubMed

Zuckerman, Daniel M; Chong, Lillian T

2017-05-22

The weighted ensemble (WE) methodology orchestrates quasi-independent parallel simulations run with intermittent communication that can enhance sampling of rare events such as protein conformational changes, folding, and binding. The WE strategy can achieve superlinear scaling-the unbiased estimation of key observables such as rate constants and equilibrium state populations to greater precision than would be possible with ordinary parallel simulation. WE software can be used to control any dynamics engine, such as standard molecular dynamics and cell-modeling packages. This article reviews the theoretical basis of WE and goes on to describe successful applications to a number of complex biological processes-protein conformational transitions, (un)binding, and assembly processes, as well as cell-scale processes in systems biology. We furthermore discuss the challenges that need to be overcome in the next phase of WE methodological development. Overall, the combined advances in WE methodology and software have enabled the simulation of long-timescale processes that would otherwise not be practical on typical computing resources using standard simulation.

Intra-articular viscosupplementation of hyaluronic acids in an experimental osteoarthritis model.

PubMed

Oliveira, Marcello Zaia; Albano, Mauro Batista; Stirma, Guilherme Augusto; Namba, Mario Massatomo; Vidigal, Leandro; Cunha, Luiz Antonio Munhoz da

2018-01-01

To analyze, from the immunohistochemical perspective, the effects of hyaluronic acid of different molecular weights in an experimental model of osteoarthritis in rabbits. Forty-four male California rabbits were randomly assigned to three different groups (PR, S, and P) and submitted to the resection of the anterior cruciate ligament of the right knee. Three weeks after the surgical procedure, three intra-articular weekly injections were carried out with low-molecular-weight native hyaluronic acid (Hyalgan ® ) to PR group, high molecular weight branched chain hyaluronic acid (Synvisc ® ) to group S, and saline solution 0.9% to group P. All animals were sacrificed 12 weeks after the surgical procedure, and the tibial plateaus of the infiltrated knees were then dissected. Histological sections of cartilage from the tibial plateau support areas were stained with immunohistochemical markers in order to investigate the amount of metalloproteases (MMPs 3 and 13) and their inhibitors (TIMPs 1 and 3). The staining intensity was quantified on a Zeiss Imager.Z2 Metasystems microscope and analyzed by Metafer4 Msearch software. The chondroprotective effect of the hyaluronic acids used in the study was demonstrated when compared to the control group. However, the comparison between them presented no significant statistical difference regarding chondroprotection. The injection of saline solution demonstrated signs of OA development, while adding native hyaluronic acid of low molecular weight (Hyalgan ® ) and hyaluronic acid of high molecular weight (Synvisc ® ) protected the articular cartilage in this model of OA.

Does glimepiride alter the pharmacokinetics of sildenafil citrate in diabetic nephropathy animals: investigating mechanism of interaction by molecular modeling studies.

PubMed

Tripathi, Alok Shiomurti; Timiri, Ajay Kumar; Mazumder, Papiya Mitra; Chandewar, Anil

2015-10-01

The present study evaluates possible drug interactions between glimepiride (GLIM) and sildenafil citrate (SIL) in streptozotocin (STZ)-induced diabetic nephropathic (DN) animals and also postulates the possible mechanism of interaction based on molecular modeling studies. Diabetic nephropathy was induced by single dose of STZ (60 mg kg(-1), i.p.) and was confirmed by assessing blood and urine biochemical parameters 28 days after induction. Selected DN animals were used to explore the drug interaction between GLIM (0.5 mg kg(-1), p.o.) and SIL (2.5 mg kg(-1), p.o.) on the 29th and 70th day of the protocol. Possible drug interaction was assessed by evaluating the plasma drug concentration using HPLC-UV and changes in biochemical parameters in blood and urine were also determined. The mechanism of the interaction was postulated from the results of a molecular modeling study using the Maestro module of Schrodinger software. DN was confirmed as there was significant alteration in blood and urine biochemical parameters in STZ-treated groups. The concentration of SIL increased significantly (P < 0.001) in rat plasma when co-administered with GLIM on the 70th day of the protocol. Molecular modeling revealed important interactions with rat serum albumin and CYP2C9. GLIM has a strong hydrophobic interaction with binding site residues of rat serum albumin compared to SIL, whereas for CYP2C9, GLIM forms a stronger hydrogen bond than SIL with polar contacts and hydrophobic interactions. The present study concludes that bioavailability of SIL increases when co-administered chronically with GLIM in the management of DN animals, and the mechanism is supported by molecular modeling studies.

SeqAPASS (Sequence Alignment to Predict Across Species Susceptibility) software and documentation

EPA Science Inventory

SeqAPASS is a software application facilitates rapid and streamlined, yet transparent, comparisons of the similarity of toxicologically-significant molecular targets across species. The present application facilitates analysis of primary amino acid sequence similarity (including ...

Predicting physical properties of emerging compounds with limited physical and chemical data: QSAR model uncertainty and applicability to military munitions.

PubMed

Bennett, Erin R; Clausen, Jay; Linkov, Eugene; Linkov, Igor

2009-11-01

Reliable, up-front information on physical and biological properties of emerging materials is essential before making a decision and investment to formulate, synthesize, scale-up, test, and manufacture a new material for use in both military and civilian applications. Multiple quantitative structure-activity relationships (QSARs) software tools are available for predicting a material's physical/chemical properties and environmental effects. Even though information on emerging materials is often limited, QSAR software output is treated without sufficient uncertainty analysis. We hypothesize that uncertainty and variability in material properties and uncertainty in model prediction can be too large to provide meaningful results. To test this hypothesis, we predicted octanol water partitioning coefficients (logP) for multiple, similar compounds with limited physical-chemical properties using six different commercial logP calculators (KOWWIN, MarvinSketch, ACD/Labs, ALogP, CLogP, SPARC). Analysis was done for materials with largely uncertain properties that were similar, based on molecular formula, to military compounds (RDX, BTTN, TNT) and pharmaceuticals (Carbamazepine, Gemfibrizol). We have also compared QSAR modeling results for a well-studied pesticide and pesticide breakdown product (Atrazine, DDE). Our analysis shows variability due to structural variations of the emerging chemicals may be several orders of magnitude. The model uncertainty across six software packages was very high (10 orders of magnitude) for emerging materials while it was low for traditional chemicals (e.g. Atrazine). Thus the use of QSAR models for emerging materials screening requires extensive model validation and coupling QSAR output with available empirical data and other relevant information.

TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD.

PubMed

Vermaas, Josh V; Hardy, David J; Stone, John E; Tajkhorshid, Emad; Kohlmeyer, Axel

2016-06-27

Molecular dynamics (MD) simulation engines use a variety of different approaches for modeling molecular systems with force fields that govern their dynamics and describe their topology. These different approaches introduce incompatibilities between engines, and previously published software bridges the gaps between many popular MD packages, such as between CHARMM and AMBER or GROMACS and LAMMPS. While there are many structure building tools available that generate topologies and structures in CHARMM format, only recently have mechanisms been developed to convert their results into GROMACS input. We present an approach to convert CHARMM-formatted topology and parameters into a format suitable for simulation with GROMACS by expanding the functionality of TopoTools, a plugin integrated within the widely used molecular visualization and analysis software VMD. The conversion process was diligently tested on a comprehensive set of biological molecules in vacuo. The resulting comparison between energy terms shows that the translation performed was lossless as the energies were unchanged for identical starting configurations. By applying the conversion process to conventional benchmark systems that mimic typical modestly sized MD systems, we explore the effect of the implementation choices made in CHARMM, NAMD, and GROMACS. The newly available automatic conversion capability breaks down barriers between simulation tools and user communities and allows users to easily compare simulation programs and leverage their unique features without the tedium of constructing a topology twice.

Tools for Modeling & Simulation of Molecular and Nanoelectronics Devices

DTIC Science & Technology

2012-06-14

implemented a prototype DFT simulation software using two different open source Finite Element (FE) libraries: DEALII and FENICS . These two libraries have been...ATK. In the first part of this Phase I project we investigated two different candidate finite element libraries, DEAL II and FENICS . Although both...element libraries, Deal.II and FEniCS /dolfin, for use as back-ends to a finite element DFT in ATK, Quantum Insight and QuantumWise A/S, October 2011.

Solvation Structure and Thermodynamic Mapping (SSTMap): An Open-Source, Flexible Package for the Analysis of Water in Molecular Dynamics Trajectories.

PubMed

Haider, Kamran; Cruz, Anthony; Ramsey, Steven; Gilson, Michael K; Kurtzman, Tom

2018-01-09

We have developed SSTMap, a software package for mapping structural and thermodynamic water properties in molecular dynamics trajectories. The package introduces automated analysis and mapping of local measures of frustration and enhancement of water structure. The thermodynamic calculations are based on Inhomogeneous Fluid Solvation Theory (IST), which is implemented using both site-based and grid-based approaches. The package also extends the applicability of solvation analysis calculations to multiple molecular dynamics (MD) simulation programs by using existing cross-platform tools for parsing MD parameter and trajectory files. SSTMap is implemented in Python and contains both command-line tools and a Python module to facilitate flexibility in setting up calculations and for automated generation of large data sets involving analysis of multiple solutes. Output is generated in formats compatible with popular Python data science packages. This tool will be used by the molecular modeling community for computational analysis of water in problems of biophysical interest such as ligand binding and protein function.

Analysis of Circadian Leaf Movements.

PubMed

Müller, Niels A; Jiménez-Gómez, José M

2016-01-01

The circadian clock is a molecular timekeeper that controls a wide variety of biological processes. In plants, clock outputs range from the molecular level, with rhythmic gene expression and metabolite content, to physiological processes such as stomatal conductance or leaf movements. Any of these outputs can be used as markers to monitor the state of the circadian clock. In the model plant Arabidopsis thaliana, much of the current knowledge about the clock has been gained from time course experiments profiling expression of endogenous genes or reporter constructs regulated by the circadian clock. Since these methods require labor-intensive sample preparation or transformation, monitoring leaf movements is an interesting alternative, especially in non-model species and for natural variation studies. Technological improvements both in digital photography and image analysis allow cheap and easy monitoring of circadian leaf movements. In this chapter we present a protocol that uses an autonomous point and shoot camera and free software to monitor circadian leaf movements in tomato.

Molecular Isotopic Distribution Analysis (MIDAs) with Adjustable Mass Accuracy

NASA Astrophysics Data System (ADS)

Alves, Gelio; Ogurtsov, Aleksey Y.; Yu, Yi-Kuo

2014-01-01

In this paper, we present Molecular Isotopic Distribution Analysis (MIDAs), a new software tool designed to compute molecular isotopic distributions with adjustable accuracies. MIDAs offers two algorithms, one polynomial-based and one Fourier-transform-based, both of which compute molecular isotopic distributions accurately and efficiently. The polynomial-based algorithm contains few novel aspects, whereas the Fourier-transform-based algorithm consists mainly of improvements to other existing Fourier-transform-based algorithms. We have benchmarked the performance of the two algorithms implemented in MIDAs with that of eight software packages (BRAIN, Emass, Mercury, Mercury5, NeutronCluster, Qmass, JFC, IC) using a consensus set of benchmark molecules. Under the proposed evaluation criteria, MIDAs's algorithms, JFC, and Emass compute with comparable accuracy the coarse-grained (low-resolution) isotopic distributions and are more accurate than the other software packages. For fine-grained isotopic distributions, we compared IC, MIDAs's polynomial algorithm, and MIDAs's Fourier transform algorithm. Among the three, IC and MIDAs's polynomial algorithm compute isotopic distributions that better resemble their corresponding exact fine-grained (high-resolution) isotopic distributions. MIDAs can be accessed freely through a user-friendly web-interface at http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/midas/index.html.

GlycCompSoft: Software for Automated Comparison of Low Molecular Weight Heparins Using Top-Down LC/MS Data

PubMed Central

Li, Lingyun; Zhang, Fuming; Hu, Min; Ren, Fuji; Chi, Lianli; Linhardt, Robert J.

2016-01-01

Low molecular weight heparins are complex polycomponent drugs that have recently become amenable to top-down analysis using liquid chromatography-mass spectrometry. Even using open source deconvolution software, DeconTools, and automatic structural assignment software, GlycReSoft, the comparison of two or more low molecular weight heparins is extremely time-consuming, taking about a week for an expert analyst and provides no guarantee of accuracy. Efficient data processing tools are required to improve analysis. This study uses the programming language of Microsoft Excel™ Visual Basic for Applications to extend its standard functionality for macro functions and specific mathematical modules for mass spectrometric data processing. The program developed enables the comparison of top-down analytical glycomics data on two or more low molecular weight heparins. The current study describes a new program, GlycCompSoft, which has a low error rate with good time efficiency in the automatic processing of large data sets. The experimental results based on three lots of Lovenox®, Clexane® and three generic enoxaparin samples show that the run time of GlycCompSoft decreases from 11 to 2 seconds when the data processed decreases from 18000 to 1500 rows. PMID:27942011

Molecular Isotopic Distribution Analysis (MIDAs) with adjustable mass accuracy.

PubMed

Alves, Gelio; Ogurtsov, Aleksey Y; Yu, Yi-Kuo

2014-01-01

In this paper, we present Molecular Isotopic Distribution Analysis (MIDAs), a new software tool designed to compute molecular isotopic distributions with adjustable accuracies. MIDAs offers two algorithms, one polynomial-based and one Fourier-transform-based, both of which compute molecular isotopic distributions accurately and efficiently. The polynomial-based algorithm contains few novel aspects, whereas the Fourier-transform-based algorithm consists mainly of improvements to other existing Fourier-transform-based algorithms. We have benchmarked the performance of the two algorithms implemented in MIDAs with that of eight software packages (BRAIN, Emass, Mercury, Mercury5, NeutronCluster, Qmass, JFC, IC) using a consensus set of benchmark molecules. Under the proposed evaluation criteria, MIDAs's algorithms, JFC, and Emass compute with comparable accuracy the coarse-grained (low-resolution) isotopic distributions and are more accurate than the other software packages. For fine-grained isotopic distributions, we compared IC, MIDAs's polynomial algorithm, and MIDAs's Fourier transform algorithm. Among the three, IC and MIDAs's polynomial algorithm compute isotopic distributions that better resemble their corresponding exact fine-grained (high-resolution) isotopic distributions. MIDAs can be accessed freely through a user-friendly web-interface at http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/midas/index.html.

Logic integer programming models for signaling networks.

PubMed

Haus, Utz-Uwe; Niermann, Kathrin; Truemper, Klaus; Weismantel, Robert

2009-05-01

We propose a static and a dynamic approach to model biological signaling networks, and show how each can be used to answer relevant biological questions. For this, we use the two different mathematical tools of Propositional Logic and Integer Programming. The power of discrete mathematics for handling qualitative as well as quantitative data has so far not been exploited in molecular biology, which is mostly driven by experimental research, relying on first-order or statistical models. The arising logic statements and integer programs are analyzed and can be solved with standard software. For a restricted class of problems the logic models reduce to a polynomial-time solvable satisfiability algorithm. Additionally, a more dynamic model enables enumeration of possible time resolutions in poly-logarithmic time. Computational experiments are included.

Molecular docking.

PubMed

Morris, Garrett M; Lim-Wilby, Marguerita

2008-01-01

Molecular docking is a key tool in structural molecular biology and computer-assisted drug design. The goal of ligand-protein docking is to predict the predominant binding mode(s) of a ligand with a protein of known three-dimensional structure. Successful docking methods search high-dimensional spaces effectively and use a scoring function that correctly ranks candidate dockings. Docking can be used to perform virtual screening on large libraries of compounds, rank the results, and propose structural hypotheses of how the ligands inhibit the target, which is invaluable in lead optimization. The setting up of the input structures for the docking is just as important as the docking itself, and analyzing the results of stochastic search methods can sometimes be unclear. This chapter discusses the background and theory of molecular docking software, and covers the usage of some of the most-cited docking software.

High-Performance First-Principles Molecular Dynamics for Predictive Theory and Modeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gygi, Francois; Galli, Giulia; Schwegler, Eric

This project focused on developing high-performance software tools for First-Principles Molecular Dynamics (FPMD) simulations, and applying them in investigations of materials relevant to energy conversion processes. FPMD is an atomistic simulation method that combines a quantum-mechanical description of electronic structure with the statistical description provided by molecular dynamics (MD) simulations. This reliance on fundamental principles allows FPMD simulations to provide a consistent description of structural, dynamical and electronic properties of a material. This is particularly useful in systems for which reliable empirical models are lacking. FPMD simulations are increasingly used as a predictive tool for applications such as batteries, solarmore » energy conversion, light-emitting devices, electro-chemical energy conversion devices and other materials. During the course of the project, several new features were developed and added to the open-source Qbox FPMD code. The code was further optimized for scalable operation of large-scale, Leadership-Class DOE computers. When combined with Many-Body Perturbation Theory (MBPT) calculations, this infrastructure was used to investigate structural and electronic properties of liquid water, ice, aqueous solutions, nanoparticles and solid-liquid interfaces. Computing both ionic trajectories and electronic structure in a consistent manner enabled the simulation of several spectroscopic properties, such as Raman spectra, infrared spectra, and sum-frequency generation spectra. The accuracy of the approximations used allowed for direct comparisons of results with experimental data such as optical spectra, X-ray and neutron diffraction spectra. The software infrastructure developed in this project, as applied to various investigations of solids, liquids and interfaces, demonstrates that FPMD simulations can provide a detailed, atomic-scale picture of structural, vibrational and electronic properties of complex systems relevant to energy conversion devices.« less

Three-dimensional printing of human skeletal muscle cells: An interdisciplinary approach for studying biological systems.

PubMed

Bagley, James R; Galpin, Andrew J

2015-01-01

Interdisciplinary exploration is vital to education in the 21st century. This manuscript outlines an innovative laboratory-based teaching method that combines elements of biochemistry/molecular biology, kinesiology/health science, computer science, and manufacturing engineering to give students the ability to better conceptualize complex biological systems. Here, we utilize technology available at most universities to print three-dimensional (3D) scale models of actual human muscle cells (myofibers) out of bioplastic materials. The same methodological approach could be applied to nearly any cell type or molecular structure. This advancement is significant because historically, two-dimensional (2D) myocellular images have proven insufficient for detailed analysis of organelle organization and morphology. 3D imaging fills this void by providing accurate and quantifiable myofiber structural data. Manipulating tangible 3D models combats 2D limitation and gives students new perspectives and alternative learning experiences that may assist their understanding. This approach also exposes learners to 1) human muscle cell extraction and isolation, 2) targeted fluorescence labeling, 3) confocal microscopy, 4) image processing (via open-source software), and 5) 3D printing bioplastic scale-models (×500 larger than the actual cells). Creating these physical models may further student's interest in the invisible world of molecular and cellular biology. Furthermore, this interdisciplinary laboratory project gives instructors of all biological disciplines a new teaching tool to foster integrative thinking. © 2015 The International Union of Biochemistry and Molecular Biology.

Quantification of video-taped images in microcirculation research using inexpensive imaging software (Adobe Photoshop).

PubMed

Brunner, J; Krummenauer, F; Lehr, H A

2000-04-01

Study end-points in microcirculation research are usually video-taped images rather than numeric computer print-outs. Analysis of these video-taped images for the quantification of microcirculatory parameters usually requires computer-based image analysis systems. Most software programs for image analysis are custom-made, expensive, and limited in their applicability to selected parameters and study end-points. We demonstrate herein that an inexpensive, commercially available computer software (Adobe Photoshop), run on a Macintosh G3 computer with inbuilt graphic capture board provides versatile, easy to use tools for the quantification of digitized video images. Using images obtained by intravital fluorescence microscopy from the pre- and postischemic muscle microcirculation in the skinfold chamber model in hamsters, Photoshop allows simple and rapid quantification (i) of microvessel diameters, (ii) of the functional capillary density and (iii) of postischemic leakage of FITC-labeled high molecular weight dextran from postcapillary venules. We present evidence of the technical accuracy of the software tools and of a high degree of interobserver reliability. Inexpensive commercially available imaging programs (i.e., Adobe Photoshop) provide versatile tools for image analysis with a wide range of potential applications in microcirculation research.

Computer-aided design of DNA origami structures.

PubMed

Selnihhin, Denis; Andersen, Ebbe Sloth

2015-01-01

The DNA origami method enables the creation of complex nanoscale objects that can be used to organize molecular components and to function as reconfigurable mechanical devices. Of relevance to synthetic biology, DNA origami structures can be delivered to cells where they can perform complicated sense-and-act tasks, and can be used as scaffolds to organize enzymes for enhanced synthesis. The design of DNA origami structures is a complicated matter and is most efficiently done using dedicated software packages. This chapter describes a procedure for designing DNA origami structures using a combination of state-of-the-art software tools. First, we introduce the basic method for calculating crossover positions between DNA helices and the standard crossover patterns for flat, square, and honeycomb DNA origami lattices. Second, we provide a step-by-step tutorial for the design of a simple DNA origami biosensor device, from schematic idea to blueprint creation and to 3D modeling and animation, and explain how careful modeling can facilitate later experimentation in the laboratory.

Atlas - a data warehouse for integrative bioinformatics.

PubMed

Shah, Sohrab P; Huang, Yong; Xu, Tao; Yuen, Macaire M S; Ling, John; Ouellette, B F Francis

2005-02-21

We present a biological data warehouse called Atlas that locally stores and integrates biological sequences, molecular interactions, homology information, functional annotations of genes, and biological ontologies. The goal of the system is to provide data, as well as a software infrastructure for bioinformatics research and development. The Atlas system is based on relational data models that we developed for each of the source data types. Data stored within these relational models are managed through Structured Query Language (SQL) calls that are implemented in a set of Application Programming Interfaces (APIs). The APIs include three languages: C++, Java, and Perl. The methods in these API libraries are used to construct a set of loader applications, which parse and load the source datasets into the Atlas database, and a set of toolbox applications which facilitate data retrieval. Atlas stores and integrates local instances of GenBank, RefSeq, UniProt, Human Protein Reference Database (HPRD), Biomolecular Interaction Network Database (BIND), Database of Interacting Proteins (DIP), Molecular Interactions Database (MINT), IntAct, NCBI Taxonomy, Gene Ontology (GO), Online Mendelian Inheritance in Man (OMIM), LocusLink, Entrez Gene and HomoloGene. The retrieval APIs and toolbox applications are critical components that offer end-users flexible, easy, integrated access to this data. We present use cases that use Atlas to integrate these sources for genome annotation, inference of molecular interactions across species, and gene-disease associations. The Atlas biological data warehouse serves as data infrastructure for bioinformatics research and development. It forms the backbone of the research activities in our laboratory and facilitates the integration of disparate, heterogeneous biological sources of data enabling new scientific inferences. Atlas achieves integration of diverse data sets at two levels. First, Atlas stores data of similar types using common data models, enforcing the relationships between data types. Second, integration is achieved through a combination of APIs, ontology, and tools. The Atlas software is freely available under the GNU General Public License at: http://bioinformatics.ubc.ca/atlas/

Atlas – a data warehouse for integrative bioinformatics

PubMed Central

Shah, Sohrab P; Huang, Yong; Xu, Tao; Yuen, Macaire MS; Ling, John; Ouellette, BF Francis

2005-01-01

Background We present a biological data warehouse called Atlas that locally stores and integrates biological sequences, molecular interactions, homology information, functional annotations of genes, and biological ontologies. The goal of the system is to provide data, as well as a software infrastructure for bioinformatics research and development. Description The Atlas system is based on relational data models that we developed for each of the source data types. Data stored within these relational models are managed through Structured Query Language (SQL) calls that are implemented in a set of Application Programming Interfaces (APIs). The APIs include three languages: C++, Java, and Perl. The methods in these API libraries are used to construct a set of loader applications, which parse and load the source datasets into the Atlas database, and a set of toolbox applications which facilitate data retrieval. Atlas stores and integrates local instances of GenBank, RefSeq, UniProt, Human Protein Reference Database (HPRD), Biomolecular Interaction Network Database (BIND), Database of Interacting Proteins (DIP), Molecular Interactions Database (MINT), IntAct, NCBI Taxonomy, Gene Ontology (GO), Online Mendelian Inheritance in Man (OMIM), LocusLink, Entrez Gene and HomoloGene. The retrieval APIs and toolbox applications are critical components that offer end-users flexible, easy, integrated access to this data. We present use cases that use Atlas to integrate these sources for genome annotation, inference of molecular interactions across species, and gene-disease associations. Conclusion The Atlas biological data warehouse serves as data infrastructure for bioinformatics research and development. It forms the backbone of the research activities in our laboratory and facilitates the integration of disparate, heterogeneous biological sources of data enabling new scientific inferences. Atlas achieves integration of diverse data sets at two levels. First, Atlas stores data of similar types using common data models, enforcing the relationships between data types. Second, integration is achieved through a combination of APIs, ontology, and tools. The Atlas software is freely available under the GNU General Public License at: PMID:15723693

RITRACKS: A Software for Simulation of Stochastic Radiation Track Structure, Micro and Nanodosimetry, Radiation Chemistry and DNA Damage for Heavy Ions

NASA Technical Reports Server (NTRS)

Plante, I; Wu, H

2014-01-01

The code RITRACKS (Relativistic Ion Tracks) has been developed over the last few years at the NASA Johnson Space Center to simulate the effects of ionizing radiations at the microscopic scale, to understand the effects of space radiation at the biological level. The fundamental part of this code is the stochastic simulation of radiation track structure of heavy ions, an important component of space radiations. The code can calculate many relevant quantities such as the radial dose, voxel dose, and may also be used to calculate the dose in spherical and cylindrical targets of various sizes. Recently, we have incorporated DNA structure and damage simulations at the molecular scale in RITRACKS. The direct effect of radiations is simulated by introducing a slight modification of the existing particle transport algorithms, using the Binary-Encounter-Bethe model of ionization cross sections for each molecular orbitals of DNA. The simulation of radiation chemistry is done by a step-by-step diffusion-reaction program based on the Green's functions of the diffusion equation]. This approach is also used to simulate the indirect effect of ionizing radiation on DNA. The software can be installed independently on PC and tablets using the Windows operating system and does not require any coding from the user. It includes a Graphic User Interface (GUI) and a 3D OpenGL visualization interface. The calculations are executed simultaneously (in parallel) on multiple CPUs. The main features of the software will be presented.

WESTPA: An interoperable, highly scalable software package for weighted ensemble simulation and analysis

PubMed Central

Zwier, Matthew C.; Adelman, Joshua L.; Kaus, Joseph W.; Pratt, Adam J.; Wong, Kim F.; Rego, Nicholas B.; Suárez, Ernesto; Lettieri, Steven; Wang, David W.; Grabe, Michael; Zuckerman, Daniel M.; Chong, Lillian T.

2015-01-01

The weighted ensemble (WE) path sampling approach orchestrates an ensemble of parallel calculations with intermittent communication to enhance the sampling of rare events, such as molecular associations or conformational changes in proteins or peptides. Trajectories are replicated and pruned in a way that focuses computational effort on under-explored regions of configuration space while maintaining rigorous kinetics. To enable the simulation of rare events at any scale (e.g. atomistic, cellular), we have developed an open-source, interoperable, and highly scalable software package for the execution and analysis of WE simulations: WESTPA (The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis). WESTPA scales to thousands of CPU cores and includes a suite of analysis tools that have been implemented in a massively parallel fashion. The software has been designed to interface conveniently with any dynamics engine and has already been used with a variety of molecular dynamics (e.g. GROMACS, NAMD, OpenMM, AMBER) and cell-modeling packages (e.g. BioNetGen, MCell). WESTPA has been in production use for over a year, and its utility has been demonstrated for a broad set of problems, ranging from atomically detailed host-guest associations to non-spatial chemical kinetics of cellular signaling networks. The following describes the design and features of WESTPA, including the facilities it provides for running WE simulations, storing and analyzing WE simulation data, as well as examples of input and output. PMID:26392815

Automatic Evolution of Molecular Nanotechnology Designs

NASA Technical Reports Server (NTRS)

Globus, Al; Lawton, John; Wipke, Todd; Saini, Subhash (Technical Monitor)

1998-01-01

This paper describes strategies for automatically generating designs for analog circuits at the molecular level. Software maps out the edges and vertices of potential nanotechnology systems on graphs, then selects appropriate ones through evolutionary or genetic paradigms.

Multiscale Computation. Needs and Opportunities for BER Science

DOE Office of Scientific and Technical Information (OSTI.GOV)

Scheibe, Timothy D.; Smith, Jeremy C.

2015-01-01

The Environmental Molecular Sciences Laboratory (EMSL), a scientific user facility managed by Pacific Northwest National Laboratory for the U.S. Department of Energy, Office of Biological and Environmental Research (BER), conducted a one-day workshop on August 26, 2014 on the topic of “Multiscale Computation: Needs and Opportunities for BER Science.” Twenty invited participants, from various computational disciplines within the BER program research areas, were charged with the following objectives; Identify BER-relevant models and their potential cross-scale linkages that could be exploited to better connect molecular-scale research to BER research at larger scales and; Identify critical science directions that will motivate EMSLmore » decisions regarding future computational (hardware and software) architectures.« less

MOLSIM: A modular molecular simulation software

PubMed Central

Jurij, Reščič

2015-01-01

The modular software MOLSIM for all‐atom molecular and coarse‐grained simulations is presented with focus on the underlying concepts used. The software possesses four unique features: (1) it is an integrated software for molecular dynamic, Monte Carlo, and Brownian dynamics simulations; (2) simulated objects are constructed in a hierarchical fashion representing atoms, rigid molecules and colloids, flexible chains, hierarchical polymers, and cross‐linked networks; (3) long‐range interactions involving charges, dipoles and/or anisotropic dipole polarizabilities are handled either with the standard Ewald sum, the smooth particle mesh Ewald sum, or the reaction‐field technique; (4) statistical uncertainties are provided for all calculated observables. In addition, MOLSIM supports various statistical ensembles, and several types of simulation cells and boundary conditions are available. Intermolecular interactions comprise tabulated pairwise potentials for speed and uniformity and many‐body interactions involve anisotropic polarizabilities. Intramolecular interactions include bond, angle, and crosslink potentials. A very large set of analyses of static and dynamic properties is provided. The capability of MOLSIM can be extended by user‐providing routines controlling, for example, start conditions, intermolecular potentials, and analyses. An extensive set of case studies in the field of soft matter is presented covering colloids, polymers, and crosslinked networks. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:25994597

SHAPEMOL: the companion to SHAPE in the molecular era of ALMA and HERSCHEL

NASA Astrophysics Data System (ADS)

Santander-García, M.; Bujarrabal, V.; Alcolea, J.

2013-05-01

Modern instrumentation in radioastronomy constitutes a valuable tool for studying the Universe: ALMA will reach unprecedented sensitivities and spatial resolution, while Herschel/HIFI has opened a new window (most of the sub-mm and far infrared ranges are only accessible from space) for probing molecular warm gas (˜50-1000 K), complementing ground-based telescopes, which are better suited to study molecular molecular gas with temperatures under ˜100 K. On the other hand, the SHAPE software has emerged in the last few years as the standard tool for determinging the morphology and velocity field of different kinds of gaseous nebulae (mainly planetary nebulae, protoplanetary nebulae and nebulae around massive stars, although it can also be applied to H II regions and molecular clouds) via spatio-kinematical modelling. Standard SHAPE implements radiative transfer solving, but it is only available for atomic species and not for molecules. Being aware of the growing importance of the development of tools for easying the analyses of molecular data from new era observatories, we introduce the computer code shapemol, a plug-in for SHAPE with which we intend to fill the so far empty molecular niche. shapemol enables spatio-kinematic modeling with accurate non-LTE calculations of line excitation and radiative transfer in molecular species. This code has been succesfully tested in the study of the excitation conditions of the molecular envelope of the planetary nebula NGC 7027 using data from Herschel/HIFI and IRAM 30m. Currently, it allows radiative transfer solving in the ^{12}CO and ^{13}CO J=1-0 to J=17-16 lines. shapemol, used along SHAPE, allows to easily generate synthetic maps to test against interferometric observations, as well as synthetic line profiles to match single-dish observations.

A systematic quantitative approach to rational drug design and discovery of novel human carbonic anhydrase IX inhibitors.

PubMed

Sethi, Kalyan K; Verma, Saurabh M

2014-08-01

Drug design involves the design of small molecules that are complementary in shape and charge to the biomolecular target with which they interact and therefore will bind to it. Three-dimensional quantitative structure-activity relationship (3D-QSAR) studies were performed for a series of carbonic anhydrase IX inhibitors using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) techniques with the help of SYBYL 7.1 software. The large set of 36 different aromatic/heterocyclic sulfamates carbonic anhydrase (CA, EC 4.2.1.1) inhibitors, such as hCA IX, was chosen for this study. The conventional ligand-based 3D-QSAR studies were performed based on the low energy conformations employing database alignment rule. The ligand-based model gave q(2) values 0.802 and 0.829 and r(2) values 1.000 and 0.994 for CoMFA and CoMSIA, respectively, and the predictive ability of the model was validated. The predicted r(2) values are 0.999 and 0.502 for CoMFA and CoMSIA, respectively. SEA (steric, electrostatic, hydrogen bond acceptor) of CoMSIA has the significant contribution for the model development. The docking of inhibitors into hCA IX active site using Glide XP (Schrödinger) software revealed the vital interactions and binding conformation of the inhibitors. The CoMFA and CoMSIA field contour maps are well in agreement with the structural characteristics of the binding pocket of hCA IX active site, which suggests that the information rendered by 3D-QSAR models and the docking interactions can provide guidelines for the development of improved hCA IX inhibitors as leads for various types of metastatic cancers including those of cervical, renal, breast and head and neck origin.

DiSCaMB: a software library for aspherical atom model X-ray scattering factor calculations with CPUs and GPUs.

PubMed

Chodkiewicz, Michał L; Migacz, Szymon; Rudnicki, Witold; Makal, Anna; Kalinowski, Jarosław A; Moriarty, Nigel W; Grosse-Kunstleve, Ralf W; Afonine, Pavel V; Adams, Paul D; Dominiak, Paulina Maria

2018-02-01

It has been recently established that the accuracy of structural parameters from X-ray refinement of crystal structures can be improved by using a bank of aspherical pseudoatoms instead of the classical spherical model of atomic form factors. This comes, however, at the cost of increased complexity of the underlying calculations. In order to facilitate the adoption of this more advanced electron density model by the broader community of crystallographers, a new software implementation called DiSCaMB , 'densities in structural chemistry and molecular biology', has been developed. It addresses the challenge of providing for high performance on modern computing architectures. With parallelization options for both multi-core processors and graphics processing units (using CUDA), the library features calculation of X-ray scattering factors and their derivatives with respect to structural parameters, gives access to intermediate steps of the scattering factor calculations (thus allowing for experimentation with modifications of the underlying electron density model), and provides tools for basic structural crystallographic operations. Permissively (MIT) licensed, DiSCaMB is an open-source C++ library that can be embedded in both academic and commercial tools for X-ray structure refinement.

CLMSVault: A Software Suite for Protein Cross-Linking Mass-Spectrometry Data Analysis and Visualization.

PubMed

Courcelles, Mathieu; Coulombe-Huntington, Jasmin; Cossette, Émilie; Gingras, Anne-Claude; Thibault, Pierre; Tyers, Mike

2017-07-07

Protein cross-linking mass spectrometry (CL-MS) enables the sensitive detection of protein interactions and the inference of protein complex topology. The detection of chemical cross-links between protein residues can identify intra- and interprotein contact sites or provide physical constraints for molecular modeling of protein structure. Recent innovations in cross-linker design, sample preparation, mass spectrometry, and software tools have significantly improved CL-MS approaches. Although a number of algorithms now exist for the identification of cross-linked peptides from mass spectral data, a dearth of user-friendly analysis tools represent a practical bottleneck to the broad adoption of the approach. To facilitate the analysis of CL-MS data, we developed CLMSVault, a software suite designed to leverage existing CL-MS algorithms and provide intuitive and flexible tools for cross-platform data interpretation. CLMSVault stores and combines complementary information obtained from different cross-linkers and search algorithms. CLMSVault provides filtering, comparison, and visualization tools to support CL-MS analyses and includes a workflow for label-free quantification of cross-linked peptides. An embedded 3D viewer enables the visualization of quantitative data and the mapping of cross-linked sites onto PDB structural models. We demonstrate the application of CLMSVault for the analysis of a noncovalent Cdc34-ubiquitin protein complex cross-linked under different conditions. CLMSVault is open-source software (available at https://gitlab.com/courcelm/clmsvault.git ), and a live demo is available at http://democlmsvault.tyerslab.com/ .

Avoiding Defect Nucleation during Equilibration in Molecular Dynamics Simulations with ReaxFF

DTIC Science & Technology

2015-04-01

respectively. All simulations are performed using the LAMMPS computer code.12 2 Fig. 1 a) Initial and b) final configurations of the molecular centers...Plimpton S. Fast parallel algorithms for short-range molecular dynamics. Comput J Phys. 1995;117:1–19. (Software available at http:// lammps .sandia.gov

A composite computational model of liver glucose homeostasis. I. Building the composite model.

PubMed

Hetherington, J; Sumner, T; Seymour, R M; Li, L; Rey, M Varela; Yamaji, S; Saffrey, P; Margoninski, O; Bogle, I D L; Finkelstein, A; Warner, A

2012-04-07

A computational model of the glucagon/insulin-driven liver glucohomeostasis function, focusing on the buffering of glucose into glycogen, has been developed. The model exemplifies an 'engineering' approach to modelling in systems biology, and was produced by linking together seven component models of separate aspects of the physiology. The component models use a variety of modelling paradigms and degrees of simplification. Model parameters were determined by an iterative hybrid of fitting to high-scale physiological data, and determination from small-scale in vitro experiments or molecular biological techniques. The component models were not originally designed for inclusion within such a composite model, but were integrated, with modification, using our published modelling software and computational frameworks. This approach facilitates the development of large and complex composite models, although, inevitably, some compromises must be made when composing the individual models. Composite models of this form have not previously been demonstrated.

Produced water re-injection in a non-fresh water aquifer with geochemical reaction, hydrodynamic molecular dispersion and adsorption kinetics controlling: model development and numerical simulation

NASA Astrophysics Data System (ADS)

Obe, Ibidapo; Fashanu, T. A.; Idialu, Peter O.; Akintola, Tope O.; Abhulimen, Kingsley E.

2017-06-01

An improved produced water reinjection (PWRI) model that incorporates filtration, geochemical reaction, molecular transport, and mass adsorption kinetics was developed to predict cake deposition and injectivity performance in hydrocarbon aquifers in Nigeria oil fields. Thus, the improved PWRI model considered contributions of geochemical reaction, adsorption kinetics, and hydrodynamic molecular dispersion mechanism to alter the injectivity and deposition of suspended solids on aquifer wall resulting in cake formation in pores during PWRI and transport of active constituents in hydrocarbon reservoirs. The injectivity decline and cake deposition for specific case studies of hydrocarbon aquifers in Nigeria oil fields were characterized with respect to its well geometry, lithology, and calibrations data and simulated in COMSOL multiphysics software environment. The PWRI model was validated by comparisons to assessments of previous field studies based on data and results supplied by operator and regulator. The results of simulation showed that PWRI performance was altered because of temporal variations and declinations of permeability, injectivity, and cake precipitation, which were observed to be dependent on active adsorption and geochemical reaction kinetics coupled with filtration scheme and molecular dispersion. From the observed results and findings, transition time t r to cake nucleation and growth were dependent on aquifer constituents, well capacity, filtration coefficients, particle-to-grain size ratio, water quality, and more importantly, particle-to-grain adsorption kinetics. Thus, the results showed that injectivity decline and permeability damage were direct contributions of geochemical reaction, hydrodynamic molecular diffusion, and adsorption kinetics to the internal filtration mechanism, which are largely dependent on the initial conditions of concentration of active constituents of produced water and aquifer capacity.

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories.

PubMed

McGibbon, Robert T; Beauchamp, Kyle A; Harrigan, Matthew P; Klein, Christoph; Swails, Jason M; Hernández, Carlos X; Schwantes, Christian R; Wang, Lee-Ping; Lane, Thomas J; Pande, Vijay S

2015-10-20

As molecular dynamics (MD) simulations continue to evolve into powerful computational tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use software tools for the analysis of these simulations is growing. We have developed MDTraj, a modern, lightweight, and fast software package for analyzing MD simulations. MDTraj reads and writes trajectory data in a wide variety of commonly used formats. It provides a large number of trajectory analysis capabilities including minimal root-mean-square-deviation calculations, secondary structure assignment, and the extraction of common order parameters. The package has a strong focus on interoperability with the wider scientific Python ecosystem, bridging the gap between MD data and the rapidly growing collection of industry-standard statistical analysis and visualization tools in Python. MDTraj is a powerful and user-friendly software package that simplifies the analysis of MD data and connects these datasets with the modern interactive data science software ecosystem in Python. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

PubMed Central

McGibbon, Robert T.; Beauchamp, Kyle A.; Harrigan, Matthew P.; Klein, Christoph; Swails, Jason M.; Hernández, Carlos X.; Schwantes, Christian R.; Wang, Lee-Ping; Lane, Thomas J.; Pande, Vijay S.

2015-01-01

As molecular dynamics (MD) simulations continue to evolve into powerful computational tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use software tools for the analysis of these simulations is growing. We have developed MDTraj, a modern, lightweight, and fast software package for analyzing MD simulations. MDTraj reads and writes trajectory data in a wide variety of commonly used formats. It provides a large number of trajectory analysis capabilities including minimal root-mean-square-deviation calculations, secondary structure assignment, and the extraction of common order parameters. The package has a strong focus on interoperability with the wider scientific Python ecosystem, bridging the gap between MD data and the rapidly growing collection of industry-standard statistical analysis and visualization tools in Python. MDTraj is a powerful and user-friendly software package that simplifies the analysis of MD data and connects these datasets with the modern interactive data science software ecosystem in Python. PMID:26488642

An autonomous molecular computer for logical control of gene expression.

PubMed

Benenson, Yaakov; Gil, Binyamin; Ben-Dor, Uri; Adar, Rivka; Shapiro, Ehud

2004-05-27

Early biomolecular computer research focused on laboratory-scale, human-operated computers for complex computational problems. Recently, simple molecular-scale autonomous programmable computers were demonstrated allowing both input and output information to be in molecular form. Such computers, using biological molecules as input data and biologically active molecules as outputs, could produce a system for 'logical' control of biological processes. Here we describe an autonomous biomolecular computer that, at least in vitro, logically analyses the levels of messenger RNA species, and in response produces a molecule capable of affecting levels of gene expression. The computer operates at a concentration of close to a trillion computers per microlitre and consists of three programmable modules: a computation module, that is, a stochastic molecular automaton; an input module, by which specific mRNA levels or point mutations regulate software molecule concentrations, and hence automaton transition probabilities; and an output module, capable of controlled release of a short single-stranded DNA molecule. This approach might be applied in vivo to biochemical sensing, genetic engineering and even medical diagnosis and treatment. As a proof of principle we programmed the computer to identify and analyse mRNA of disease-related genes associated with models of small-cell lung cancer and prostate cancer, and to produce a single-stranded DNA molecule modelled after an anticancer drug.

Electronic coarse graining enhances the predictive power of molecular simulation allowing challenges in water physics to be addressed

NASA Astrophysics Data System (ADS)

Cipcigan, Flaviu S.; Sokhan, Vlad P.; Crain, Jason; Martyna, Glenn J.

2016-12-01

One key factor that limits the predictive power of molecular dynamics simulations is the accuracy and transferability of the input force field. Force fields are challenged by heterogeneous environments, where electronic responses give rise to biologically important forces such as many-body polarisation and dispersion. The importance of polarisation in the condensed phase was recognised early on, as described by Cochran in 1959 [Philosophical Magazine 4 (1959) 1082-1086] [32]. Currently in molecular simulation, dispersion forces are treated at the two-body level and in the dipole limit, although the importance of three-body terms in the condensed phase was demonstrated by Barker in the 1980s [Phys. Rev. Lett. 57 (1986) 230-233] [72]. One approach for treating both polarisation and dispersion on an equal basis is to coarse grain the electrons surrounding a molecular moiety to a single quantum harmonic oscillator (cf. Hirschfelder, Curtiss and Bird 1954 [The Molecular Theory of Gases and Liquids (1954)] [37]). The approach, when solved in strong coupling beyond the dipole limit, gives a description of long-range forces that includes two- and many-body terms to all orders. In the last decade, the tools necessary to implement the strong coupling limit have been developed, culminating in a transferable model of water with excellent predictive power across the phase diagram. Transferability arises since the environment automatically identifies the important long range interactions, rather than the modeller through a limited set of expressions. Here, we discuss the role of electronic coarse-graining in predictive multiscale materials modelling and describe the first implementation of the method in a general purpose molecular dynamics software: QDO_MD.

Quantitative structure-retention relationships of flavonoids unraveled by immobilized artificial membrane chromatography.

PubMed

Santoro, Adriana Leandra; Carrilho, Emanuel; Lanças, Fernando Mauro; Montanari, Carlos Alberto

2016-06-10

The pharmacokinetic properties of flavonoids with differing degrees of lipophilicity were investigated using immobilized artificial membranes (IAMs) as the stationary phase in high performance liquid chromatography (HPLC). For each flavonoid compound, we investigated whether the type of column used affected the correlation between the retention factors and the calculated octanol/water partition (log Poct). Three-dimensional (3D) molecular descriptors were calculated from the molecular structure of each compound using i) VolSurf software, ii) the GRID method (computational procedure for determining energetically favorable binding sites in molecules of known structure using a probe for calculating the 3D molecular interaction fields, between the probe and the molecule), and iii) the relationship between partition and molecular structure, analyzed in terms of physicochemical descriptors. The VolSurf built-in Caco-2 model was used to estimate compound permeability. The extent to which the datasets obtained from different columns differ both from each other and from both the calculated log Poct and the predicted permeability in Caco-2 cells was examined by principal component analysis (PCA). The immobilized membrane partition coefficients (kIAM) were analyzed using molecular descriptors in partial least square regression (PLS) and a quantitative structure-retention relationship was generated for the chromatographic retention in the cholesterol column. The cholesterol column provided the best correlation with the permeability predicted by the Caco-2 cell model and a good fit model with great prediction power was obtained for its retention data (R(2)=0.96 and Q(2)=0.85 with four latent variables). Copyright © 2015 Elsevier B.V. All rights reserved.

Web-Based Job Submission Interface for the GAMESS Computational Chemistry Program

ERIC Educational Resources Information Center

Perri, M. J.; Weber, S. H.

2014-01-01

A Web site is described that facilitates use of the free computational chemistry software: General Atomic and Molecular Electronic Structure System (GAMESS). Its goal is to provide an opportunity for undergraduate students to perform computational chemistry experiments without the need to purchase expensive software.

PrePhyloPro: phylogenetic profile-based prediction of whole proteome linkages

PubMed Central

Niu, Yulong; Liu, Chengcheng; Moghimyfiroozabad, Shayan; Yang, Yi

2017-01-01

Direct and indirect functional links between proteins as well as their interactions as part of larger protein complexes or common signaling pathways may be predicted by analyzing the correlation of their evolutionary patterns. Based on phylogenetic profiling, here we present a highly scalable and time-efficient computational framework for predicting linkages within the whole human proteome. We have validated this method through analysis of 3,697 human pathways and molecular complexes and a comparison of our results with the prediction outcomes of previously published co-occurrency model-based and normalization methods. Here we also introduce PrePhyloPro, a web-based software that uses our method for accurately predicting proteome-wide linkages. We present data on interactions of human mitochondrial proteins, verifying the performance of this software. PrePhyloPro is freely available at http://prephylopro.org/phyloprofile/. PMID:28875072

Electron tunneling in proteins program.

PubMed

Hagras, Muhammad A; Stuchebrukhov, Alexei A

2016-06-05

We developed a unique integrated software package (called Electron Tunneling in Proteins Program or ETP) which provides an environment with different capabilities such as tunneling current calculation, semi-empirical quantum mechanical calculation, and molecular modeling simulation for calculation and analysis of electron transfer reactions in proteins. ETP program is developed as a cross-platform client-server program in which all the different calculations are conducted at the server side while only the client terminal displays the resulting calculation outputs in the different supported representations. ETP program is integrated with a set of well-known computational software packages including Gaussian, BALLVIEW, Dowser, pKip, and APBS. In addition, ETP program supports various visualization methods for the tunneling calculation results that assist in a more comprehensive understanding of the tunneling process. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

A Model for Assessing the Liability of Seemingly Correct Software

NASA Technical Reports Server (NTRS)

Voas, Jeffrey M.; Voas, Larry K.; Miller, Keith W.

1991-01-01

Current research on software reliability does not lend itself to quantitatively assessing the risk posed by a piece of life-critical software. Black-box software reliability models are too general and make too many assumptions to be applied confidently to assessing the risk of life-critical software. We present a model for assessing the risk caused by a piece of software; this model combines software testing results and Hamlet's probable correctness model. We show how this model can assess software risk for those who insure against a loss that can occur if life-critical software fails.

Building cell models and simulations from microscope images.

PubMed

Murphy, Robert F

2016-03-01

The use of fluorescence microscopy has undergone a major revolution over the past twenty years, both with the development of dramatic new technologies and with the widespread adoption of image analysis and machine learning methods. Many open source software tools provide the ability to use these methods in a wide range of studies, and many molecular and cellular phenotypes can now be automatically distinguished. This article presents the next major challenge in microscopy automation, the creation of accurate models of cell organization directly from images, and reviews the progress that has been made towards this challenge. Copyright © 2015 Elsevier Inc. All rights reserved.

PyMOL mControl: Manipulating Molecular Visualization with Mobile Devices

ERIC Educational Resources Information Center

Lam, Wendy W. T.; Siu, Shirley W. I.

2017-01-01

Viewing and manipulating three-dimensional (3D) structures in molecular graphics software are essential tasks for researchers and students to understand the functions of molecules. Currently, the way to manipulate a 3D molecular object is mainly based on mouse-and-keyboard control that is usually difficult and tedious to learn. While gesture-based…

DyNAMiC Workbench: an integrated development environment for dynamic DNA nanotechnology

PubMed Central

Grun, Casey; Werfel, Justin; Zhang, David Yu; Yin, Peng

2015-01-01

Dynamic DNA nanotechnology provides a promising avenue for implementing sophisticated assembly processes, mechanical behaviours, sensing and computation at the nanoscale. However, design of these systems is complex and error-prone, because the need to control the kinetic pathway of a system greatly increases the number of design constraints and possible failure modes for the system. Previous tools have automated some parts of the design workflow, but an integrated solution is lacking. Here, we present software implementing a three ‘tier’ design process: a high-level visual programming language is used to describe systems, a molecular compiler builds a DNA implementation and nucleotide sequences are generated and optimized. Additionally, our software includes tools for analysing and ‘debugging’ the designs in silico, and for importing/exporting designs to other commonly used software systems. The software we present is built on many existing pieces of software, but is integrated into a single package—accessible using a Web-based interface at http://molecular-systems.net/workbench. We hope that the deep integration between tools and the flexibility of this design process will lead to better experimental results, fewer experimental design iterations and the development of more complex DNA nanosystems. PMID:26423437

Quantitative structure activity relationship studies of piperazinyl phenylalanine derivatives as VLA-4/VCAM-1 inhibitors.

PubMed

Bhargava, Dinesh; Karthikeyan, C; Moorthy, N S H N; Trivedi, Piyush

2009-09-01

QSAR study was carried out for a series of piperazinyl phenylalanine derivatives exhibiting VLA-4/VCAM-1 inhibitory activity to find out the structural features responsible for the biological activity. The QSAR study was carried out on V-life Molecular Design Suite software and the derived best QSAR model by partial least square (forward) regression method showed 85.67% variation in biological activity. The statistically significant model with high correlation coefficient (r2=0.85) was selected for further study and the resulted validation parameters of the model, crossed squared correlation coefficient (q2=0.76 and pred_r2=0.42) show the model has good predictive ability. The model showed that the parameters SaaNEindex, SsClcount slogP,and 4PathCount are highly correlated with VLA-4/VCAM-1 inhibitory activity of piperazinyl phenylalanine derivatives. The result of the study suggests that the chlorine atoms in the molecule and fourth order fragmentation patterns in the molecular skeleton favour VLA-4/VCAM-1 inhibition shown by the title compounds whereas lipophilicity and nitrogen bonded to aromatic bond are not conducive for VLA-4/VCAM-1 inhibitory activity.

A molecular model for the active site of S-adenosyl- l-homocysteine hydrolase

NASA Astrophysics Data System (ADS)

Yeh, Jerry C.; Borchardt, Ronald T.; Vedani, Angelo

1991-06-01

S-adenosyl- l-homocysteine hydrolase (AdoHcy hydrolase, EC 3.3.1.1.), a specific target for antiviral drug design, catalyzes the hydrolysis of AdoHcy to adenosine (Ado) and homocysteine (Hcy) as well as the synthesis of AdoHcy from Ado and Hcy. The enzyme isolated from different sources has been shown to contain tightly bound NAD+. Based on the 2.0 Å-resolution X-ray crystal structure of dogfish lactate dehydrogenase (LDH), which is functionally homologous to AdoHcy hydrolase, and the primary sequence of rat liver AdoHcy hydrolase, we have derived a molecular model of an extended active site for AdoHcy hydrolase. The computational mutation was performed using the software MUTAR (Yeh et al., University of Kansas, Lawrence), followed by molecular mechanics optimizations using the programs AMBER (Singh et al., University of California, San Francisco) and YETI (Vedani, University of Kansas). Solvation of the model structure was achieved by use of the program SOLVGEN (Jacober, University of Kansas); 56 water molecules were explicitly included in all refinements. Some of these may be involved in the catalytic reaction. We also studied a model of the complex of AdoHcy hydrolase with NAD+, as well as the ternary complexes of the redox reaction catalyzed by AdoHcy hydrolase and has been used to differentiate the relative binding strength of inhibitors.

Cross-Link Guided Molecular Modeling with ROSETTA

PubMed Central

Leitner, Alexander; Rosenberger, George; Aebersold, Ruedi; Malmström, Lars

2013-01-01

Chemical cross-links identified by mass spectrometry generate distance restraints that reveal low-resolution structural information on proteins and protein complexes. The technology to reliably generate such data has become mature and robust enough to shift the focus to the question of how these distance restraints can be best integrated into molecular modeling calculations. Here, we introduce three workflows for incorporating distance restraints generated by chemical cross-linking and mass spectrometry into ROSETTA protocols for comparative and de novo modeling and protein-protein docking. We demonstrate that the cross-link validation and visualization software Xwalk facilitates successful cross-link data integration. Besides the protocols we introduce XLdb, a database of chemical cross-links from 14 different publications with 506 intra-protein and 62 inter-protein cross-links, where each cross-link can be mapped on an experimental structure from the Protein Data Bank. Finally, we demonstrate on a protein-protein docking reference data set the impact of virtual cross-links on protein docking calculations and show that an inter-protein cross-link can reduce on average the RMSD of a docking prediction by 5.0 Å. The methods and results presented here provide guidelines for the effective integration of chemical cross-link data in molecular modeling calculations and should advance the structural analysis of particularly large and transient protein complexes via hybrid structural biology methods. PMID:24069194

DROIDS 1.20: A GUI-Based Pipeline for GPU-Accelerated Comparative Protein Dynamics.

PubMed

Babbitt, Gregory A; Mortensen, Jamie S; Coppola, Erin E; Adams, Lily E; Liao, Justin K

2018-03-13

Traditional informatics in comparative genomics work only with static representations of biomolecules (i.e., sequence and structure), thereby ignoring the molecular dynamics (MD) of proteins that define function in the cell. A comparative approach applied to MD would connect this very short timescale process, defined in femtoseconds, to one of the longest in the universe: molecular evolution measured in millions of years. Here, we leverage advances in graphics-processing-unit-accelerated MD simulation software to develop a comparative method of MD analysis and visualization that can be applied to any two homologous Protein Data Bank structures. Our open-source pipeline, DROIDS (Detecting Relative Outlier Impacts in Dynamic Simulations), works in conjunction with existing molecular modeling software to convert any Linux gaming personal computer into a "comparative computational microscope" for observing the biophysical effects of mutations and other chemical changes in proteins. DROIDS implements structural alignment and Benjamini-Hochberg-corrected Kolmogorov-Smirnov statistics to compare nanosecond-scale atom bond fluctuations on the protein backbone, color mapping the significant differences identified in protein MD with single-amino-acid resolution. DROIDS is simple to use, incorporating graphical user interface control for Amber16 MD simulations, cpptraj analysis, and the final statistical and visual representations in R graphics and UCSF Chimera. We demonstrate that DROIDS can be utilized to visually investigate molecular evolution and disease-related functional changes in MD due to genetic mutation and epigenetic modification. DROIDS can also be used to potentially investigate binding interactions of pharmaceuticals, toxins, or other biomolecules in a functional evolutionary context as well. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

skeleSim: an extensible, general framework for population genetic simulation in R

PubMed Central

Parobek, Christian M.; Archer, Frederick I.; DePrenger-Levin, Michelle E.; Hoban, Sean M.; Liggins, Libby; Strand, Allan E.

2016-01-01

Simulations are a key tool in molecular ecology for inference and forecasting, as well as for evaluating new methods. Due to growing computational power and a diversity of software with different capabilities, simulations are becoming increasingly powerful and useful. However, the widespread use of simulations by geneticists and ecologists is hindered by difficulties in understanding these softwares’ complex capabilities, composing code and input files, a daunting bioinformatics barrier, and a steep conceptual learning curve. skeleSim (an R package) guides users in choosing appropriate simulations, setting parameters, calculating genetic summary statistics, and organizing data output, in a reproducible pipeline within the R environment. skeleSim is designed to be an extensible framework that can ‘wrap’ around any simulation software (inside or outside the R environment) and be extended to calculate and graph any genetic summary statistics. Currently, skeleSim implements coalescent and forward-time models available in the fastsimcoal2 and rmetasim simulation engines to produce null distributions for multiple population genetic statistics and marker types, under a variety of demographic conditions. skeleSim is intended to make simulations easier while still allowing full model complexity to ensure that simulations play a fundamental role in molecular ecology investigations. skeleSim can also serve as a teaching tool: demonstrating the outcomes of stochastic population genetic processes; teaching general concepts of simulations; and providing an introduction to the R environment with a user-friendly graphical user interface (using shiny). PMID:27736016

The fundamentals behind solving for unknown molecular structures using computer-assisted structure elucidation: a free software package at the undergraduate and graduate levels.

PubMed

Moser, Arvin; Pautler, Brent G

2016-05-15

The successful elucidation of an unknown compound's molecular structure often requires an analyst with profound knowledge and experience of advanced spectroscopic techniques, such as Nuclear Magnetic Resonance (NMR) spectroscopy and mass spectrometry. The implementation of Computer-Assisted Structure Elucidation (CASE) software in solving for unknown structures, such as isolated natural products and/or reaction impurities, can serve both as elucidation and teaching tools. As such, the introduction of CASE software with 112 exercises to train students in conjunction with the traditional pen and paper approach will strengthen their overall understanding of solving unknowns and explore of various structural end points to determine the validity of the results quickly. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Integration of genomic and medical data into a 3D atlas of human anatomy.

PubMed

Turinsky, Andrei L; Fanea, Elena; Trinh, Quang; Dong, Xiaoli; Stromer, Julie N; Shu, Xueling; Wat, Stephen; Hallgrímsson, Benedikt; Hill, Jonathan W; Edwards, Carol; Grosenick, Brenda; Yajima, Masumi; Sensen, Christoph W

2008-01-01

We have developed a framework for the visual integration and exploration of multi-scale biomedical data, which includes anatomical and molecular components. We have also created a Java-based software system that integrates molecular information, such as gene expression data, into a three-dimensional digital atlas of the male adult human anatomy. Our atlas is structured according to the Terminologia Anatomica. The underlying data-indexing mechanism uses open standards and semantic ontology-processing tools to establish the associations between heterogeneous data types. The software system makes an extensive use of virtual reality visualization.

Bringing macromolecular machinery to life using 3D animation.

PubMed

Iwasa, Janet H

2015-04-01

Over the past decade, there has been a rapid rise in the use of three-dimensional (3D) animation to depict molecular and cellular processes. Much of the growth in molecular animation has been in the educational arena, but increasingly, 3D animation software is finding its way into research laboratories. In this review, I will discuss a number of ways in which 3d animation software can play a valuable role in visualizing and communicating macromolecular structures and dynamics. I will also consider the challenges of using animation tools within the research sphere. Copyright © 2015. Published by Elsevier Ltd.

Using collective variables to drive molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Fiorin, Giacomo; Klein, Michael L.; Hénin, Jérôme

2013-12-01

A software framework is introduced that facilitates the application of biasing algorithms to collective variables of the type commonly employed to drive massively parallel molecular dynamics (MD) simulations. The modular framework that is presented enables one to combine existing collective variables into new ones, and combine any chosen collective variable with available biasing methods. The latter include the classic time-dependent biases referred to as steered MD and targeted MD, the temperature-accelerated MD algorithm, as well as the adaptive free-energy biases called metadynamics and adaptive biasing force. The present modular software is extensible, and portable between commonly used MD simulation engines.

PHARMAVIRTUA: Educational Software for Teaching and Learning Basic Pharmacology

ERIC Educational Resources Information Center

Fidalgo-Neto, Antonio Augusto; Alberto, Anael Viana Pinto; Bonavita, André Gustavo Calvano; Bezerra, Rômulo José Soares; Berçot, Felipe Faria; Lopes, Renato Matos; Alves, Luiz Anastacio

2014-01-01

Information and communication technologies have become important tools for teaching scientific subjects such as anatomy and histology as well as other, nondescriptive subjects like physiology and pharmacology. Software has been used to facilitate the learning of specific concepts at the cellular and molecular levels in the biological and health…

Modeling SMAP Spacecraft Attitude Control Estimation Error Using Signal Generation Model

NASA Technical Reports Server (NTRS)

Rizvi, Farheen

2016-01-01

Two ground simulation software are used to model the SMAP spacecraft dynamics. The CAST software uses a higher fidelity model than the ADAMS software. The ADAMS software models the spacecraft plant, controller and actuator models, and assumes a perfect sensor and estimator model. In this simulation study, the spacecraft dynamics results from the ADAMS software are used as CAST software is unavailable. The main source of spacecraft dynamics error in the higher fidelity CAST software is due to the estimation error. A signal generation model is developed to capture the effect of this estimation error in the overall spacecraft dynamics. Then, this signal generation model is included in the ADAMS software spacecraft dynamics estimate such that the results are similar to CAST. This signal generation model has similar characteristics mean, variance and power spectral density as the true CAST estimation error. In this way, ADAMS software can still be used while capturing the higher fidelity spacecraft dynamics modeling from CAST software.

Electronic coarse graining enhances the predictive power of molecular simulation allowing challenges in water physics to be addressed

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cipcigan, Flaviu S., E-mail: flaviu.cipcigan@ed.ac.uk; National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW; Sokhan, Vlad P.

One key factor that limits the predictive power of molecular dynamics simulations is the accuracy and transferability of the input force field. Force fields are challenged by heterogeneous environments, where electronic responses give rise to biologically important forces such as many-body polarisation and dispersion. The importance of polarisation in the condensed phase was recognised early on, as described by Cochran in 1959 [Philosophical Magazine 4 (1959) 1082–1086] [32]. Currently in molecular simulation, dispersion forces are treated at the two-body level and in the dipole limit, although the importance of three-body terms in the condensed phase was demonstrated by Barker inmore » the 1980s [Phys. Rev. Lett. 57 (1986) 230–233] [72]. One approach for treating both polarisation and dispersion on an equal basis is to coarse grain the electrons surrounding a molecular moiety to a single quantum harmonic oscillator (cf. Hirschfelder, Curtiss and Bird 1954 [The Molecular Theory of Gases and Liquids (1954)] [37]). The approach, when solved in strong coupling beyond the dipole limit, gives a description of long-range forces that includes two- and many-body terms to all orders. In the last decade, the tools necessary to implement the strong coupling limit have been developed, culminating in a transferable model of water with excellent predictive power across the phase diagram. Transferability arises since the environment automatically identifies the important long range interactions, rather than the modeler through a limited set of expressions. Here, we discuss the role of electronic coarse-graining in predictive multiscale materials modelling and describe the first implementation of the method in a general purpose molecular dynamics software: QDO-MD. - Highlights: • Electronic coarse graining unites many-body dispersion and polarisation beyond the dipole limit. • It consists of replacing the electrons of a molecule using a quantum harmonic oscillator, called a Quantum Drude Oscillator. • We present the first general implementation of Quantum Drude Oscillators in the molecular dynamics package QDO-MD. • We highlight the successful construction of a new, transferable molecular model of water: QDO-water. - Graphical abstract:.« less

Electrophoresis gel image processing and analysis using the KODAK 1D software.

PubMed

Pizzonia, J

2001-06-01

The present article reports on the performance of the KODAK 1D Image Analysis Software for the acquisition of information from electrophoresis experiments and highlights the utility of several mathematical functions for subsequent image processing, analysis, and presentation. Digital images of Coomassie-stained polyacrylamide protein gels containing molecular weight standards and ethidium bromide stained agarose gels containing DNA mass standards are acquired using the KODAK Electrophoresis Documentation and Analysis System 290 (EDAS 290). The KODAK 1D software is used to optimize lane and band identification using features such as isomolecular weight lines. Mathematical functions for mass standard representation are presented, and two methods for estimation of unknown band mass are compared. Given the progressive transition of electrophoresis data acquisition and daily reporting in peer-reviewed journals to digital formats ranging from 8-bit systems such as EDAS 290 to more expensive 16-bit systems, the utility of algorithms such as Gaussian modeling, which can correct geometric aberrations such as clipping due to signal saturation common at lower bit depth levels, is discussed. Finally, image-processing tools that can facilitate image preparation for presentation are demonstrated.

LIQUID: an-open source software for identifying lipids in LC-MS/MS-based lipidomics data.

PubMed

Kyle, Jennifer E; Crowell, Kevin L; Casey, Cameron P; Fujimoto, Grant M; Kim, Sangtae; Dautel, Sydney E; Smith, Richard D; Payne, Samuel H; Metz, Thomas O

2017-06-01

We introduce an open-source software, LIQUID, for semi-automated processing and visualization of LC-MS/MS-based lipidomics data. LIQUID provides users with the capability to process high throughput data and contains a customizable target library and scoring model per project needs. The graphical user interface provides visualization of multiple lines of spectral evidence for each lipid identification, allowing rapid examination of data for making confident identifications of lipid molecular species. LIQUID was compared to other freely available software commonly used to identify lipids and other small molecules (e.g. CFM-ID, MetFrag, GNPS, LipidBlast and MS-DIAL), and was found to have a faster processing time to arrive at a higher number of validated lipid identifications. LIQUID is available at http://github.com/PNNL-Comp-Mass-Spec/LIQUID . jennifer.kyle@pnnl.gov or thomas.metz@pnnl.gov. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

GIDL: a rule based expert system for GenBank Intelligent Data Loading into the Molecular Biodiversity database

PubMed Central

2012-01-01

Background In the scientific biodiversity community, it is increasingly perceived the need to build a bridge between molecular and traditional biodiversity studies. We believe that the information technology could have a preeminent role in integrating the information generated by these studies with the large amount of molecular data we can find in bioinformatics public databases. This work is primarily aimed at building a bioinformatic infrastructure for the integration of public and private biodiversity data through the development of GIDL, an Intelligent Data Loader coupled with the Molecular Biodiversity Database. The system presented here organizes in an ontological way and locally stores the sequence and annotation data contained in the GenBank primary database. Methods The GIDL architecture consists of a relational database and of an intelligent data loader software. The relational database schema is designed to manage biodiversity information (Molecular Biodiversity Database) and it is organized in four areas: MolecularData, Experiment, Collection and Taxonomy. The MolecularData area is inspired to an established standard in Generic Model Organism Databases, the Chado relational schema. The peculiarity of Chado, and also its strength, is the adoption of an ontological schema which makes use of the Sequence Ontology. The Intelligent Data Loader (IDL) component of GIDL is an Extract, Transform and Load software able to parse data, to discover hidden information in the GenBank entries and to populate the Molecular Biodiversity Database. The IDL is composed by three main modules: the Parser, able to parse GenBank flat files; the Reasoner, which automatically builds CLIPS facts mapping the biological knowledge expressed by the Sequence Ontology; the DBFiller, which translates the CLIPS facts into ordered SQL statements used to populate the database. In GIDL Semantic Web technologies have been adopted due to their advantages in data representation, integration and processing. Results and conclusions Entries coming from Virus (814,122), Plant (1,365,360) and Invertebrate (959,065) divisions of GenBank rel.180 have been loaded in the Molecular Biodiversity Database by GIDL. Our system, combining the Sequence Ontology and the Chado schema, allows a more powerful query expressiveness compared with the most commonly used sequence retrieval systems like Entrez or SRS. PMID:22536971

Modeling the drugs' passive transfer in the body based on their chromatographic behavior.

PubMed

Kouskoura, Maria G; Kachrimanis, Kyriakos G; Markopoulou, Catherine K

2014-11-01

One of the most challenging aims in modern analytical chemistry and pharmaceutical analysis is to create models for drugs' behavior based on simulation experiments. Since drugs' effects are closely related to their molecular properties, numerous characteristics of drugs are used in order to acquire a model of passive absorption and transfer in the human body. Importantly, such direction in innovative bioanalytical methodologies is also of stressful need in the area of personalized medicine to implement nanotechnological and genomics advancements. Simulation experiments were carried out by examining and interpreting the chromatographic behavior of 113 analytes/drugs (400 observations) in RP-HPLC. The dataset employed for this purpose included 73 descriptors which are referring to the physicochemical properties of the mobile phase mixture in different proportions, the physicochemical properties of the analytes and the structural characteristics of their molecules. A series of different software packages was used to calculate all the descriptors apart from those referring to the structure of analytes. The correlation of the descriptors with the retention time of the analytes eluted from a C4 column with an aqueous mobile phase was employed as dataset to introduce the behavior models in the human body. Their evaluation with a Partial Least Squares (PLS) software proved that the chromatographic behavior of a drug on a lipophilic stationary and a polar mobile phase is directly related to its drug-ability. At the same time, the behavior of an unknown drug in the human body can be predicted with reliability via the Artificial Neural Networks (ANNs) software. Copyright © 2014 Elsevier B.V. All rights reserved.

Direct NOE simulation from long MD trajectories.

PubMed

Chalmers, G; Glushka, J N; Foley, B L; Woods, R J; Prestegard, J H

2016-04-01

A software package, MD2NOE, is presented which calculates Nuclear Overhauser Effect (NOE) build-up curves directly from molecular dynamics (MD) trajectories. It differs from traditional approaches in that it calculates correlation functions directly from the trajectory instead of extracting inverse sixth power distance terms as an intermediate step in calculating NOEs. This is particularly important for molecules that sample conformational states on a timescale similar to molecular reorientation. The package is tested on sucrose and results are shown to differ in small but significant ways from those calculated using an inverse sixth power assumption. Results are also compared to experiment and found to be in reasonable agreement despite an expected underestimation of water viscosity by the water model selected. Copyright © 2016 Elsevier Inc. All rights reserved.

A parallel algorithm for step- and chain-growth polymerization in molecular dynamics.

PubMed

de Buyl, Pierre; Nies, Erik

2015-04-07

Classical Molecular Dynamics (MD) simulations provide insight into the properties of many soft-matter systems. In some situations, it is interesting to model the creation of chemical bonds, a process that is not part of the MD framework. In this context, we propose a parallel algorithm for step- and chain-growth polymerization that is based on a generic reaction scheme, works at a given intrinsic rate and produces continuous trajectories. We present an implementation in the ESPResSo++ simulation software and compare it with the corresponding feature in LAMMPS. For chain growth, our results are compared to the existing simulation literature. For step growth, a rate equation is proposed for the evolution of the crosslinker population that compares well to the simulations for low crosslinker functionality or for short times.

A parallel algorithm for step- and chain-growth polymerization in molecular dynamics

NASA Astrophysics Data System (ADS)

de Buyl, Pierre; Nies, Erik

2015-04-01

Classical Molecular Dynamics (MD) simulations provide insight into the properties of many soft-matter systems. In some situations, it is interesting to model the creation of chemical bonds, a process that is not part of the MD framework. In this context, we propose a parallel algorithm for step- and chain-growth polymerization that is based on a generic reaction scheme, works at a given intrinsic rate and produces continuous trajectories. We present an implementation in the ESPResSo++ simulation software and compare it with the corresponding feature in LAMMPS. For chain growth, our results are compared to the existing simulation literature. For step growth, a rate equation is proposed for the evolution of the crosslinker population that compares well to the simulations for low crosslinker functionality or for short times.

TRIMS: Validating T2 Molecular Effects for Neutrino Mass Experiments

NASA Astrophysics Data System (ADS)

Lin, Ying-Ting; Bodine, Laura; Enomoto, Sanshiro; Kallander, Matthew; Machado, Eric; Parno, Diana; Robertson, Hamish; Trims Collaboration

2017-01-01

The upcoming KATRIN and Project 8 experiments will measure the model-independent effective neutrino mass through the kinematics near the endpoint of tritium beta-decay. A critical systematic, however, is the understanding of the molecular final-state distribution populated by tritium decay. In fact, the current theory incorporated in the KATRIN analysis framework predicts an observable that disagrees with an experimental result from the 1950s. The Tritium Recoil-Ion Mass Spectrometer (TRIMS) experiment will reexamine branching ratio of the molecular tritium (T2) beta decay to the bound state (3HeT+). TRIMS consists of a magnet-guided time-of-flight mass spectrometer with a detector located on each end. By measuring the kinetic energy and time-of-flight difference of the ions and beta particles reaching the detectors, we will be able to distinguish molecular ions from atomic ones and hence derive the ratio in question.We will give an update on simulation software, analysis tools, and the apparatus, including early commissioning results. U.S. Department of Energy Office of Science, Office of Nuclear Physics, Award Number DE-FG02-97ER41020.

SAMPL4 & DOCK3.7: lessons for automated docking procedures

NASA Astrophysics Data System (ADS)

Coleman, Ryan G.; Sterling, Teague; Weiss, Dahlia R.

2014-03-01

The SAMPL4 challenges were used to test current automated methods for solvation energy, virtual screening, pose and affinity prediction of the molecular docking pipeline DOCK 3.7. Additionally, first-order models of binding affinity were proposed as milestones for any method predicting binding affinity. Several important discoveries about the molecular docking software were made during the challenge: (1) Solvation energies of ligands were five-fold worse than any other method used in SAMPL4, including methods that were similarly fast, (2) HIV Integrase is a challenging target, but automated docking on the correct allosteric site performed well in terms of virtual screening and pose prediction (compared to other methods) but affinity prediction, as expected, was very poor, (3) Molecular docking grid sizes can be very important, serious errors were discovered with default settings that have been adjusted for all future work. Overall, lessons from SAMPL4 suggest many changes to molecular docking tools, not just DOCK 3.7, that could improve the state of the art. Future difficulties and projects will be discussed.

Statistical modelling of software reliability

NASA Technical Reports Server (NTRS)

Miller, Douglas R.

1991-01-01

During the six-month period from 1 April 1991 to 30 September 1991 the following research papers in statistical modeling of software reliability appeared: (1) A Nonparametric Software Reliability Growth Model; (2) On the Use and the Performance of Software Reliability Growth Models; (3) Research and Development Issues in Software Reliability Engineering; (4) Special Issues on Software; and (5) Software Reliability and Safety.

CoMD Implementation Suite in Emerging Programming Models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Haque, Riyaz; Reeve, Sam; Juallmes, Luc

CoMD-Em is a software implementation suite of the CoMD [4] proxy app using different emerging programming models. It is intended to analyze the features and capabilities of novel programming models that could help ensure code and performance portability and scalability across heterogeneous platforms while improving programmer productivity. Another goal is to provide the authors and venders with some meaningful feedback regarding the capabilities and limitations of their models. The actual application is a classical molecular dynamics (MD) simulation using either the Lennard-Jones method (LJ) or the embedded atom method (EAM) for primary particle interaction. The code can be extended tomore » support alternate interaction models. The code is expected ro run on a wide class of heterogeneous hardware configurations like shard/distributed/hybrid memory, GPU's and any other platform supported by the underlying programming model.« less

Hybrid deterministic/stochastic simulation of complex biochemical systems.

PubMed

Lecca, Paola; Bagagiolo, Fabio; Scarpa, Marina

2017-11-21

In a biological cell, cellular functions and the genetic regulatory apparatus are implemented and controlled by complex networks of chemical reactions involving genes, proteins, and enzymes. Accurate computational models are indispensable means for understanding the mechanisms behind the evolution of a complex system, not always explored with wet lab experiments. To serve their purpose, computational models, however, should be able to describe and simulate the complexity of a biological system in many of its aspects. Moreover, it should be implemented by efficient algorithms requiring the shortest possible execution time, to avoid enlarging excessively the time elapsing between data analysis and any subsequent experiment. Besides the features of their topological structure, the complexity of biological networks also refers to their dynamics, that is often non-linear and stiff. The stiffness is due to the presence of molecular species whose abundance fluctuates by many orders of magnitude. A fully stochastic simulation of a stiff system is computationally time-expensive. On the other hand, continuous models are less costly, but they fail to capture the stochastic behaviour of small populations of molecular species. We introduce a new efficient hybrid stochastic-deterministic computational model and the software tool MoBioS (MOlecular Biology Simulator) implementing it. The mathematical model of MoBioS uses continuous differential equations to describe the deterministic reactions and a Gillespie-like algorithm to describe the stochastic ones. Unlike the majority of current hybrid methods, the MoBioS algorithm divides the reactions' set into fast reactions, moderate reactions, and slow reactions and implements a hysteresis switching between the stochastic model and the deterministic model. Fast reactions are approximated as continuous-deterministic processes and modelled by deterministic rate equations. Moderate reactions are those whose reaction waiting time is greater than the fast reaction waiting time but smaller than the slow reaction waiting time. A moderate reaction is approximated as a stochastic (deterministic) process if it was classified as a stochastic (deterministic) process at the time at which it crosses the threshold of low (high) waiting time. A Gillespie First Reaction Method is implemented to select and execute the slow reactions. The performances of MoBios were tested on a typical example of hybrid dynamics: that is the DNA transcription regulation. The simulated dynamic profile of the reagents' abundance and the estimate of the error introduced by the fully deterministic approach were used to evaluate the consistency of the computational model and that of the software tool.

S&MPO - An information system for ozone spectroscopy on the WEB

NASA Astrophysics Data System (ADS)

Babikov, Yurii L.; Mikhailenko, Semen N.; Barbe, Alain; Tyuterev, Vladimir G.

2014-09-01

Spectroscopy and Molecular Properties of Ozone ("S&MPO") is an Internet accessible information system devoted to high resolution spectroscopy of the ozone molecule, related properties and data sources. S&MPO contains information on original spectroscopic data (line positions, line intensities, energies, transition moments, spectroscopic parameters) recovered from comprehensive analyses and modeling of experimental spectra as well as associated software for data representation written in PHP Java Script, C++ and FORTRAN. The line-by-line list of vibration-rotation transitions and other information is organized as a relational database under control of MySQL database tools. The main S&MPO goal is to provide access to all available information on vibration-rotation molecular states and transitions under extended conditions based on extrapolations of laboratory measurements using validated theoretical models. Applications for the S&MPO may include: education/training in molecular physics, radiative processes, laser physics; spectroscopic applications (analysis, Fourier transform spectroscopy, atmospheric optics, optical standards, spectroscopic atlases); applications to environment studies and atmospheric physics (remote sensing); data supply for specific databases; and to photochemistry (laser excitation, multiphoton processes). The system is accessible via Internet on two sites: http://smpo.iao.ru and http://smpo.univ-reims.fr.

Optical measurement of transverse molecular diffusion in a microchannel.

PubMed Central

Kamholz, A E; Schilling, E A; Yager, P

2001-01-01

Quantitative analysis of molecular diffusion is a necessity for the efficient design of most microfluidic devices as well as an important biophysical method in its own right. This study demonstrates the rapid measurement of diffusion coefficients of large and small molecules in a microfluidic device, the T-sensor, by means of conventional epifluorescence microscopy. Data were collected by monitoring the transverse flux of analyte from a sample stream into a second stream flowing alongside it. As indicated by the low Reynolds numbers of the system (< 1), flow is laminar, and molecular transport between streams occurs only by diffusion. Quantitative determinations were made by fitting data with predictions of a one-dimensional model. Analysis was made of the flow development and its effect on the distribution of diffusing analyte using a three-dimensional modeling software package. Diffusion coefficients were measured for four fluorescently labeled molecules: fluorescein-biotin, insulin, ovalbumin, and streptavidin. The resulting values differed from accepted results by an average of 2.4%. Microfluidic system parameters can be selected to achieve accurate diffusion coefficient measurements and to optimize other microfluidic devices that rely on precise transverse transport of molecules. PMID:11259309

QSAR models to predict mutagenicity of acrylates, methacrylates and alpha,beta-unsaturated carbonyl compounds.

PubMed

Pérez-Garrido, Alfonso; Helguera, Aliuska Morales; Rodríguez, Francisco Girón; Cordeiro, M Natália D S

2010-05-01

The purpose of this study is to develop a quantitative structure-activity relationship (QSAR) model that can distinguish mutagenic from non-mutagenic species with alpha,beta-unsaturated carbonyl moiety using two endpoints for this activity - Ames test and mammalian cell gene mutation test - and also to gather information about the molecular features that most contribute to eliminate the mutagenic effects of these chemicals. Two data sets were used for modeling the two mutagenicity endpoints: (1) Ames test and (2) mammalian cells mutagenesis. The first one comprised 220 molecules, while the second one 48 substances, ranging from acrylates, methacrylates to alpha,beta-unsaturated carbonyl compounds. The QSAR models were developed by applying linear discriminant analysis (LDA) along with different sets of descriptors computed using the DRAGON software. For both endpoints, there was a concordance of 89% in the prediction and 97% confidentiality by combining the three models for the Ames test mutagenicity. We have also identified several structural alerts to assist the design of new monomers. These individual models and especially their combination are attractive from the point of view of molecular modeling and could be used for the prediction and design of new monomers that do not pose a human health risk. 2010 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

Smoldyn: particle-based simulation with rule-based modeling, improved molecular interaction and a library interface.

PubMed

Andrews, Steven S

2017-03-01

Smoldyn is a spatial and stochastic biochemical simulator. It treats each molecule of interest as an individual particle in continuous space, simulating molecular diffusion, molecule-membrane interactions and chemical reactions, all with good accuracy. This article presents several new features. Smoldyn now supports two types of rule-based modeling. These are a wildcard method, which is very convenient, and the BioNetGen package with extensions for spatial simulation, which is better for complicated models. Smoldyn also includes new algorithms for simulating the diffusion of surface-bound molecules and molecules with excluded volume. Both are exact in the limit of short time steps and reasonably good with longer steps. In addition, Smoldyn supports single-molecule tracking simulations. Finally, the Smoldyn source code can be accessed through a C/C ++ language library interface. Smoldyn software, documentation, code, and examples are at http://www.smoldyn.org . steven.s.andrews@gmail.com. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Reviews: The Molecular Animator.

ERIC Educational Resources Information Center

Journal of Chemical Education, 1987

1987-01-01

Provided is a review of a chemical software package. The package makes possible an instructional technique that is not effective by any other means, namely the ability to view molecular shapes in three dimensions. The program can be used with either IBM or Apple hardware. (RH)

Automatic identification approach for high-performance liquid chromatography-multiple reaction monitoring fatty acid global profiling.

PubMed

Tie, Cai; Hu, Ting; Jia, Zhi-Xin; Zhang, Jin-Lan

2015-08-18

Fatty acids (FAs) are a group of lipid molecules that are essential to organisms. As potential biomarkers for different diseases, FAs have attracted increasing attention from both biological researchers and the pharmaceutical industry. A sensitive and accurate method for globally profiling and identifying FAs is required for biomarker discovery. The high selectivity and sensitivity of high-performance liquid chromatography-multiple reaction monitoring (HPLC-MRM) gives it great potential to fulfill the need to identify FAs from complicated matrices. This paper developed a new approach for global FA profiling and identification for HPLC-MRM FA data mining. Mathematical models for identifying FAs were simulated using the isotope-induced retention time (RT) shift (IRS) and peak area ratios between parallel isotope peaks for a series of FA standards. The FA structures were predicated using another model based on the RT and molecular weight. Fully automated FA identification software was coded using the Qt platform based on these mathematical models. Different samples were used to verify the software. A high identification efficiency (greater than 75%) was observed when 96 FA species were identified in plasma. This FAs identification strategy promises to accelerate FA research and applications.

Mass spectrometry based lipid(ome) analyzer and molecular platform: a new software to interpret and analyze electrospray and/or matrix-assisted laser desorption/ionization mass spectrometric data of lipids: a case study from Mycobacterium tuberculosis.

PubMed

Sabareesh, Varatharajan; Singh, Gurpreet

2013-04-01

Mass Spectrometry based Lipid(ome) Analyzer and Molecular Platform (MS-LAMP) is a new software capable of aiding in interpreting electrospray ionization (ESI) and/or matrix-assisted laser desorption/ionization (MALDI) mass spectrometric data of lipids. The graphical user interface (GUI) of this standalone programme is built using Perl::Tk. Two databases have been developed and constituted within MS-LAMP, on the basis of Mycobacterium tuberculosis (M. tb) lipid database (www.mrl.colostate.edu) and that of Lipid Metabolites and Pathways Strategy Consortium (LIPID MAPS; www.lipidmaps.org). Different types of queries entered through GUI would interrogate with a chosen database. The queries can be molecular mass(es) or mass-to-charge (m/z) value(s) and molecular formula. LIPID MAPS identifier also can be used to search but not for M. tb lipids. Multiple choices have been provided to select diverse ion types and lipids. Satisfying to input parameters, a glimpse of various lipid categories and their population distribution can be viewed in the output. Additionally, molecular structures of lipids in the output can be seen using ChemSketch (www.acdlabs.com), which has been linked to the programme. Furthermore, a version of MS-LAMP for use in Linux operating system is separately available, wherein PyMOL can be used to view molecular structures that result as output from General Lipidome MS-LAMP. The utility of this software is demonstrated using ESI mass spectrometric data of lipid extracts of M. tb grown under two different pH (5.5 and 7.0) conditions. Copyright © 2013 John Wiley & Sons, Ltd.

IADE: a system for intelligent automatic design of bioisosteric analogs

NASA Astrophysics Data System (ADS)

Ertl, Peter; Lewis, Richard

2012-11-01

IADE, a software system supporting molecular modellers through the automatic design of non-classical bioisosteric analogs, scaffold hopping and fragment growing, is presented. The program combines sophisticated cheminformatics functionalities for constructing novel analogs and filtering them based on their drug-likeness and synthetic accessibility using automatic structure-based design capabilities: the best candidates are selected according to their similarity to the template ligand and to their interactions with the protein binding site. IADE works in an iterative manner, improving the fitness of designed molecules in every generation until structures with optimal properties are identified. The program frees molecular modellers from routine, repetitive tasks, allowing them to focus on analysis and evaluation of the automatically designed analogs, considerably enhancing their work efficiency as well as the area of chemical space that can be covered. The performance of IADE is illustrated through a case study of the design of a nonclassical bioisosteric analog of a farnesyltransferase inhibitor—an analog that has won a recent "Design a Molecule" competition.

IADE: a system for intelligent automatic design of bioisosteric analogs.

PubMed

Ertl, Peter; Lewis, Richard

2012-11-01

IADE, a software system supporting molecular modellers through the automatic design of non-classical bioisosteric analogs, scaffold hopping and fragment growing, is presented. The program combines sophisticated cheminformatics functionalities for constructing novel analogs and filtering them based on their drug-likeness and synthetic accessibility using automatic structure-based design capabilities: the best candidates are selected according to their similarity to the template ligand and to their interactions with the protein binding site. IADE works in an iterative manner, improving the fitness of designed molecules in every generation until structures with optimal properties are identified. The program frees molecular modellers from routine, repetitive tasks, allowing them to focus on analysis and evaluation of the automatically designed analogs, considerably enhancing their work efficiency as well as the area of chemical space that can be covered. The performance of IADE is illustrated through a case study of the design of a nonclassical bioisosteric analog of a farnesyltransferase inhibitor--an analog that has won a recent "Design a Molecule" competition.

Model Driven Engineering with Ontology Technologies

NASA Astrophysics Data System (ADS)

Staab, Steffen; Walter, Tobias; Gröner, Gerd; Parreiras, Fernando Silva

Ontologies constitute formal models of some aspect of the world that may be used for drawing interesting logical conclusions even for large models. Software models capture relevant characteristics of a software artifact to be developed, yet, most often these software models have limited formal semantics, or the underlying (often graphical) software language varies from case to case in a way that makes it hard if not impossible to fix its semantics. In this contribution, we survey the use of ontology technologies for software modeling in order to carry over advantages from ontology technologies to the software modeling domain. It will turn out that ontology-based metamodels constitute a core means for exploiting expressive ontology reasoning in the software modeling domain while remaining flexible enough to accommodate varying needs of software modelers.

beta-Aminoalcohols as Potential Reactivators of Aged Sarin-/Soman-Inhibited Acetylcholinesterase

DTIC Science & Technology

2017-02-08

This approach includes high - quality quantum mechanical/molecular mechanical calcula- tions, providing reliable reactivation steps and energetics...I. V. Khavrutskii Department of Defense Biotechnology High Performance Computing Software Applications Institute Telemedicine and Advanced...b] Dr. A. Wallqvist Department of Defense Biotechnology High Performance Computing Software Applications Institute Telemedicine and Advanced

GW100: Benchmarking G0W0 for Molecular Systems.

PubMed

van Setten, Michiel J; Caruso, Fabio; Sharifzadeh, Sahar; Ren, Xinguo; Scheffler, Matthias; Liu, Fang; Lischner, Johannes; Lin, Lin; Deslippe, Jack R; Louie, Steven G; Yang, Chao; Weigend, Florian; Neaton, Jeffrey B; Evers, Ferdinand; Rinke, Patrick

2015-12-08

We present the GW100 set. GW100 is a benchmark set of the ionization potentials and electron affinities of 100 molecules computed with the GW method using three independent GW codes and different GW methodologies. The quasi-particle energies of the highest-occupied molecular orbitals (HOMO) and lowest-unoccupied molecular orbitals (LUMO) are calculated for the GW100 set at the G0W0@PBE level using the software packages TURBOMOLE, FHI-aims, and BerkeleyGW. The use of these three codes allows for a quantitative comparison of the type of basis set (plane wave or local orbital) and handling of unoccupied states, the treatment of core and valence electrons (all electron or pseudopotentials), the treatment of the frequency dependence of the self-energy (full frequency or more approximate plasmon-pole models), and the algorithm for solving the quasi-particle equation. Primary results include reference values for future benchmarks, best practices for convergence within a particular approach, and average error bars for the most common approximations.

High Performance Molecular Visualization: In-Situ and Parallel Rendering with EGL.

PubMed

Stone, John E; Messmer, Peter; Sisneros, Robert; Schulten, Klaus

2016-05-01

Large scale molecular dynamics simulations produce terabytes of data that is impractical to transfer to remote facilities. It is therefore necessary to perform visualization tasks in-situ as the data are generated, or by running interactive remote visualization sessions and batch analyses co-located with direct access to high performance storage systems. A significant challenge for deploying visualization software within clouds, clusters, and supercomputers involves the operating system software required to initialize and manage graphics acceleration hardware. Recently, it has become possible for applications to use the Embedded-system Graphics Library (EGL) to eliminate the requirement for windowing system software on compute nodes, thereby eliminating a significant obstacle to broader use of high performance visualization applications. We outline the potential benefits of this approach in the context of visualization applications used in the cloud, on commodity clusters, and supercomputers. We discuss the implementation of EGL support in VMD, a widely used molecular visualization application, and we outline benefits of the approach for molecular visualization tasks on petascale computers, clouds, and remote visualization servers. We then provide a brief evaluation of the use of EGL in VMD, with tests using developmental graphics drivers on conventional workstations and on Amazon EC2 G2 GPU-accelerated cloud instance types. We expect that the techniques described here will be of broad benefit to many other visualization applications.

High Performance Molecular Visualization: In-Situ and Parallel Rendering with EGL

PubMed Central

Stone, John E.; Messmer, Peter; Sisneros, Robert; Schulten, Klaus

2016-01-01

Large scale molecular dynamics simulations produce terabytes of data that is impractical to transfer to remote facilities. It is therefore necessary to perform visualization tasks in-situ as the data are generated, or by running interactive remote visualization sessions and batch analyses co-located with direct access to high performance storage systems. A significant challenge for deploying visualization software within clouds, clusters, and supercomputers involves the operating system software required to initialize and manage graphics acceleration hardware. Recently, it has become possible for applications to use the Embedded-system Graphics Library (EGL) to eliminate the requirement for windowing system software on compute nodes, thereby eliminating a significant obstacle to broader use of high performance visualization applications. We outline the potential benefits of this approach in the context of visualization applications used in the cloud, on commodity clusters, and supercomputers. We discuss the implementation of EGL support in VMD, a widely used molecular visualization application, and we outline benefits of the approach for molecular visualization tasks on petascale computers, clouds, and remote visualization servers. We then provide a brief evaluation of the use of EGL in VMD, with tests using developmental graphics drivers on conventional workstations and on Amazon EC2 G2 GPU-accelerated cloud instance types. We expect that the techniques described here will be of broad benefit to many other visualization applications. PMID:27747137

Equilibrium expert: an add-in to Microsoft Excel for multiple binding equilibrium simulations and parameter estimations.

PubMed

Raguin, Olivier; Gruaz-Guyon, Anne; Barbet, Jacques

2002-11-01

An add-in to Microsoft Excel was developed to simulate multiple binding equilibriums. A partition function, readily written even when the equilibrium is complex, describes the experimental system. It involves the concentrations of the different free molecular species and of the different complexes present in the experiment. As a result, the software is not restricted to a series of predefined experimental setups but can handle a large variety of problems involving up to nine independent molecular species. Binding parameters are estimated by nonlinear least-square fitting of experimental measurements as supplied by the user. The fitting process allows user-defined weighting of the experimental data. The flexibility of the software and the way it may be used to describe common experimental situations and to deal with usual problems such as tracer reactivity or nonspecific binding is demonstrated by a few examples. The software is available free of charge upon request.

DFTBaby: A software package for non-adiabatic molecular dynamics simulations based on long-range corrected tight-binding TD-DFT(B)

NASA Astrophysics Data System (ADS)

Humeniuk, Alexander; Mitrić, Roland

2017-12-01

A software package, called DFTBaby, is published, which provides the electronic structure needed for running non-adiabatic molecular dynamics simulations at the level of tight-binding DFT. A long-range correction is incorporated to avoid spurious charge transfer states. Excited state energies, their analytic gradients and scalar non-adiabatic couplings are computed using tight-binding TD-DFT. These quantities are fed into a molecular dynamics code, which integrates Newton's equations of motion for the nuclei together with the electronic Schrödinger equation. Non-adiabatic effects are included by surface hopping. As an example, the program is applied to the optimization of excited states and non-adiabatic dynamics of polyfluorene. The python and Fortran source code is available at http://www.dftbaby.chemie.uni-wuerzburg.de.

A comprehensive physiologically based pharmacokinetic ...

EPA Pesticide Factsheets

Published physiologically based pharmacokinetic (PBPK) models from peer-reviewed articles are often well-parameterized, thoroughly-vetted, and can be utilized as excellent resources for the construction of models pertaining to related chemicals. Specifically, chemical-specific parameters and in vivo pharmacokinetic data used to calibrate these published models can act as valuable starting points for model development of new chemicals with similar molecular structures. A knowledgebase for published PBPK-related articles was compiled to support PBPK model construction for new chemicals based on their close analogues within the knowledgebase, and a web-based interface was developed to allow users to query those close analogues. A list of 689 unique chemicals and their corresponding 1751 articles was created after analysis of 2,245 PBPK-related articles. For each model, the PMID, chemical name, major metabolites, species, gender, life stages and tissue compartments were extracted from the published articles. PaDEL-Descriptor, a Chemistry Development Kit based software, was used to calculate molecular fingerprints. Tanimoto index was implemented in the user interface as measurement of structural similarity. The utility of the PBPK knowledgebase and web-based user interface was demonstrated using two case studies with ethylbenzene and gefitinib. Our PBPK knowledgebase is a novel tool for ranking chemicals based on similarities to other chemicals associated with existi

GneimoSim: A Modular Internal Coordinates Molecular Dynamics Simulation Package

PubMed Central

Larsen, Adrien B.; Wagner, Jeffrey R.; Kandel, Saugat; Salomon-Ferrer, Romelia; Vaidehi, Nagarajan; Jain, Abhinandan

2014-01-01

The Generalized Newton Euler Inverse Mass Operator (GNEIMO) method is an advanced method for internal coordinates molecular dynamics (ICMD). GNEIMO includes several theoretical and algorithmic advancements that address longstanding challenges with ICMD simulations. In this paper we describe the GneimoSim ICMD software package that implements the GNEIMO method. We believe that GneimoSim is the first software package to include advanced features such as the equipartition principle derived for internal coordinates, and a method for including the Fixman potential to eliminate systematic statistical biases introduced by the use of hard constraints. Moreover, by design, GneimoSim is extensible and can be easily interfaced with third party force field packages for ICMD simulations. Currently, GneimoSim includes interfaces to LAMMPS, OpenMM, Rosetta force field calculation packages. The availability of a comprehensive Python interface to the underlying C++ classes and their methods provides a powerful and versatile mechanism for users to develop simulation scripts to configure the simulation and control the simulation flow. GneimoSim has been used extensively for studying the dynamics of protein structures, refinement of protein homology models, and for simulating large scale protein conformational changes with enhanced sampling methods. GneimoSim is not limited to proteins and can also be used for the simulation of polymeric materials. PMID:25263538

GneimoSim: a modular internal coordinates molecular dynamics simulation package.

PubMed

Larsen, Adrien B; Wagner, Jeffrey R; Kandel, Saugat; Salomon-Ferrer, Romelia; Vaidehi, Nagarajan; Jain, Abhinandan

2014-12-05

The generalized Newton-Euler inverse mass operator (GNEIMO) method is an advanced method for internal coordinates molecular dynamics (ICMD). GNEIMO includes several theoretical and algorithmic advancements that address longstanding challenges with ICMD simulations. In this article, we describe the GneimoSim ICMD software package that implements the GNEIMO method. We believe that GneimoSim is the first software package to include advanced features such as the equipartition principle derived for internal coordinates, and a method for including the Fixman potential to eliminate systematic statistical biases introduced by the use of hard constraints. Moreover, by design, GneimoSim is extensible and can be easily interfaced with third party force field packages for ICMD simulations. Currently, GneimoSim includes interfaces to LAMMPS, OpenMM, and Rosetta force field calculation packages. The availability of a comprehensive Python interface to the underlying C++ classes and their methods provides a powerful and versatile mechanism for users to develop simulation scripts to configure the simulation and control the simulation flow. GneimoSim has been used extensively for studying the dynamics of protein structures, refinement of protein homology models, and for simulating large scale protein conformational changes with enhanced sampling methods. GneimoSim is not limited to proteins and can also be used for the simulation of polymeric materials. © 2014 Wiley Periodicals, Inc.

Generic domain models in software engineering

NASA Technical Reports Server (NTRS)

Maiden, Neil

1992-01-01

This paper outlines three research directions related to domain-specific software development: (1) reuse of generic models for domain-specific software development; (2) empirical evidence to determine these generic models, namely elicitation of mental knowledge schema possessed by expert software developers; and (3) exploitation of generic domain models to assist modelling of specific applications. It focuses on knowledge acquisition for domain-specific software development, with emphasis on tool support for the most important phases of software development.

An autonomous molecular computer for logical control of gene expression

PubMed Central

Benenson, Yaakov; Gil, Binyamin; Ben-Dor, Uri; Adar, Rivka; Shapiro, Ehud

2013-01-01

Early biomolecular computer research focused on laboratory-scale, human-operated computers for complex computational problems1–7. Recently, simple molecular-scale autonomous programmable computers were demonstrated8–15 allowing both input and output information to be in molecular form. Such computers, using biological molecules as input data and biologically active molecules as outputs, could produce a system for ‘logical’ control of biological processes. Here we describe an autonomous biomolecular computer that, at least in vitro, logically analyses the levels of messenger RNA species, and in response produces a molecule capable of affecting levels of gene expression. The computer operates at a concentration of close to a trillion computers per microlitre and consists of three programmable modules: a computation module, that is, a stochastic molecular automaton12–17; an input module, by which specific mRNA levels or point mutations regulate software molecule concentrations, and hence automaton transition probabilities; and an output module, capable of controlled release of a short single-stranded DNA molecule. This approach might be applied in vivo to biochemical sensing, genetic engineering and even medical diagnosis and treatment. As a proof of principle we programmed the computer to identify and analyse mRNA of disease-related genes18–22 associated with models of small-cell lung cancer and prostate cancer, and to produce a single-stranded DNA molecule modelled after an anticancer drug. PMID:15116117

Molecular simulation of methane adsorption characteristics on coal macromolecule

NASA Astrophysics Data System (ADS)

Yang, Zhiyuan; He, Xiaoxiao; Meng, Zhuoyue; Xue, Wenying

2018-02-01

In this paper, the molecular model of anthracite named Wender2 was selected to study the adsorption behaviour of single component CH4 and the competitive adsorption of CH4/CO2, CH4/H2O and CH4/N2. The molecular model of anthracite was established by molecular simulation software (Materials Studio 8.0), and Grand Canonical Monte Carlo (GCMC) simulations were carried out to investigate the single and binary component adsorption. The effects of pressure and temperature on the adsorption position, adsorption energy and adsorption capacity were mainly discussed. The results show that for the single component adsorption, the adsorption capacity of CH4 increases rapidly with the pressure ascending, and then tends to be stable after the first step. The low temperature is favourable for the adsorption of CH4, and the high temperature promotes desorption quantity of CH4 from the coal. Adsorbent molecules are preferentially adsorbed on the edge of coal macromolecules. The order of adsorption capacity of CH4/CO2, CH4/H2O and CH4/N2 in the binary component is H2O>CO2>CH4>N2. The change of pressure has little effect on the adsorption capacity of the adsorbent in the competitive adsorption, but it has a great influence on the adsorption capacity of the adsorbent, and there is a positive correlation between them.

XaNSoNS: GPU-accelerated simulator of diffraction patterns of nanoparticles

NASA Astrophysics Data System (ADS)

Neverov, V. S.

XaNSoNS is an open source software with GPU support, which simulates X-ray and neutron 1D (or 2D) diffraction patterns and pair-distribution functions (PDF) for amorphous or crystalline nanoparticles (up to ∼107 atoms) of heterogeneous structural content. Among the multiple parameters of the structure the user may specify atomic displacements, site occupancies, molecular displacements and molecular rotations. The software uses general equations nonspecific to crystalline structures to calculate the scattering intensity. It supports four major standards of parallel computing: MPI, OpenMP, Nvidia CUDA and OpenCL, enabling it to run on various architectures, from CPU-based HPCs to consumer-level GPUs.

Automatic Molecular Design using Evolutionary Techniques

NASA Technical Reports Server (NTRS)

Globus, Al; Lawton, John; Wipke, Todd; Saini, Subhash (Technical Monitor)

1998-01-01

Molecular nanotechnology is the precise, three-dimensional control of materials and devices at the atomic scale. An important part of nanotechnology is the design of molecules for specific purposes. This paper describes early results using genetic software techniques to automatically design molecules under the control of a fitness function. The fitness function must be capable of determining which of two arbitrary molecules is better for a specific task. The software begins by generating a population of random molecules. The population is then evolved towards greater fitness by randomly combining parts of the better individuals to create new molecules. These new molecules then replace some of the worst molecules in the population. The unique aspect of our approach is that we apply genetic crossover to molecules represented by graphs, i.e., sets of atoms and the bonds that connect them. We present evidence suggesting that crossover alone, operating on graphs, can evolve any possible molecule given an appropriate fitness function and a population containing both rings and chains. Prior work evolved strings or trees that were subsequently processed to generate molecular graphs. In principle, genetic graph software should be able to evolve other graph representable systems such as circuits, transportation networks, metabolic pathways, computer networks, etc.

GAPP: A Proteogenomic Software for Genome Annotation and Global Profiling of Post-translational Modifications in Prokaryotes.

PubMed

Zhang, Jia; Yang, Ming-Kun; Zeng, Honghui; Ge, Feng

2016-11-01

Although the number of sequenced prokaryotic genomes is growing rapidly, experimentally verified annotation of prokaryotic genome remains patchy and challenging. To facilitate genome annotation efforts for prokaryotes, we developed an open source software called GAPP for genome annotation and global profiling of post-translational modifications (PTMs) in prokaryotes. With a single command, it provides a standard workflow to validate and refine predicted genetic models and discover diverse PTM events. We demonstrated the utility of GAPP using proteomic data from Helicobacter pylori, one of the major human pathogens that is responsible for many gastric diseases. Our results confirmed 84.9% of the existing predicted H. pylori proteins, identified 20 novel protein coding genes, and corrected four existing gene models with regard to translation initiation sites. In particular, GAPP revealed a large repertoire of PTMs using the same proteomic data and provided a rich resource that can be used to examine the functions of reversible modifications in this human pathogen. This software is a powerful tool for genome annotation and global discovery of PTMs and is applicable to any sequenced prokaryotic organism; we expect that it will become an integral part of ongoing genome annotation efforts for prokaryotes. GAPP is freely available at https://sourceforge.net/projects/gappproteogenomic/. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Buying in to bioinformatics: an introduction to commercial sequence analysis software

PubMed Central

2015-01-01

Advancements in high-throughput nucleotide sequencing techniques have brought with them state-of-the-art bioinformatics programs and software packages. Given the importance of molecular sequence data in contemporary life science research, these software suites are becoming an essential component of many labs and classrooms, and as such are frequently designed for non-computer specialists and marketed as one-stop bioinformatics toolkits. Although beautifully designed and powerful, user-friendly bioinformatics packages can be expensive and, as more arrive on the market each year, it can be difficult for researchers, teachers and students to choose the right software for their needs, especially if they do not have a bioinformatics background. This review highlights some of the currently available and most popular commercial bioinformatics packages, discussing their prices, usability, features and suitability for teaching. Although several commercial bioinformatics programs are arguably overpriced and overhyped, many are well designed, sophisticated and, in my opinion, worth the investment. If you are just beginning your foray into molecular sequence analysis or an experienced genomicist, I encourage you to explore proprietary software bundles. They have the potential to streamline your research, increase your productivity, energize your classroom and, if anything, add a bit of zest to the often dry detached world of bioinformatics. PMID:25183247

Buying in to bioinformatics: an introduction to commercial sequence analysis software.

PubMed

Smith, David Roy

2015-07-01

Advancements in high-throughput nucleotide sequencing techniques have brought with them state-of-the-art bioinformatics programs and software packages. Given the importance of molecular sequence data in contemporary life science research, these software suites are becoming an essential component of many labs and classrooms, and as such are frequently designed for non-computer specialists and marketed as one-stop bioinformatics toolkits. Although beautifully designed and powerful, user-friendly bioinformatics packages can be expensive and, as more arrive on the market each year, it can be difficult for researchers, teachers and students to choose the right software for their needs, especially if they do not have a bioinformatics background. This review highlights some of the currently available and most popular commercial bioinformatics packages, discussing their prices, usability, features and suitability for teaching. Although several commercial bioinformatics programs are arguably overpriced and overhyped, many are well designed, sophisticated and, in my opinion, worth the investment. If you are just beginning your foray into molecular sequence analysis or an experienced genomicist, I encourage you to explore proprietary software bundles. They have the potential to streamline your research, increase your productivity, energize your classroom and, if anything, add a bit of zest to the often dry detached world of bioinformatics. © The Author 2014. Published by Oxford University Press.

MAX: Multiplatform Applications for XAFS

NASA Astrophysics Data System (ADS)

Alain, Michalowicz; Jacques, Moscovici; Diane, Muller-Bouvet; Karine, Provost

2009-11-01

MAX is a new EXAFS and XANES analysis package, replacing our old "EXAFS pour le Mac" software suite. The major improvement is the ability to work with strictly the same code, compiled at once for Microsoft Windows, Apple MacOSX and LINUX systems, justifying the title "Multiplatform Applications for XAFS". It is organized as four modules: ABSORBIX (X-ray absorbance and fluorescence self-absorption calculations), CHEROKEE (EXAFS and XANES data treatment), ROUNDMIDNIGHT (EXAFS modeling and fit) and CRYSTALFFREV (from crystal structures and molecular modeling to FEFF EXAFS and XANES theoretical calculations). Most features developed in "EXAFS pour le Mac" are still available, but with much improvements in the user's interface, data treatment algorithms and new functionalities.

Characterization of Disulfide-Linked Peptides Using Tandem Mass Spectrometry Coupled with Automated Data Analysis Software

NASA Astrophysics Data System (ADS)

Liang, Zhidan; McGuinness, Kenneth N.; Crespo, Alejandro; Zhong, Wendy

2018-05-01

Disulfide bond formation is critical for maintaining structure stability and function of many peptides and proteins. Mass spectrometry has become an important tool for the elucidation of molecular connectivity. However, the interpretation of the tandem mass spectral data of disulfide-linked peptides has been a major challenge due to the lack of appropriate tools. Developing proper data analysis software is essential to quickly characterize disulfide-linked peptides. A thorough and in-depth understanding of how disulfide-linked peptides fragment in mass spectrometer is a key in developing software to interpret the tandem mass spectra of these peptides. Two model peptides with inter- and intra-chain disulfide linkages were used to study fragmentation behavior in both collisional-activated dissociation (CAD) and electron-based dissociation (ExD) experiments. Fragments generated from CAD and ExD can be categorized into three major types, which result from different S-S and C-S bond cleavage patterns. DiSulFinder is a computer algorithm that was newly developed based on the fragmentation observed in these peptides. The software is vendor neutral and capable of quickly and accurately identifying a variety of fragments generated from disulfide-linked peptides. DiSulFinder identifies peptide backbone fragments with S-S and C-S bond cleavages and, more importantly, can also identify fragments with the S-S bond still intact to aid disulfide linkage determination. With the assistance of this software, more comprehensive disulfide connectivity characterization can be achieved. [Figure not available: see fulltext.

Characterization of Disulfide-Linked Peptides Using Tandem Mass Spectrometry Coupled with Automated Data Analysis Software

NASA Astrophysics Data System (ADS)

Liang, Zhidan; McGuinness, Kenneth N.; Crespo, Alejandro; Zhong, Wendy

2018-01-01

Disulfide bond formation is critical for maintaining structure stability and function of many peptides and proteins. Mass spectrometry has become an important tool for the elucidation of molecular connectivity. However, the interpretation of the tandem mass spectral data of disulfide-linked peptides has been a major challenge due to the lack of appropriate tools. Developing proper data analysis software is essential to quickly characterize disulfide-linked peptides. A thorough and in-depth understanding of how disulfide-linked peptides fragment in mass spectrometer is a key in developing software to interpret the tandem mass spectra of these peptides. Two model peptides with inter- and intra-chain disulfide linkages were used to study fragmentation behavior in both collisional-activated dissociation (CAD) and electron-based dissociation (ExD) experiments. Fragments generated from CAD and ExD can be categorized into three major types, which result from different S-S and C-S bond cleavage patterns. DiSulFinder is a computer algorithm that was newly developed based on the fragmentation observed in these peptides. The software is vendor neutral and capable of quickly and accurately identifying a variety of fragments generated from disulfide-linked peptides. DiSulFinder identifies peptide backbone fragments with S-S and C-S bond cleavages and, more importantly, can also identify fragments with the S-S bond still intact to aid disulfide linkage determination. With the assistance of this software, more comprehensive disulfide connectivity characterization can be achieved. [Figure not available: see fulltext.

MaMiCo: Transient multi-instance molecular-continuum flow simulation on supercomputers

NASA Astrophysics Data System (ADS)

Neumann, Philipp; Bian, Xin

2017-11-01

We present extensions of the macro-micro-coupling tool MaMiCo, which was designed to couple continuum fluid dynamics solvers with discrete particle dynamics. To enable local extraction of smooth flow field quantities especially on rather short time scales, sampling over an ensemble of molecular dynamics simulations is introduced. We provide details on these extensions including the transient coupling algorithm, open boundary forcing, and multi-instance sampling. Furthermore, we validate the coupling in Couette flow using different particle simulation software packages and particle models, i.e. molecular dynamics and dissipative particle dynamics. Finally, we demonstrate the parallel scalability of the molecular-continuum simulations by using up to 65 536 compute cores of the supercomputer Shaheen II located at KAUST. Program Files doi:http://dx.doi.org/10.17632/w7rgdrhb85.1 Licensing provisions: BSD 3-clause Programming language: C, C++ External routines/libraries: For compiling: SCons, MPI (optional) Subprograms used: ESPResSo, LAMMPS, ls1 mardyn, waLBerla For installation procedures of the MaMiCo interfaces, see the README files in the respective code directories located in coupling/interface/impl. Journal reference of previous version: P. Neumann, H. Flohr, R. Arora, P. Jarmatz, N. Tchipev, H.-J. Bungartz. MaMiCo: Software design for parallel molecular-continuum flow simulations, Computer Physics Communications 200: 324-335, 2016 Does the new version supersede the previous version?: Yes. The functionality of the previous version is completely retained in the new version. Nature of problem: Coupled molecular-continuum simulation for multi-resolution fluid dynamics: parts of the domain are resolved by molecular dynamics or another particle-based solver whereas large parts are covered by a mesh-based CFD solver, e.g. a lattice Boltzmann automaton. Solution method: We couple existing MD and CFD solvers via MaMiCo (macro-micro coupling tool). Data exchange and coupling algorithmics are abstracted and incorporated in MaMiCo. Once an algorithm is set up in MaMiCo, it can be used and extended, even if other solvers are used (as soon as the respective interfaces are implemented/available). Reasons for the new version: We have incorporated a new algorithm to simulate transient molecular-continuum systems and to automatically sample data over multiple MD runs that can be executed simultaneously (on, e.g., a compute cluster). MaMiCo has further been extended by an interface to incorporate boundary forcing to account for open molecular dynamics boundaries. Besides support for coupling with various MD and CFD frameworks, the new version contains a test case that allows to run molecular-continuum Couette flow simulations out-of-the-box. No external tools or simulation codes are required anymore. However, the user is free to switch from the included MD simulation package to LAMMPS. For details on how to run the transient Couette problem, see the file README in the folder coupling/tests, Remark on MaMiCo V1.1. Summary of revisions: Open boundary forcing; Multi-instance MD sampling; support for transient molecular-continuum systems Restrictions: Currently, only single-centered systems are supported. For access to the LAMMPS-based implementation of DPD boundary forcing, please contact Xin Bian, xin.bian@tum.de. Additional comments: Please see file license_mamico.txt for further details regarding distribution and advertising of this software.

Simulation tools for particle-based reaction-diffusion dynamics in continuous space

PubMed Central

2014-01-01

Particle-based reaction-diffusion algorithms facilitate the modeling of the diffusional motion of individual molecules and the reactions between them in cellular environments. A physically realistic model, depending on the system at hand and the questions asked, would require different levels of modeling detail such as particle diffusion, geometrical confinement, particle volume exclusion or particle-particle interaction potentials. Higher levels of detail usually correspond to increased number of parameters and higher computational cost. Certain systems however, require these investments to be modeled adequately. Here we present a review on the current field of particle-based reaction-diffusion software packages operating on continuous space. Four nested levels of modeling detail are identified that capture incrementing amount of detail. Their applicability to different biological questions is discussed, arching from straight diffusion simulations to sophisticated and expensive models that bridge towards coarse grained molecular dynamics. PMID:25737778

A model for the solution structure of the rod arrestin tetramer.

PubMed

Hanson, Susan M; Dawson, Eric S; Francis, Derek J; Van Eps, Ned; Klug, Candice S; Hubbell, Wayne L; Meiler, Jens; Gurevich, Vsevolod V

2008-06-01

Visual rod arrestin has the ability to self-associate at physiological concentrations. We previously demonstrated that only monomeric arrestin can bind the receptor and that the arrestin tetramer in solution differs from that in the crystal. We employed the Rosetta docking software to generate molecular models of the physiologically relevant solution tetramer based on the monomeric arrestin crystal structure. The resulting models were filtered using the Rosetta energy function, experimental intersubunit distances measured with DEER spectroscopy, and intersubunit contact sites identified by mutagenesis and site-directed spin labeling. This resulted in a unique model for subsequent evaluation. The validity of the model is strongly supported by model-directed crosslinking and targeted mutagenesis that yields arrestin variants deficient in self-association. The structure of the solution tetramer explains its inability to bind rhodopsin and paves the way for experimental studies of the physiological role of rod arrestin self-association.

DEVELOPMENT OF A PORTABLE SOFTWARE LANGUAGE FOR PHYSIOLOGICALLY-BASED PHARMACOKINETIC (PBPK) MODELS

EPA Science Inventory

The PBPK modeling community has had a long-standing problem with modeling software compatibility. The numerous software packages used for PBPK models are, at best, minimally compatible. This creates problems ranging from model obsolescence due to software support discontinuation...

Molecular mechanisms of protein aggregation from global fitting of kinetic models.

PubMed

Meisl, Georg; Kirkegaard, Julius B; Arosio, Paolo; Michaels, Thomas C T; Vendruscolo, Michele; Dobson, Christopher M; Linse, Sara; Knowles, Tuomas P J

2016-02-01

The elucidation of the molecular mechanisms by which soluble proteins convert into their amyloid forms is a fundamental prerequisite for understanding and controlling disorders that are linked to protein aggregation, such as Alzheimer's and Parkinson's diseases. However, because of the complexity associated with aggregation reaction networks, the analysis of kinetic data of protein aggregation to obtain the underlying mechanisms represents a complex task. Here we describe a framework, using quantitative kinetic assays and global fitting, to determine and to verify a molecular mechanism for aggregation reactions that is compatible with experimental kinetic data. We implement this approach in a web-based software, AmyloFit. Our procedure starts from the results of kinetic experiments that measure the concentration of aggregate mass as a function of time. We illustrate the approach with results from the aggregation of the β-amyloid (Aβ) peptides measured using thioflavin T, but the method is suitable for data from any similar kinetic experiment measuring the accumulation of aggregate mass as a function of time; the input data are in the form of a tab-separated text file. We also outline general experimental strategies and practical considerations for obtaining kinetic data of sufficient quality to draw detailed mechanistic conclusions, and the procedure starts with instructions for extensive data quality control. For the core part of the analysis, we provide an online platform (http://www.amylofit.ch.cam.ac.uk) that enables robust global analysis of kinetic data without the need for extensive programming or detailed mathematical knowledge. The software automates repetitive tasks and guides users through the key steps of kinetic analysis: determination of constraints to be placed on the aggregation mechanism based on the concentration dependence of the aggregation reaction, choosing from several fundamental models describing assembly into linear aggregates and fitting the chosen models using an advanced minimization algorithm to yield the reaction orders and rate constants. Finally, we outline how to use this approach to investigate which targets potential inhibitors of amyloid formation bind to and where in the reaction mechanism they act. The protocol, from processing data to determining mechanisms, can be completed in <1 d.

Cost Estimation of Software Development and the Implications for the Program Manager

DTIC Science & Technology

1992-06-01

Software Lifecycle Model (SLIM), the Jensen System-4 model, the Software Productivity, Quality, and Reliability Estimator ( SPQR \\20), the Constructive...function models in current use are the Software Productivity, Quality, and Reliability Estimator ( SPQR /20) and the Software Architecture Sizing and...Estimator ( SPQR /20) was developed by T. Capers Jones of Software Productivity Research, Inc., in 1985. The model is intended to estimate the outcome

Software reliability models for critical applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pham, H.; Pham, M.

This report presents the results of the first phase of the ongoing EG G Idaho, Inc. Software Reliability Research Program. The program is studying the existing software reliability models and proposes a state-of-the-art software reliability model that is relevant to the nuclear reactor control environment. This report consists of three parts: (1) summaries of the literature review of existing software reliability and fault tolerant software reliability models and their related issues, (2) proposed technique for software reliability enhancement, and (3) general discussion and future research. The development of this proposed state-of-the-art software reliability model will be performed in the secondmore » place. 407 refs., 4 figs., 2 tabs.« less

Software reliability models for critical applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pham, H.; Pham, M.

This report presents the results of the first phase of the ongoing EG&G Idaho, Inc. Software Reliability Research Program. The program is studying the existing software reliability models and proposes a state-of-the-art software reliability model that is relevant to the nuclear reactor control environment. This report consists of three parts: (1) summaries of the literature review of existing software reliability and fault tolerant software reliability models and their related issues, (2) proposed technique for software reliability enhancement, and (3) general discussion and future research. The development of this proposed state-of-the-art software reliability model will be performed in the second place.more » 407 refs., 4 figs., 2 tabs.« less

Radiobiological modeling with MarCell software

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hasan, J.S.; Jones, T.D.

1999-01-01

A nonlinear system of differential equations that models the bone marrow cellular kinetics associated with radiation injury, molecular repair, and compensatory cell proliferation has been extensively documented. Recently, that model has been implemented as MarCell, a user-friendly MS-DOS computer program that allows users with little knowledge of the original model to evaluate complex radiation exposure scenarios. The software allows modeling with the following radiations: tritium beta, 100 kVp X, 250 kVp X, 22 MV X, {sup 60}Co, {sup 137}Cs, 2 MeV electrons, triga neutrons, D-T neutrons, and 3 blends of mixed-field fission radiations. The possible cell lineages are stem, stroma,more » and leukemia/lymphoma, and the available species include mouse, rat, dog, sheep, swine, burro, and man. An attractive mathematical feature is that any protracted protocol can be expressed as an equivalent prompt dose for either the source used or for a reference, such as 250 kVp X rays or {sup 60}Co. Output from MarCell includes: risk of 30-day mortality; risk of cancer and leukemia based either on cytopenia or compensatory cell proliferation; cell survival plots as a function of time or dose; and 4-week recovery kinetics following treatment. In this article, the program`s applicability and ease of use are demonstrated by evaluating a medical total body irradiation protocol and a nuclear fallout scenario.« less

Particle-based simulations of self-motile suspensions

NASA Astrophysics Data System (ADS)

Hinz, Denis F.; Panchenko, Alexander; Kim, Tae-Yeon; Fried, Eliot

2015-11-01

A simple model for simulating flows of active suspensions is investigated. The approach is based on dissipative particle dynamics. While the model is potentially applicable to a wide range of self-propelled particle systems, the specific class of self-motile bacterial suspensions is considered as a modeling scenario. To mimic the rod-like geometry of a bacterium, two dissipative particle dynamics particles are connected by a stiff harmonic spring to form an aggregate dissipative particle dynamics molecule. Bacterial motility is modeled through a constant self-propulsion force applied along the axis of each such aggregate molecule. The model accounts for hydrodynamic interactions between self-propelled agents through the pairwise dissipative interactions conventional to dissipative particle dynamics. Numerical simulations are performed using a customized version of the open-source software package LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) software package. Detailed studies of the influence of agent concentration, pairwise dissipative interactions, and Stokes friction on the statistics of the system are provided. The simulations are used to explore the influence of hydrodynamic interactions in active suspensions. For high agent concentrations in combination with dominating pairwise dissipative forces, strongly correlated motion patterns and a fluid-like spectral distributions of kinetic energy are found. In contrast, systems dominated by Stokes friction exhibit weaker spatial correlations of the velocity field. These results indicate that hydrodynamic interactions may play an important role in the formation of spatially extended structures in active suspensions.

In silico study of in vitro GPCR assays by QSAR modeling ...

EPA Pesticide Factsheets

The U.S. EPA is screening thousands of chemicals of environmental interest in hundreds of in vitro high-throughput screening (HTS) assays (the ToxCast program). One goal is to prioritize chemicals for more detailed analyses based on activity in molecular initiating events (MIE) of adverse outcome pathways (AOPs). However, the chemical space of interest for environmental exposure is much wider than this set of chemicals. Thus, there is a need to fill data gaps with in silico methods, and quantitative structure-activity relationships (QSARs) are a proven and cost effective approach to predict biological activity. ToxCast in turn provides relatively large datasets that are ideal for training and testing QSAR models. The overall goal of the study described here was to develop QSAR models to fill the data gaps in a larger environmental database of ~32k structures. The specific aim of the current work was to build QSAR models for 18 G-Protein Coupled Receptor (GPCR) assays, part of the aminergic category. Two QSAR modeling strategies were adopted: classification models were developed to separate chemicals into active/non-active classes, and then regression models were built to predict the potency values of the bioassays for the active chemicals. Multiple software programs were used to calculate constitutional, topological and substructural molecular descriptors from two-dimensional (2D) chemical structures. Model-fitting methods included PLSDA (partial least squares d

Molecular Descriptors

NASA Astrophysics Data System (ADS)

Consonni, Viviana; Todeschini, Roberto

In the last decades, several scientific researches have been focused on studying how to encompass and convert - by a theoretical pathway - the information encoded in the molecular structure into one or more numbers used to establish quantitative relationships between structures and properties, biological activities, or other experimental properties. Molecular descriptors are formally mathematical representations of a molecule obtained by a well-specified algorithm applied to a defined molecular representation or a well-specified experimental procedure. They play a fundamental role in chemistry, pharmaceutical sciences, environmental protection policy, toxicology, ecotoxicology, health research, and quality control. Evidence of the interest of the scientific community in the molecular descriptors is provided by the huge number of descriptors proposed up today: more than 5000 descriptors derived from different theories and approaches are defined in the literature and most of them can be calculated by means of dedicated software applications. Molecular descriptors are of outstanding importance in the research fields of quantitative structure-activity relationships (QSARs) and quantitative structure-property relationships (QSPRs), where they are the independent chemical information used to predict the properties of interest. Along with the definition of appropriate molecular descriptors, the molecular structure representation and the mathematical tools for deriving and assessing models are other fundamental components of the QSAR/QSPR approach. The remarkable progress during the last few years in chemometrics and chemoinformatics has led to new strategies for finding mathematical meaningful relationships between the molecular structure and biological activities, physico-chemical, toxicological, and environmental properties of chemicals. Different approaches for deriving molecular descriptors here reviewed and some of the most relevant descriptors are presented in detail with numerical examples.

Adaptive MCMC in Bayesian phylogenetics: an application to analyzing partitioned data in BEAST.

PubMed

Baele, Guy; Lemey, Philippe; Rambaut, Andrew; Suchard, Marc A

2017-06-15

Advances in sequencing technology continue to deliver increasingly large molecular sequence datasets that are often heavily partitioned in order to accurately model the underlying evolutionary processes. In phylogenetic analyses, partitioning strategies involve estimating conditionally independent models of molecular evolution for different genes and different positions within those genes, requiring a large number of evolutionary parameters that have to be estimated, leading to an increased computational burden for such analyses. The past two decades have also seen the rise of multi-core processors, both in the central processing unit (CPU) and Graphics processing unit processor markets, enabling massively parallel computations that are not yet fully exploited by many software packages for multipartite analyses. We here propose a Markov chain Monte Carlo (MCMC) approach using an adaptive multivariate transition kernel to estimate in parallel a large number of parameters, split across partitioned data, by exploiting multi-core processing. Across several real-world examples, we demonstrate that our approach enables the estimation of these multipartite parameters more efficiently than standard approaches that typically use a mixture of univariate transition kernels. In one case, when estimating the relative rate parameter of the non-coding partition in a heterochronous dataset, MCMC integration efficiency improves by > 14-fold. Our implementation is part of the BEAST code base, a widely used open source software package to perform Bayesian phylogenetic inference. guy.baele@kuleuven.be. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Assessment of the health effects of chemicals in humans: II. Construction of an adverse effects database for QSAR modeling.

PubMed

Matthews, Edwin J; Kruhlak, Naomi L; Weaver, James L; Benz, R Daniel; Contrera, Joseph F

2004-12-01

The FDA's Spontaneous Reporting System (SRS) database contains over 1.5 million adverse drug reaction (ADR) reports for 8620 drugs/biologics that are listed for 1191 Coding Symbols for Thesaurus of Adverse Reaction (COSTAR) terms of adverse effects. We have linked the trade names of the drugs to 1861 generic names and retrieved molecular structures for each chemical to obtain a set of 1515 organic chemicals that are suitable for modeling with commercially available QSAR software packages. ADR report data for 631 of these compounds were extracted and pooled for the first five years that each drug was marketed. Patient exposure was estimated during this period using pharmaceutical shipping units obtained from IMS Health. Significant drug effects were identified using a Reporting Index (RI), where RI = (# ADR reports / # shipping units) x 1,000,000. MCASE/MC4PC software was used to identify the optimal conditions for defining a significant adverse effect finding. Results suggest that a significant effect in our database is characterized by > or = 4 ADR reports and > or = 20,000 shipping units during five years of marketing, and an RI > or = 4.0. Furthermore, for a test chemical to be evaluated as active it must contain a statistically significant molecular structural alert, called a decision alert, in two or more toxicologically related endpoints. We also report the use of a composite module, which pools observations from two or more toxicologically related COSTAR term endpoints to provide signal enhancement for detecting adverse effects.

TADSim: Discrete Event-based Performance Prediction for Temperature Accelerated Dynamics

DOE PAGES

Mniszewski, Susan M.; Junghans, Christoph; Voter, Arthur F.; ...

2015-04-16

Next-generation high-performance computing will require more scalable and flexible performance prediction tools to evaluate software--hardware co-design choices relevant to scientific applications and hardware architectures. Here, we present a new class of tools called application simulators—parameterized fast-running proxies of large-scale scientific applications using parallel discrete event simulation. Parameterized choices for the algorithmic method and hardware options provide a rich space for design exploration and allow us to quickly find well-performing software--hardware combinations. We demonstrate our approach with a TADSim simulator that models the temperature-accelerated dynamics (TAD) method, an algorithmically complex and parameter-rich member of the accelerated molecular dynamics (AMD) family ofmore » molecular dynamics methods. The essence of the TAD application is captured without the computational expense and resource usage of the full code. We accomplish this by identifying the time-intensive elements, quantifying algorithm steps in terms of those elements, abstracting them out, and replacing them by the passage of time. We use TADSim to quickly characterize the runtime performance and algorithmic behavior for the otherwise long-running simulation code. We extend TADSim to model algorithm extensions, such as speculative spawning of the compute-bound stages, and predict performance improvements without having to implement such a method. Validation against the actual TAD code shows close agreement for the evolution of an example physical system, a silver surface. Finally, focused parameter scans have allowed us to study algorithm parameter choices over far more scenarios than would be possible with the actual simulation. This has led to interesting performance-related insights and suggested extensions.« less

Usability Prediction & Ranking of SDLC Models Using Fuzzy Hierarchical Usability Model

NASA Astrophysics Data System (ADS)

Gupta, Deepak; Ahlawat, Anil K.; Sagar, Kalpna

2017-06-01

Evaluation of software quality is an important aspect for controlling and managing the software. By such evaluation, improvements in software process can be made. The software quality is significantly dependent on software usability. Many researchers have proposed numbers of usability models. Each model considers a set of usability factors but do not cover all the usability aspects. Practical implementation of these models is still missing, as there is a lack of precise definition of usability. Also, it is very difficult to integrate these models into current software engineering practices. In order to overcome these challenges, this paper aims to define the term `usability' using the proposed hierarchical usability model with its detailed taxonomy. The taxonomy considers generic evaluation criteria for identifying the quality components, which brings together factors, attributes and characteristics defined in various HCI and software models. For the first time, the usability model is also implemented to predict more accurate usability values. The proposed system is named as fuzzy hierarchical usability model that can be easily integrated into the current software engineering practices. In order to validate the work, a dataset of six software development life cycle models is created and employed. These models are ranked according to their predicted usability values. This research also focuses on the detailed comparison of proposed model with the existing usability models.

Workshop on Molecular Animation

PubMed Central

Bromberg, Sarina; Chiu, Wah; Ferrin, Thomas E.

2011-01-01

Summary February 25–26, 2010, in San Francisco, the Resource for Biocomputing, Visualization and Informatics (RBVI) and the National Center for Macromolecular Imaging (NCMI) hosted a molecular animation workshop for 21 structural biologists, molecular animators, and creators of molecular visualization software. Molecular animation aims to visualize scientific understanding of biomolecular processes and structures. The primary goal of the workshop was to identify the necessary tools for: producing high quality molecular animations, understanding complex molecular and cellular structures, creating publication supplementary materials and conference presentations, and teaching science to students and the public. Another use of molecular animation emerged in the workshop: helping to focus scientific inquiry about the motions of molecules and enhancing informal communication within and between laboratories. PMID:20947014

XML Encoding of Features Describing Rule-Based Modeling of Reaction Networks with Multi-Component Molecular Complexes

PubMed Central

Blinov, Michael L.; Moraru, Ion I.

2011-01-01

Multi-state molecules and multi-component complexes are commonly involved in cellular signaling. Accounting for molecules that have multiple potential states, such as a protein that may be phosphorylated on multiple residues, and molecules that combine to form heterogeneous complexes located among multiple compartments, generates an effect of combinatorial complexity. Models involving relatively few signaling molecules can include thousands of distinct chemical species. Several software tools (StochSim, BioNetGen) are already available to deal with combinatorial complexity. Such tools need information standards if models are to be shared, jointly evaluated and developed. Here we discuss XML conventions that can be adopted for modeling biochemical reaction networks described by user-specified reaction rules. These could form a basis for possible future extensions of the Systems Biology Markup Language (SBML). PMID:21464833

Remote network control plasma diagnostic system for Tokamak T-10

NASA Astrophysics Data System (ADS)

Troynov, V. I.; Zimin, A. M.; Krupin, V. A.; Notkin, G. E.; Nurgaliev, M. R.

2016-09-01

The parameters of molecular plasma in closed magnetic trap is studied in this paper. Using the system of molecular diagnostics, which was designed by the authors on the «Tokamak T-10» facility, the radiation of hydrogen isotopes at the plasma edge is investigated. The scheme of optical radiation registration within visible spectrum is described. For visualization, identification and processing of registered molecular spectra a new software is developed using MatLab environment. The software also includes electronic atlas of electronic-vibrational-rotational transitions for molecules of protium and deuterium. To register radiation from limiter cross-section a network control system is designed using the means of the Internet/Intranet. Remote control system diagram and methods are given. The examples of web-interfaces for working out equipment control scenarios and viewing of results are provided. After test run in Intranet, the remote diagnostic system will be accessible through Internet.

Genetic Algorithms and Their Application to the Protein Folding Problem

DTIC Science & Technology

1993-12-01

and symbolic methods, random methods such as Monte Carlo simulation and simulated annealing, distance geometry, and molecular dynamics. Many of these...calculated energies with those obtained using the molecular simulation software package called CHARMm. 10 9) Test both the simple and parallel simpie genetic...homology-based, and simplification techniques. 3.21 Molecular Dynamics. Perhaps the most natural approach is to actually simulate the folding process. This

Benchmarking of HPCC: A novel 3D molecular representation combining shape and pharmacophoric descriptors for efficient molecular similarity assessments.

PubMed

Karaboga, Arnaud S; Petronin, Florent; Marchetti, Gino; Souchet, Michel; Maigret, Bernard

2013-04-01

Since 3D molecular shape is an important determinant of biological activity, designing accurate 3D molecular representations is still of high interest. Several chemoinformatic approaches have been developed to try to describe accurate molecular shapes. Here, we present a novel 3D molecular description, namely harmonic pharma chemistry coefficient (HPCC), combining a ligand-centric pharmacophoric description projected onto a spherical harmonic based shape of a ligand. The performance of HPCC was evaluated by comparison to the standard ROCS software in a ligand-based virtual screening (VS) approach using the publicly available directory of useful decoys (DUD) data set comprising over 100,000 compounds distributed across 40 protein targets. Our results were analyzed using commonly reported statistics such as the area under the curve (AUC) and normalized sum of logarithms of ranks (NSLR) metrics. Overall, our HPCC 3D method is globally as efficient as the state-of-the-art ROCS software in terms of enrichment and slightly better for more than half of the DUD targets. Since it is largely admitted that VS results depend strongly on the nature of the protein families, we believe that the present HPCC solution is of interest over the current ligand-based VS methods. Copyright © 2013 Elsevier Inc. All rights reserved.

Prediction on the inhibition ratio of pyrrolidine derivatives on matrix metalloproteinase based on gene expression programming.

PubMed

Li, Yuqin; You, Guirong; Jia, Baoxiu; Si, Hongzong; Yao, Xiaojun

2014-01-01

Quantitative structure-activity relationships (QSAR) were developed to predict the inhibition ratio of pyrrolidine derivatives on matrix metalloproteinase via heuristic method (HM) and gene expression programming (GEP). The descriptors of 33 pyrrolidine derivatives were calculated by the software CODESSA, which can calculate quantum chemical, topological, geometrical, constitutional, and electrostatic descriptors. HM was also used for the preselection of 5 appropriate molecular descriptors. Linear and nonlinear QSAR models were developed based on the HM and GEP separately and two prediction models lead to a good correlation coefficient (R (2)) of 0.93 and 0.94. The two QSAR models are useful in predicting the inhibition ratio of pyrrolidine derivatives on matrix metalloproteinase during the discovery of new anticancer drugs and providing theory information for studying the new drugs.

Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen).

PubMed

Rambaut, Andrew; Lam, Tommy T; Max Carvalho, Luiz; Pybus, Oliver G

2016-01-01

Gene sequences sampled at different points in time can be used to infer molecular phylogenies on a natural timescale of months or years, provided that the sequences in question undergo measurable amounts of evolutionary change between sampling times. Data sets with this property are termed heterochronous and have become increasingly common in several fields of biology, most notably the molecular epidemiology of rapidly evolving viruses. Here we introduce the cross-platform software tool, TempEst (formerly known as Path-O-Gen), for the visualization and analysis of temporally sampled sequence data. Given a molecular phylogeny and the dates of sampling for each sequence, TempEst uses an interactive regression approach to explore the association between genetic divergence through time and sampling dates. TempEst can be used to (1) assess whether there is sufficient temporal signal in the data to proceed with phylogenetic molecular clock analysis, and (2) identify sequences whose genetic divergence and sampling date are incongruent. Examination of the latter can help identify data quality problems, including errors in data annotation, sample contamination, sequence recombination, or alignment error. We recommend that all users of the molecular clock models implemented in BEAST first check their data using TempEst prior to analysis.

Coarse-grained simulation of DNA using LAMMPS : An implementation of the oxDNA model and its applications.

PubMed

Henrich, Oliver; Gutiérrez Fosado, Yair Augusto; Curk, Tine; Ouldridge, Thomas E

2018-05-10

During the last decade coarse-grained nucleotide models have emerged that allow us to study DNA and RNA on unprecedented time and length scales. Among them is oxDNA, a coarse-grained, sequence-specific model that captures the hybridisation transition of DNA and many structural properties of single- and double-stranded DNA. oxDNA was previously only available as standalone software, but has now been implemented into the popular LAMMPS molecular dynamics code. This article describes the new implementation and analyses its parallel performance. Practical applications are presented that focus on single-stranded DNA, an area of research which has been so far under-investigated. The LAMMPS implementation of oxDNA lowers the entry barrier for using the oxDNA model significantly, facilitates future code development and interfacing with existing LAMMPS functionality as well as other coarse-grained and atomistic DNA models.

Linear and nonlinear models for predicting fish bioconcentration factors for pesticides.

PubMed

Yuan, Jintao; Xie, Chun; Zhang, Ting; Sun, Jinfang; Yuan, Xuejie; Yu, Shuling; Zhang, Yingbiao; Cao, Yunyuan; Yu, Xingchen; Yang, Xuan; Yao, Wu

2016-08-01

This work is devoted to the applications of the multiple linear regression (MLR), multilayer perceptron neural network (MLP NN) and projection pursuit regression (PPR) to quantitative structure-property relationship analysis of bioconcentration factors (BCFs) of pesticides tested on Bluegill (Lepomis macrochirus). Molecular descriptors of a total of 107 pesticides were calculated with the DRAGON Software and selected by inverse enhanced replacement method. Based on the selected DRAGON descriptors, a linear model was built by MLR, nonlinear models were developed using MLP NN and PPR. The robustness of the obtained models was assessed by cross-validation and external validation using test set. Outliers were also examined and deleted to improve predictive power. Comparative results revealed that PPR achieved the most accurate predictions. This study offers useful models and information for BCF prediction, risk assessment, and pesticide formulation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Networked Instructional Chemistry: Using Technology To Teach Chemistry

NASA Astrophysics Data System (ADS)

Smith, Stanley; Stovall, Iris

1996-10-01

Networked multimedia microcomputers provide new ways to help students learn chemistry and to help instructors manage the learning environment. This technology is used to replace some traditional laboratory work, collect on-line experimental data, enhance lectures and quiz sections with multimedia presentations, provide prelaboratory training for beginning nonchemistry- major organic laboratory, provide electronic homework for organic chemistry students, give graduate students access to real NMR data for analysis, and provide access to molecular modeling tools. The integration of all of these activities into an active learning environment is made possible by a client-server network of hundreds of computers. This requires not only instructional software but also classroom and course management software, computers, networking, and room management. Combining computer-based work with traditional course material is made possible with software management tools that allow the instructor to monitor the progress of each student and make available an on-line gradebook so students can see their grades and class standing. This client-server based system extends the capabilities of the earlier mainframe-based PLATO system, which was used for instructional computing. This paper outlines the components of a technology center used to support over 5,000 students per semester.

Calculation of relative free energies for ligand-protein binding, solvation, and conformational transitions using the GROMOS software.

PubMed

Riniker, Sereina; Christ, Clara D; Hansen, Halvor S; Hünenberger, Philippe H; Oostenbrink, Chris; Steiner, Denise; van Gunsteren, Wilfred F

2011-11-24

The calculation of the relative free energies of ligand-protein binding, of solvation for different compounds, and of different conformational states of a polypeptide is of considerable interest in the design or selection of potential enzyme inhibitors. Since such processes in aqueous solution generally comprise energetic and entropic contributions from many molecular configurations, adequate sampling of the relevant parts of configurational space is required and can be achieved through molecular dynamics simulations. Various techniques to obtain converged ensemble averages and their implementation in the GROMOS software for biomolecular simulation are discussed, and examples of their application to biomolecules in aqueous solution are given. © 2011 American Chemical Society

Atomdroid: a computational chemistry tool for mobile platforms.

PubMed

Feldt, Jonas; Mata, Ricardo A; Dieterich, Johannes M

2012-04-23

We present the implementation of a new molecular mechanics program designed for use in mobile platforms, the first specifically built for these devices. The software is designed to run on Android operating systems and is compatible with several modern tablet-PCs and smartphones available in the market. It includes molecular viewer/builder capabilities with integrated routines for geometry optimizations and Monte Carlo simulations. These functionalities allow it to work as a stand-alone tool. We discuss some particular development aspects, as well as the overall feasibility of using computational chemistry software packages in mobile platforms. Benchmark calculations show that through efficient implementation techniques even hand-held devices can be used to simulate midsized systems using force fields.

Surface CHEMKIN (Version 4. 0): A Fortran package for analyzing heterogeneous chemical kinetics at a solid-surface---gas-phase interface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Coltrin, M.E.; Kee, R.J.; Rupley, F.M.

1991-07-01

Heterogeneous reaction at the interface between a solid surface and adjacent gas is central to many chemical processes. Our purpose for developing the software package SURFACE CHEMKIN was motivated by our need to understand the complex surface chemistry in chemical vapor deposition systems involving silicon, silicon nitride, and gallium arsenide. However, we have developed the approach and implemented the software in a general setting. Thus, we expect it will find use in such diverse applications as chemical vapor deposition, chemical etching, combustion of solids, and catalytic processes, and for a wide range of chemical systems. We believe that it providesmore » a powerful capability to help model, understand, and optimize important industrial and research chemical processes. The SURFACE CHEMKIN software is designed to work in conjunction with the CHEMKIN-2 software, which handles the chemical kinetics in the gas phase. It may also be used in conjunction with the Transport Property Package, which provides information about molecular diffusion. Thus, these three packages provide a foundation on which a user can build applications software to analyze gas-phase and heterogeneous chemistry in flowing systems. These packages should not be considered programs'' in the ordinary sense. That is, they are not designed to accept input, solve a particular problem, and report the answer. Instead, they are software tools intended to help a user work efficiently with large systems of chemical reactions and develop Fortran representations of systems of equations that define a particular problem. It is up the user to solve the problem and interpret the answer. 11 refs., 15 figs., 5 tabs.« less

eSBMTools 1.0: enhanced native structure-based modeling tools.

PubMed

Lutz, Benjamin; Sinner, Claude; Heuermann, Geertje; Verma, Abhinav; Schug, Alexander

2013-11-01

Molecular dynamics simulations provide detailed insights into the structure and function of biomolecular systems. Thus, they complement experimental measurements by giving access to experimentally inaccessible regimes. Among the different molecular dynamics techniques, native structure-based models (SBMs) are based on energy landscape theory and the principle of minimal frustration. Typically used in protein and RNA folding simulations, they coarse-grain the biomolecular system and/or simplify the Hamiltonian resulting in modest computational requirements while achieving high agreement with experimental data. eSBMTools streamlines running and evaluating SBM in a comprehensive package and offers high flexibility in adding experimental- or bioinformatics-derived restraints. We present a software package that allows setting up, modifying and evaluating SBM for both RNA and proteins. The implemented workflows include predicting protein complexes based on bioinformatics-derived inter-protein contact information, a standardized setup of protein folding simulations based on the common PDB format, calculating reaction coordinates and evaluating the simulation by free-energy calculations with weighted histogram analysis method or by phi-values. The modules interface with the molecular dynamics simulation program GROMACS. The package is open source and written in architecture-independent Python2. http://sourceforge.net/projects/esbmtools/. alexander.schug@kit.edu. Supplementary data are available at Bioinformatics online.

Comparative simulation study of chemical synthesis of functional DADNE material.

PubMed

Liu, Min Hsien; Liu, Chuan Wen

2017-01-01

Amorphous molecular simulation to model the reaction species in the synthesis of chemically inert and energetic 1,1-diamino-2,2-dinitroethene (DADNE) explosive material was performed in this work. Nitromethane was selected as the starting reactant to undergo halogenation, nitration, deprotonation, intermolecular condensation, and dehydration to produce the target DADNE product. The Materials Studio (MS) forcite program allowed fast energy calculations and reliable geometric optimization of all aqueous molecular reaction systems (0.1-0.5 M) at 283 K and 298 K. The MS forcite-computed and Gaussian polarizable continuum model (PCM)-computed results were analyzed and compared in order to explore feasible reaction pathways under suitable conditions for the synthesis of DADNE. Through theoretical simulation, the findings revealed that synthesis was possible, and a total energy barrier of 449.6 kJ mol -1 needed to be overcome in order to carry out the reaction according to MS calculation of the energy barriers at each stage at 283 K, as shown by the reaction profiles. Local analysis of intermolecular interaction, together with calculation of the stabilization energy of each reaction system, provided information that can be used as a reference regarding molecular integrated stability. Graphical Abstract Materials Studio software has been suggested for the computation and simulation of DADNE synthesis.

LIMAO: Cross-platform software for simulating laser-induced alignment and orientation dynamics of linear-, symmetric- and asymmetric tops

NASA Astrophysics Data System (ADS)

Szidarovszky, Tamás; Jono, Maho; Yamanouchi, Kaoru

2018-07-01

A user-friendly and cross-platform software called Laser-Induced Molecular Alignment and Orientation simulator (LIMAO) has been developed. The program can be used to simulate within the rigid rotor approximation the rotational dynamics of gas phase molecules induced by linearly polarized intense laser fields at a given temperature. The software is implemented in the Java and Mathematica programming languages. The primary aim of LIMAO is to aid experimental scientists in predicting and analyzing experimental data representing laser-induced spatial alignment and orientation of molecules.

Validation and Verification of LADEE Models and Software

NASA Technical Reports Server (NTRS)

Gundy-Burlet, Karen

2013-01-01

The Lunar Atmosphere Dust Environment Explorer (LADEE) mission will orbit the moon in order to measure the density, composition and time variability of the lunar dust environment. The ground-side and onboard flight software for the mission is being developed using a Model-Based Software methodology. In this technique, models of the spacecraft and flight software are developed in a graphical dynamics modeling package. Flight Software requirements are prototyped and refined using the simulated models. After the model is shown to work as desired in this simulation framework, C-code software is automatically generated from the models. The generated software is then tested in real time Processor-in-the-Loop and Hardware-in-the-Loop test beds. Travelling Road Show test beds were used for early integration tests with payloads and other subsystems. Traditional techniques for verifying computational sciences models are used to characterize the spacecraft simulation. A lightweight set of formal methods analysis, static analysis, formal inspection and code coverage analyses are utilized to further reduce defects in the onboard flight software artifacts. These techniques are applied early and often in the development process, iteratively increasing the capabilities of the software and the fidelity of the vehicle models and test beds.

WWW Entrez: A Hypertext Retrieval Tool for Molecular Biology.

ERIC Educational Resources Information Center

Epstein, Jonathan A.; Kans, Jonathan A.; Schuler, Gregory D.

This article describes the World Wide Web (WWW) Entrez server which is based upon the National Center for Biotechnology Information's (NCBI) Entrez retrieval database and software. Entrez is a molecular sequence retrieval system that contains an integrated view of portions of Medline and all publicly available nucleotide and protein databases,…

jMetalCpp: optimizing molecular docking problems with a C++ metaheuristic framework.

PubMed

López-Camacho, Esteban; García Godoy, María Jesús; Nebro, Antonio J; Aldana-Montes, José F

2014-02-01

Molecular docking is a method for structure-based drug design and structural molecular biology, which attempts to predict the position and orientation of a small molecule (ligand) in relation to a protein (receptor) to produce a stable complex with a minimum binding energy. One of the most widely used software packages for this purpose is AutoDock, which incorporates three metaheuristic techniques. We propose the integration of AutoDock with jMetalCpp, an optimization framework, thereby providing both single- and multi-objective algorithms that can be used to effectively solve docking problems. The resulting combination of AutoDock + jMetalCpp allows users of the former to easily use the metaheuristics provided by the latter. In this way, biologists have at their disposal a richer set of optimization techniques than those already provided in AutoDock. Moreover, designers of metaheuristic techniques can use molecular docking for case studies, which can lead to more efficient algorithms oriented to solving the target problems.  jMetalCpp software adapted to AutoDock is freely available as a C++ source code at http://khaos.uma.es/AutodockjMetal/.

Computer-Aided Molecular Design of Bis-phosphine Oxide Lanthanide Extractants

DOE PAGES

McCann, Billy W.; Silva, Nuwan De; Windus, Theresa L.; ...

2016-02-17

Computer-aided molecular design and high-throughput screening of viable host architectures can significantly reduce the efforts in the design of novel ligands for efficient extraction of rare earth elements. This paper presents a computational approach to the deliberate design of bis-phosphine oxide host architectures that are structurally organized for complexation of trivalent lanthanides. Molecule building software, HostDesigner, was interfaced with molecular mechanics software, PCModel, providing a tool for generating and screening millions of potential R 2(O)P-link-P(O)R 2 ligand geometries. The molecular mechanics ranking of ligand structures is consistent with both the solution-phase free energies of complexation obtained with density functional theorymore » and the performance of known bis-phosphine oxide extractants. For the case where link is -CH 2-, evaluation of the ligand geometry provides the first characterization of a steric origin for the ‘anomalous aryl strengthening’ effect. The design approach has identified a number of novel bis-phosphine oxide ligands that are better organized for lanthanide complexation than previously studied examples.« less

MaMiCo: Software design for parallel molecular-continuum flow simulations

NASA Astrophysics Data System (ADS)

Neumann, Philipp; Flohr, Hanno; Arora, Rahul; Jarmatz, Piet; Tchipev, Nikola; Bungartz, Hans-Joachim

2016-03-01

The macro-micro-coupling tool (MaMiCo) was developed to ease the development of and modularize molecular-continuum simulations, retaining sequential and parallel performance. We demonstrate the functionality and performance of MaMiCo by coupling the spatially adaptive Lattice Boltzmann framework waLBerla with four molecular dynamics (MD) codes: the light-weight Lennard-Jones-based implementation SimpleMD, the node-level optimized software ls1 mardyn, and the community codes ESPResSo and LAMMPS. We detail interface implementations to connect each solver with MaMiCo. The coupling for each waLBerla-MD setup is validated in three-dimensional channel flow simulations which are solved by means of a state-based coupling method. We provide sequential and strong scaling measurements for the four molecular-continuum simulations. The overhead of MaMiCo is found to come at 10%-20% of the total (MD) runtime. The measurements further show that scalability of the hybrid simulations is reached on up to 500 Intel SandyBridge, and more than 1000 AMD Bulldozer compute cores.

Web-accessible molecular modeling with Rosetta: The Rosetta Online Server that Includes Everyone (ROSIE).

PubMed

Moretti, Rocco; Lyskov, Sergey; Das, Rhiju; Meiler, Jens; Gray, Jeffrey J

2018-01-01

The Rosetta molecular modeling software package provides a large number of experimentally validated tools for modeling and designing proteins, nucleic acids, and other biopolymers, with new protocols being added continually. While freely available to academic users, external usage is limited by the need for expertise in the Unix command line environment. To make Rosetta protocols available to a wider audience, we previously created a web server called Rosetta Online Server that Includes Everyone (ROSIE), which provides a common environment for hosting web-accessible Rosetta protocols. Here we describe a simplification of the ROSIE protocol specification format, one that permits easier implementation of Rosetta protocols. Whereas the previous format required creating multiple separate files in different locations, the new format allows specification of the protocol in a single file. This new, simplified protocol specification has more than doubled the number of Rosetta protocols available under ROSIE. These new applications include pK a determination, lipid accessibility calculation, ribonucleic acid redesign, protein-protein docking, protein-small molecule docking, symmetric docking, antibody docking, cyclic toxin docking, critical binding peptide determination, and mapping small molecule binding sites. ROSIE is freely available to academic users at http://rosie.rosettacommons.org. © 2017 The Protein Society.

QSAR and 3D-QSAR studies applied to compounds with anticonvulsant activity.

PubMed

Garro Martinez, Juan C; Vega-Hissi, Esteban G; Andrada, Matías F; Estrada, Mario R

2015-01-01

Quantitative structure-activity relationships (QSAR and 3D-QSAR) have been applied in the last decade to obtain a reliable statistical model for the prediction of the anticonvulsant activities of new chemical entities. However, despite the large amount of information on QSAR, no recent review has published and discussed this data in detail. In this review, the authors provide a detailed discussion of QSAR studies that have been applied to compounds with anticonvulsant activity published between the years 2003 and 2013. They also evaluate the mathematical approaches and the main software used to develop the QSAR and 3D-QSAR model. QSAR methodologies continue to attract the attention of researchers and provide valuable information for the development of new potentially active compounds including those with anticonvulsant activity. This has been helped in part by improvements in the size and performance of computers; the development of specific software and the development of novel molecular descriptors, which have given rise to new and more predictive QSAR models. The extensive development of descriptors, and the way by which descriptor values are derived, have allowed the evolution of the QSAR methods. This evolution could strengthen the QSAR methods as an important tool in research and development of new and more potent anticonvulsant agents.

Modification of S-Adenosyl-l-Homocysteine as Inhibitor of Nonstructural Protein 5 Methyltransferase Dengue Virus Through Molecular Docking and Molecular Dynamics Simulation

PubMed Central

Tambunan, Usman Sumo Friend; Nasution, Mochammad Arfin Fardiansyah; Azhima, Fauziah; Parikesit, Arli Aditya; Toepak, Erwin Prasetya; Idrus, Syarifuddin; Kerami, Djati

2017-01-01

Dengue fever is still a major threat worldwide, approximately threatening two-fifths of the world’s population in tropical and subtropical countries. Nonstructural protein 5 (NS5) methyltransferase enzyme plays a vital role in the process of messenger RNA capping of dengue by transferring methyl groups from S-adenosyl-l-methionine to N7 atom of the guanine bases of RNA and the RNA ribose group of 2′OH, resulting in S-adenosyl-l-homocysteine (SAH). The modification of SAH compound was screened using molecular docking and molecular dynamics simulation, along with computational ADME-Tox (absorption, distribution, metabolism, excretion, and toxicity) test. The 2 simulations were performed using Molecular Operating Environment (MOE) 2008.10 software, whereas the ADME-Tox test was performed using various software. The modification of SAH compound was done using several functional groups that possess different polarities and properties, resulting in 3460 ligands to be docked. After conducting docking simulation, we earned 3 best ligands (SAH-M331, SAH-M2696, and SAH-M1356) based on ΔGbinding and molecular interactions, which show better results than the standard ligands. Moreover, the results of molecular dynamics simulation show that the best ligands are still able to maintain the active site residue interaction with the binding site until the end of the simulation. After a series of molecular docking and molecular dynamics simulation were performed, we concluded that SAH-M1356 ligand is the most potential SAH-based compound to inhibit NS5 methyltransferase enzyme for treating dengue fever. PMID:28469408

QSAR Study for Carcinogenic Potency of Aromatic Amines Based on GEP and MLPs

PubMed Central

Song, Fucheng; Zhang, Anling; Liang, Hui; Cui, Lianhua; Li, Wenlian; Si, Hongzong; Duan, Yunbo; Zhai, Honglin

2016-01-01

A new analysis strategy was used to classify the carcinogenicity of aromatic amines. The physical-chemical parameters are closely related to the carcinogenicity of compounds. Quantitative structure activity relationship (QSAR) is a method of predicting the carcinogenicity of aromatic amine, which can reveal the relationship between carcinogenicity and physical-chemical parameters. This study accessed gene expression programming by APS software, the multilayer perceptrons by Weka software to predict the carcinogenicity of aromatic amines, respectively. All these methods relied on molecular descriptors calculated by CODESSA software and eight molecular descriptors were selected to build function equations. As a remarkable result, the accuracy of gene expression programming in training and test sets are 0.92 and 0.82, the accuracy of multilayer perceptrons in training and test sets are 0.84 and 0.74 respectively. The precision of the gene expression programming is obviously superior to multilayer perceptrons both in training set and test set. The QSAR application in the identification of carcinogenic compounds is a high efficiency method. PMID:27854309

MOLE 2.0: advanced approach for analysis of biomacromolecular channels

PubMed Central

2013-01-01

Background Channels and pores in biomacromolecules (proteins, nucleic acids and their complexes) play significant biological roles, e.g., in molecular recognition and enzyme substrate specificity. Results We present an advanced software tool entitled MOLE 2.0, which has been designed to analyze molecular channels and pores. Benchmark tests against other available software tools showed that MOLE 2.0 is by comparison quicker, more robust and more versatile. As a new feature, MOLE 2.0 estimates physicochemical properties of the identified channels, i.e., hydropathy, hydrophobicity, polarity, charge, and mutability. We also assessed the variability in physicochemical properties of eighty X-ray structures of two members of the cytochrome P450 superfamily. Conclusion Estimated physicochemical properties of the identified channels in the selected biomacromolecules corresponded well with the known functions of the respective channels. Thus, the predicted physicochemical properties may provide useful information about the potential functions of identified channels. The MOLE 2.0 software is available at http://mole.chemi.muni.cz. PMID:23953065

Implementation of metal-friendly EAM/FS-type semi-empirical potentials in HOOMD-blue: A GPU-accelerated molecular dynamics software

NASA Astrophysics Data System (ADS)

Yang, Lin; Zhang, Feng; Wang, Cai-Zhuang; Ho, Kai-Ming; Travesset, Alex

2018-04-01

We present an implementation of EAM and FS interatomic potentials, which are widely used in simulating metallic systems, in HOOMD-blue, a software designed to perform classical molecular dynamics simulations using GPU accelerations. We first discuss the details of our implementation and then report extensive benchmark tests. We demonstrate that single-precision floating point operations efficiently implemented on GPUs can produce sufficient accuracy when compared against double-precision codes, as demonstrated in test simulations of calculations of the glass-transition temperature of Cu64.5Zr35.5, and pair correlation function g (r) of liquid Ni3Al. Our code scales well with the size of the simulating system on NVIDIA Tesla M40 and P100 GPUs. Compared with another popular software LAMMPS running on 32 cores of AMD Opteron 6220 processors, the GPU/CPU performance ratio can reach as high as 4.6. The source code can be accessed through the HOOMD-blue web page for free by any interested user.

From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language.

PubMed

de Jong, Wibe A; Walker, Andrew M; Hanwell, Marcus D

2013-05-24

Multidisciplinary integrated research requires the ability to couple the diverse sets of data obtained from a range of complex experiments and computer simulations. Integrating data requires semantically rich information. In this paper an end-to-end use of semantically rich data in computational chemistry is demonstrated utilizing the Chemical Markup Language (CML) framework. Semantically rich data is generated by the NWChem computational chemistry software with the FoX library and utilized by the Avogadro molecular editor for analysis and visualization. The NWChem computational chemistry software has been modified and coupled to the FoX library to write CML compliant XML data files. The FoX library was expanded to represent the lexical input files and molecular orbitals used by the computational chemistry software. Draft dictionary entries and a format for molecular orbitals within CML CompChem were developed. The Avogadro application was extended to read in CML data, and display molecular geometry and electronic structure in the GUI allowing for an end-to-end solution where Avogadro can create input structures, generate input files, NWChem can run the calculation and Avogadro can then read in and analyse the CML output produced. The developments outlined in this paper will be made available in future releases of NWChem, FoX, and Avogadro. The production of CML compliant XML files for computational chemistry software such as NWChem can be accomplished relatively easily using the FoX library. The CML data can be read in by a newly developed reader in Avogadro and analysed or visualized in various ways. A community-based effort is needed to further develop the CML CompChem convention and dictionary. This will enable the long-term goal of allowing a researcher to run simple "Google-style" searches of chemistry and physics and have the results of computational calculations returned in a comprehensible form alongside articles from the published literature.

From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language

PubMed Central

2013-01-01

Background Multidisciplinary integrated research requires the ability to couple the diverse sets of data obtained from a range of complex experiments and computer simulations. Integrating data requires semantically rich information. In this paper an end-to-end use of semantically rich data in computational chemistry is demonstrated utilizing the Chemical Markup Language (CML) framework. Semantically rich data is generated by the NWChem computational chemistry software with the FoX library and utilized by the Avogadro molecular editor for analysis and visualization. Results The NWChem computational chemistry software has been modified and coupled to the FoX library to write CML compliant XML data files. The FoX library was expanded to represent the lexical input files and molecular orbitals used by the computational chemistry software. Draft dictionary entries and a format for molecular orbitals within CML CompChem were developed. The Avogadro application was extended to read in CML data, and display molecular geometry and electronic structure in the GUI allowing for an end-to-end solution where Avogadro can create input structures, generate input files, NWChem can run the calculation and Avogadro can then read in and analyse the CML output produced. The developments outlined in this paper will be made available in future releases of NWChem, FoX, and Avogadro. Conclusions The production of CML compliant XML files for computational chemistry software such as NWChem can be accomplished relatively easily using the FoX library. The CML data can be read in by a newly developed reader in Avogadro and analysed or visualized in various ways. A community-based effort is needed to further develop the CML CompChem convention and dictionary. This will enable the long-term goal of allowing a researcher to run simple “Google-style” searches of chemistry and physics and have the results of computational calculations returned in a comprehensible form alongside articles from the published literature. PMID:23705910

State-of-the-Art Resources (SOAR) for Software Vulnerability Detection, Test, and Evaluation

DTIC Science & Technology

2014-07-01

preclude in-depth analysis, and widespread use of a Software -as-a- Service ( SaaS ) model that limits data availability and application to DoD systems...provide mobile application analysis using a Software - as-a- Service ( SaaS ) model. In this case, any software to be analyzed must be sent to the...tools are only available through a SaaS model. The widespread use of a Software -as-a- Service ( SaaS ) model as a sole evaluation model limits data

RealityConvert: a tool for preparing 3D models of biochemical structures for augmented and virtual reality.

PubMed

Borrel, Alexandre; Fourches, Denis

2017-12-01

There is a growing interest for the broad use of Augmented Reality (AR) and Virtual Reality (VR) in the fields of bioinformatics and cheminformatics to visualize complex biological and chemical structures. AR and VR technologies allow for stunning and immersive experiences, offering untapped opportunities for both research and education purposes. However, preparing 3D models ready to use for AR and VR is time-consuming and requires a technical expertise that severely limits the development of new contents of potential interest for structural biologists, medicinal chemists, molecular modellers and teachers. Herein we present the RealityConvert software tool and associated website, which allow users to easily convert molecular objects to high quality 3D models directly compatible for AR and VR applications. For chemical structures, in addition to the 3D model generation, RealityConvert also generates image trackers, useful to universally call and anchor that particular 3D model when used in AR applications. The ultimate goal of RealityConvert is to facilitate and boost the development and accessibility of AR and VR contents for bioinformatics and cheminformatics applications. http://www.realityconvert.com. dfourch@ncsu.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

A UML-based metamodel for software evolution process

NASA Astrophysics Data System (ADS)

Jiang, Zuo; Zhou, Wei-Hong; Fu, Zhi-Tao; Xiong, Shun-Qing

2014-04-01

A software evolution process is a set of interrelated software processes under which the corresponding software is evolving. An object-oriented software evolution process meta-model (OO-EPMM), abstract syntax and formal OCL constraint of meta-model are presented in this paper. OO-EPMM can not only represent software development process, but also represent software evolution.

Compiler-aided systematic construction of large-scale DNA strand displacement circuits using unpurified components

NASA Astrophysics Data System (ADS)

Thubagere, Anupama J.; Thachuk, Chris; Berleant, Joseph; Johnson, Robert F.; Ardelean, Diana A.; Cherry, Kevin M.; Qian, Lulu

2017-02-01

Biochemical circuits made of rationally designed DNA molecules are proofs of concept for embedding control within complex molecular environments. They hold promise for transforming the current technologies in chemistry, biology, medicine and material science by introducing programmable and responsive behaviour to diverse molecular systems. As the transformative power of a technology depends on its accessibility, two main challenges are an automated design process and simple experimental procedures. Here we demonstrate the use of circuit design software, combined with the use of unpurified strands and simplified experimental procedures, for creating a complex DNA strand displacement circuit that consists of 78 distinct species. We develop a systematic procedure for overcoming the challenges involved in using unpurified DNA strands. We also develop a model that takes synthesis errors into consideration and semi-quantitatively reproduces the experimental data. Our methods now enable even novice researchers to successfully design and construct complex DNA strand displacement circuits.

Virtual Design of a 4-Bed Molecular Sieve for Exploration

NASA Technical Reports Server (NTRS)

Giesy, Timothy J.; Coker, Robert F.; O'Connor, Brian F.; Knox, James C.

2017-01-01

Simulations of six new 4-Bed Molecular Sieve configurations have been performed using a COMSOL (COMSOL Multiphysics - commercial software) model. The preliminary results show that reductions in desiccant bed size and sorbent bed size when compared to the International Space Station configuration are feasible while still yielding a process that handles at least 4.0 kilograms a day CO2. The results also show that changes to the CO2 sorbent are likewise feasible. Decreasing the bed sizes was found to have very little negative effect on the adsorption process; breakthrough of CO2 in the sorbent bed was observed for two of the configurations, but a small degree of CO2 breakthrough is acceptable, and water breakthrough in the desiccant beds was not observed. Both configurations for which CO2 breakthrough was observed still yield relatively high CO2 efficiency, and future investigations will focus on bed size in order to find the optimum configuration.

Optimisation of the synthesis of vancomycin-selective molecularly imprinted polymer nanoparticles using automatic photoreactor

PubMed Central

2014-01-01

A novel optimized protocol for solid-state synthesis of molecularly imprinted polymer nanoparticles (nanoMIPs) with specificity for antibiotic vancomycin is described. The experimental objective was optimization of the synthesis parameters (factors) affecting the yield of obtained nanoparticles which have been synthesized using the first prototype of an automated solid-phase synthesizer. Applications of experimental design (or design of experiments) in optimization of nanoMIP yield were carried out using MODDE 9.0 software. The factors chosen in the model were the amount of functional monomers in the polymerization mixture, irradiation time, temperature during polymerization, and elution temperature. In general, it could be concluded that the irradiation time is the most important and the temperature was the least important factor which influences the yield of nanoparticles. Overall, the response surface methodology proved to be an effective tool in reducing time required for optimization of complex experimental conditions. PMID:24685151

Optimisation of the synthesis of vancomycin-selective molecularly imprinted polymer nanoparticles using automatic photoreactor.

PubMed

Muzyka, Kateryna; Karim, Khalku; Guerreiro, Antonio; Poma, Alessandro; Piletsky, Sergey

2014-03-31

A novel optimized protocol for solid-state synthesis of molecularly imprinted polymer nanoparticles (nanoMIPs) with specificity for antibiotic vancomycin is described. The experimental objective was optimization of the synthesis parameters (factors) affecting the yield of obtained nanoparticles which have been synthesized using the first prototype of an automated solid-phase synthesizer. Applications of experimental design (or design of experiments) in optimization of nanoMIP yield were carried out using MODDE 9.0 software. The factors chosen in the model were the amount of functional monomers in the polymerization mixture, irradiation time, temperature during polymerization, and elution temperature. In general, it could be concluded that the irradiation time is the most important and the temperature was the least important factor which influences the yield of nanoparticles. Overall, the response surface methodology proved to be an effective tool in reducing time required for optimization of complex experimental conditions.

Optimisation of the synthesis of vancomycin-selective molecularly imprinted polymer nanoparticles using automatic photoreactor

NASA Astrophysics Data System (ADS)

Muzyka, Kateryna; Karim, Khalku; Guerreiro, Antonio; Poma, Alessandro; Piletsky, Sergey

2014-03-01

A novel optimized protocol for solid-state synthesis of molecularly imprinted polymer nanoparticles (nanoMIPs) with specificity for antibiotic vancomycin is described. The experimental objective was optimization of the synthesis parameters (factors) affecting the yield of obtained nanoparticles which have been synthesized using the first prototype of an automated solid-phase synthesizer. Applications of experimental design (or design of experiments) in optimization of nanoMIP yield were carried out using MODDE 9.0 software. The factors chosen in the model were the amount of functional monomers in the polymerization mixture, irradiation time, temperature during polymerization, and elution temperature. In general, it could be concluded that the irradiation time is the most important and the temperature was the least important factor which influences the yield of nanoparticles. Overall, the response surface methodology proved to be an effective tool in reducing time required for optimization of complex experimental conditions.

T.D.S. spectroscopic databank for spherical tops: DOS version

NASA Astrophysics Data System (ADS)

Tyuterev, V. G.; Babikov, Yu. L.; Tashkun, S. A.; Perevalov, V. I.; Nikitin, A.; Champion, J.-P.; Wenger, C.; Pierre, C.; Pierre, G.; Hilico, J.-C.; Loete, M.

1994-10-01

T.D.S. (Traitement de Donnees Spectroscopiques or Tomsk-Dijon-Spectroscopy project) is a computer package concerned with high resolution spectroscopy of spherical top molecules like CH4, CF4, SiH4, SiF4, SnH4, GeH4, SF6, etc. T.D.S. contains information, fundamental spectroscopic data (energies, transition moments, spectroscopic constants) recovered from comprehensive modeling and simultaneous fitting of experimental spectra, and associated software written in C. The T.D.S. goal is to provide an access to all available information on vibration-rotation molecular states and transitions including various spectroscopic processes (Stark, Raman, etc.) under extended conditions based on extrapolations of laboratory measurements using validated theoretical models. Applications for T.D.S. may include: education/training in molecular physics, quantum chemistry, laser physics; spectroscopic applications (analysis, laser spectroscopy, atmospheric optics, optical standards, spectroscopic atlases); applications to environment studies and atmospheric physics (remote sensing); data supply for specific databases; and to photochemistry (laser excitation, multiphoton processes). The reported DOS-version is designed for IBM and compatible personal computers.

Structural models of antibody variable fragments: A method for investigating binding mechanisms

NASA Astrophysics Data System (ADS)

Petit, Samuel; Brard, Frédéric; Coquerel, Gérard; Perez, Guy; Tron, François

1998-03-01

The value of comparative molecular modeling for elucidating structure-function relationships was demonstrated by analyzing six anti-nucleosome autoantibody variable fragments. Structural models were built using the automated procedure developed in the COMPOSER software, subsequently minimized with the AMBER force field, and validated according to several standard geometric and chemical criteria. Canonical class assignment from Chothia and Lesk's [Chottin and Lesk, J. Mol. Biol., 196 (1987) 901; Chothia et al., Nature, 342 (1989) 877] work was used as a supplementary validation tool for five of the six hypervariable loops. The analysis, based on the hypothesis that antigen binding could occur through electrostatic interactions, reveals a diversity of possible binding mechanisms of anti-nucleosome or anti-histone antibodies to their cognate antigen. These results lead us to postulate that anti-nucleosome autoantibodies could have different origins. Since both anti-DNA and anti-nculeosome autoantibodies are produced during the course of systemic lupus erythematosus, a non-organ specific autoimmune disease, a comparative structural and electrostatic analysis of the two populations of autoantibodies may constitute a way to elucidate their origin and the role of the antigen in tolerance breakdown. The present study illustrates some interests, advantages and limits of a methodology based on the use of comparative modeling and analysis of molecular surface properties.

SBION: A Program for Analyses of Salt-Bridges from Multiple Structure Files.

PubMed

Gupta, Parth Sarthi Sen; Mondal, Sudipta; Mondal, Buddhadev; Islam, Rifat Nawaz Ul; Banerjee, Shyamashree; Bandyopadhyay, Amal K

2014-01-01

Salt-bridge and network salt-bridge are specific electrostatic interactions that contribute to the overall stability of proteins. In hierarchical protein folding model, these interactions play crucial role in nucleation process. The advent and growth of protein structure database and its availability in public domain made an urgent need for context dependent rapid analysis of salt-bridges. While these analyses on single protein is cumbersome and time-consuming, batch analyses need efficient software for rapid topological scan of a large number of protein for extracting details on (i) fraction of salt-bridge residues (acidic and basic). (ii) Chain specific intra-molecular salt-bridges, (iii) inter-molecular salt-bridges (protein-protein interactions) in all possible binary combinations (iv) network salt-bridges and (v) secondary structure distribution of salt-bridge residues. To the best of our knowledge, such efficient software is not available in public domain. At this juncture, we have developed a program i.e. SBION which can perform all the above mentioned computations for any number of protein with any number of chain at any given distance of ion-pair. It is highly efficient, fast, error-free and user friendly. Finally we would say that our SBION indeed possesses potential for applications in the field of structural and comparative bioinformatics studies. SBION is freely available for non-commercial/academic institutions on formal request to the corresponding author (akbanerjee@biotech.buruniv.ac.in).

mdFoam+: Advanced molecular dynamics in OpenFOAM

NASA Astrophysics Data System (ADS)

Longshaw, S. M.; Borg, M. K.; Ramisetti, S. B.; Zhang, J.; Lockerby, D. A.; Emerson, D. R.; Reese, J. M.

2018-03-01

This paper introduces mdFoam+, which is an MPI parallelised molecular dynamics (MD) solver implemented entirely within the OpenFOAM software framework. It is open-source and released under the same GNU General Public License (GPL) as OpenFOAM. The source code is released as a publicly open software repository that includes detailed documentation and tutorial cases. Since mdFoam+ is designed entirely within the OpenFOAM C++ object-oriented framework, it inherits a number of key features. The code is designed for extensibility and flexibility, so it is aimed first and foremost as an MD research tool, in which new models and test cases can be developed and tested rapidly. Implementing mdFoam+ in OpenFOAM also enables easier development of hybrid methods that couple MD with continuum-based solvers. Setting up MD cases follows the standard OpenFOAM format, as mdFoam+ also relies upon the OpenFOAM dictionary-based directory structure. This ensures that useful pre- and post-processing capabilities provided by OpenFOAM remain available even though the fully Lagrangian nature of an MD simulation is not typical of most OpenFOAM applications. Results show that mdFoam+ compares well to another well-known MD code (e.g. LAMMPS) in terms of benchmark problems, although it also has additional functionality that does not exist in other open-source MD codes.

Maximum Entropy Discrimination Poisson Regression for Software Reliability Modeling.

PubMed

Chatzis, Sotirios P; Andreou, Andreas S

2015-11-01

Reliably predicting software defects is one of the most significant tasks in software engineering. Two of the major components of modern software reliability modeling approaches are: 1) extraction of salient features for software system representation, based on appropriately designed software metrics and 2) development of intricate regression models for count data, to allow effective software reliability data modeling and prediction. Surprisingly, research in the latter frontier of count data regression modeling has been rather limited. More specifically, a lack of simple and efficient algorithms for posterior computation has made the Bayesian approaches appear unattractive, and thus underdeveloped in the context of software reliability modeling. In this paper, we try to address these issues by introducing a novel Bayesian regression model for count data, based on the concept of max-margin data modeling, effected in the context of a fully Bayesian model treatment with simple and efficient posterior distribution updates. Our novel approach yields a more discriminative learning technique, making more effective use of our training data during model inference. In addition, it allows of better handling uncertainty in the modeled data, which can be a significant problem when the training data are limited. We derive elegant inference algorithms for our model under the mean-field paradigm and exhibit its effectiveness using the publicly available benchmark data sets.

A Combined Molecular Dynamics and Experimental Study of Doped Polypyrrole.

PubMed

Fonner, John M; Schmidt, Christine E; Ren, Pengyu

2010-10-01

Polypyrrole (PPy) is a biocompatible, electrically conductive polymer that has great potential for battery, sensor, and neural implant applications. Its amorphous structure and insolubility, however, limit the experimental techniques available to study its structure and properties at the atomic level. Previous theoretical studies of PPy in bulk are also scarce. Using ab initio calculations, we have constructed a molecular mechanics force field of chloride-doped PPy (PPyCl) and undoped PPy. This model has been designed to integrate into the OPLS force field, and parameters are available for the Gromacs and TINKER software packages. Molecular dynamics (MD) simulations of bulk PPy and PPyCl have been performed using this force field, and the effects of chain packing and electrostatic scaling on the bulk polymer density have been investigated. The density of flotation of PPyCl films has been measured experimentally. Amorphous X-ray diffraction of PPyCl was obtained and correlated with atomic structures sampled from MD simulations. The force field reported here is foundational for bridging the gap between experimental measurements and theoretical calculations for PPy based materials.

Enhancing in vivo tumor boundary delineation with structured illumination fluorescence molecular imaging and spatial gradient mapping

NASA Astrophysics Data System (ADS)

Sun, Jessica; Miller, Jessica P.; Hathi, Deep; Zhou, Haiying; Achilefu, Samuel; Shokeen, Monica; Akers, Walter J.

2016-08-01

Fluorescence imaging, in combination with tumor-avid near-infrared (NIR) fluorescent molecular probes, provides high specificity and sensitivity for cancer detection in preclinical animal models, and more recently, assistance during oncologic surgery. However, conventional camera-based fluorescence imaging techniques are heavily surface-weighted such that surface reflection from skin or other nontumor tissue and nonspecific fluorescence signals dominate, obscuring true cancer-specific signals and blurring tumor boundaries. To address this challenge, we applied structured illumination fluorescence molecular imaging (SIFMI) in live animals for automated subtraction of nonspecific surface signals to better delineate accumulation of an NIR fluorescent probe targeting α4β1 integrin in mice bearing subcutaneous plasma cell xenografts. SIFMI demonstrated a fivefold improvement in tumor-to-background contrast when compared with other full-field fluorescence imaging methods and required significantly reduced scanning time compared with diffuse optical spectroscopy imaging. Furthermore, the spatial gradient mapping enhanced highlighting of tumor boundaries. Through the relatively simple hardware and software modifications described, SIFMI can be integrated with clinical fluorescence imaging systems, enhancing intraoperative tumor boundary delineation from the uninvolved tissue.

Molecular dynamics study of mechanical properties of carbon nanotube reinforced aluminum composites

NASA Astrophysics Data System (ADS)

Srivastava, Ashish Kumar; Mokhalingam, A.; Singh, Akhileshwar; Kumar, Dinesh

2016-05-01

Atomistic simulations were conducted to estimate the effect of the carbon nanotube (CNT) reinforcement on the mechanical behavior of CNT-reinforced aluminum (Al) nanocomposite. The periodic system of CNT-Al nanocomposite was built and simulated using molecular dynamics (MD) software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator). The mechanical properties of the nanocomposite were investigated by the application of uniaxial load on one end of the representative volume element (RVE) and fixing the other end. The interactions between the atoms of Al were modeled using embedded atom method (EAM) potentials, whereas Adaptive Intermolecular Reactive Empirical Bond Order (AIREBO) potential was used for the interactions among carbon atoms and these pair potentials are coupled with the Lennard-Jones (LJ) potential. The results show that the incorporation of CNT into the Al matrix can increase the Young's modulus of the nanocomposite substantially. In the present case, i.e. for approximately 9 with % reinforcement of CNT can increase the axial Young's modulus of the Al matrix up to 77 % as compared to pure Al.

Modelling and Display of the Ultraviolet Sky

NASA Astrophysics Data System (ADS)

Daniels, J.; Henry, R.; Murthy, J.; Allen, M.; McGlynn, T. A.; Scollick, K.

1994-12-01

A computer program is currently under development to model in 3D - one dimension of which is wavelength - all the known and major speculated sources of ultraviolet (900 A - 3100 A ) radiation over the celestial sphere. The software is being written in Fortran 77 and IDL and currently operates under IRIX (the operating system of the Silicon Graphics Iris Machine); all output models are in FITS format. Models along with display software will become available to the astronomical community. The Ultraviolet Sky Model currently includes the Zodiacal Light, Point Sources of Emission, and the Diffuse Galactic Light. The Ultraviolet Sky Model is currently displayed using SkyView: a package under development at NASA/ GSFC, which allows users to retrieve and display publically available all-sky astronomical survey data (covering many wavebands) over the Internet. We present a demonstration of the SkyView display of the Ultraviolet Model. The modelling is a five year development project: the work illustrated here represents product output at the end of year one. Future work includes enhancements to the current models and incorporation of the following models: Galactic Molecular Hydrogen Fluorescence; Galactic Highly Ionized Atomic Line Emission; Integrated Extragalactic Light; and speculated sources in the intergalactic medium such as Ionized Plasma and radiation from Non-Baryonic Particle Decay. We also present a poster which summarizes the components of the Ultraviolet Sky Model and outlines a further package that will be used to display the Ultraviolet Model. This work is supported by United States Air Force Contract F19628-93-K-0004. Dr J. Daniels is supported with a post-doctoral Fellowship from the Leverhulme Foundation, London, United Kingdom. We are also grateful for the encouragement of Dr Stephen Price (Phillips Laboratory, Hanscomb Air Force Base, MA)

Virtual network computing: cross-platform remote display and collaboration software.

PubMed

Konerding, D E

1999-04-01

VNC (Virtual Network Computing) is a computer program written to address the problem of cross-platform remote desktop/application display. VNC uses a client/server model in which an image of the desktop of the server is transmitted to the client and displayed. The client collects mouse and keyboard input from the user and transmits them back to the server. The VNC client and server can run on Windows 95/98/NT, MacOS, and Unix (including Linux) operating systems. VNC is multi-user on Unix machines (any number of servers can be run are unrelated to the primary display of the computer), while it is effectively single-user on Macintosh and Windows machines (only one server can be run, displaying the contents of the primary display of the server). The VNC servers can be configured to allow more than one client to connect at one time, effectively allowing collaboration through the shared desktop. I describe the function of VNC, provide details of installation, describe how it achieves its goal, and evaluate the use of VNC for molecular modelling. VNC is an extremely useful tool for collaboration, instruction, software development, and debugging of graphical programs with remote users.

DnaSAM: Software to perform neutrality testing for large datasets with complex null models.

PubMed

Eckert, Andrew J; Liechty, John D; Tearse, Brandon R; Pande, Barnaly; Neale, David B

2010-05-01

Patterns of DNA sequence polymorphisms can be used to understand the processes of demography and adaptation within natural populations. High-throughput generation of DNA sequence data has historically been the bottleneck with respect to data processing and experimental inference. Advances in marker technologies have largely solved this problem. Currently, the limiting step is computational, with most molecular population genetic software allowing a gene-by-gene analysis through a graphical user interface. An easy-to-use analysis program that allows both high-throughput processing of multiple sequence alignments along with the flexibility to simulate data under complex demographic scenarios is currently lacking. We introduce a new program, named DnaSAM, which allows high-throughput estimation of DNA sequence diversity and neutrality statistics from experimental data along with the ability to test those statistics via Monte Carlo coalescent simulations. These simulations are conducted using the ms program, which is able to incorporate several genetic parameters (e.g. recombination) and demographic scenarios (e.g. population bottlenecks). The output is a set of diversity and neutrality statistics with associated probability values under a user-specified null model that are stored in easy to manipulate text file. © 2009 Blackwell Publishing Ltd.

Structure-activity relationships of cannabinoids: A joint CoMFA and pseudoreceptor modelling study

NASA Astrophysics Data System (ADS)

Schmetzer, Silke; Greenidge, Paulette; Kovar, Karl-Artur; Schulze-Alexandru, Meike; Folkers, Gerd

1997-05-01

A cannabinoid pseudoreceptor model for the CB1-receptor has been constructed for 31 cannabinoids using the molecular modelling software YAK. Additionally, two CoMFA studies were performed on these ligands, the first of which was conducted prior to the building of the pseudoreceptor. Its pharmacophore is identical with the initial superposition of ligands used for pseudoreceptor construction. In contrast, the ligand alignment for the second CoMFA study was taken directly from the final cannabinoid pseudoreceptor model. This altered alignment gives markedly improved cross-validated r2 values as compared to those obtained from the original alignment with{{r}}_{{{cross}}}^2 values of 0.79 and 0.63, respectively, for five components. However, the pharmacophore alignment has the better predictive ability. Both the CoMFA and pseudoreceptor methods predict the free energy of binding of test ligands well.

DOT2: Macromolecular Docking With Improved Biophysical Models

PubMed Central

Roberts, Victoria A.; Thompson, Elaine E.; Pique, Michael E.; Perez, Martin S.; Eyck, Lynn Ten

2015-01-01

Computational docking is a useful tool for predicting macromolecular complexes, which are often difficult to determine experimentally. Here we present the DOT2 software suite, an updated version of the DOT intermolecular docking program. DOT2 provides straightforward, automated construction of improved biophysical models based on molecular coordinates, offering checkpoints that guide the user to include critical features. DOT has been updated to run more quickly, allow flexibility in grid size and spacing, and generate a complete list of favorable candidate configu-rations. Output can be filtered by experimental data and rescored by the sum of electrostatic and atomic desolvation energies. We show that this rescoring method improves the ranking of correct complexes for a wide range of macromolecular interactions, and demonstrate that biologically relevant models are essential for biologically relevant results. The flexibility and versatility of DOT2 accommodate realistic models of complex biological systems, improving the likelihood of a successful docking outcome. PMID:23695987

Implicit solvation model for density-functional study of nanocrystal surfaces and reaction pathways

NASA Astrophysics Data System (ADS)

Mathew, Kiran; Sundararaman, Ravishankar; Letchworth-Weaver, Kendra; Arias, T. A.; Hennig, Richard G.

2014-02-01

Solid-liquid interfaces are at the heart of many modern-day technologies and provide a challenge to many materials simulation methods. A realistic first-principles computational study of such systems entails the inclusion of solvent effects. In this work, we implement an implicit solvation model that has a firm theoretical foundation into the widely used density-functional code Vienna ab initio Software Package. The implicit solvation model follows the framework of joint density functional theory. We describe the framework, our algorithm and implementation, and benchmarks for small molecular systems. We apply the solvation model to study the surface energies of different facets of semiconducting and metallic nanocrystals and the SN2 reaction pathway. We find that solvation reduces the surface energies of the nanocrystals, especially for the semiconducting ones and increases the energy barrier of the SN2 reaction.

A measurement system for large, complex software programs

NASA Technical Reports Server (NTRS)

Rone, Kyle Y.; Olson, Kitty M.; Davis, Nathan E.

1994-01-01

This paper describes measurement systems required to forecast, measure, and control activities for large, complex software development and support programs. Initial software cost and quality analysis provides the foundation for meaningful management decisions as a project evolves. In modeling the cost and quality of software systems, the relationship between the functionality, quality, cost, and schedule of the product must be considered. This explicit relationship is dictated by the criticality of the software being developed. This balance between cost and quality is a viable software engineering trade-off throughout the life cycle. Therefore, the ability to accurately estimate the cost and quality of software systems is essential to providing reliable software on time and within budget. Software cost models relate the product error rate to the percent of the project labor that is required for independent verification and validation. The criticality of the software determines which cost model is used to estimate the labor required to develop the software. Software quality models yield an expected error discovery rate based on the software size, criticality, software development environment, and the level of competence of the project and developers with respect to the processes being employed.

Teaching the Structure of Immunoglobulins by Molecular Visualization and SDS-PAGE Analysis

ERIC Educational Resources Information Center

Rižner, Tea Lanišnik

2014-01-01

This laboratory class combines molecular visualization and laboratory experimentation to teach the structure of the immunoglobulins (Ig). In the first part of the class, the three-dimensional structures of the human IgG and IgM molecules available through the RCSB PDB database are visualized using freely available software. In the second part, IgG…

[Relevance of big data for molecular diagnostics].

PubMed

Bonin-Andresen, M; Smiljanovic, B; Stuhlmüller, B; Sörensen, T; Grützkau, A; Häupl, T

2018-04-01

Big data analysis raises the expectation that computerized algorithms may extract new knowledge from otherwise unmanageable vast data sets. What are the algorithms behind the big data discussion? In principle, high throughput technologies in molecular research already introduced big data and the development and application of analysis tools into the field of rheumatology some 15 years ago. This includes especially omics technologies, such as genomics, transcriptomics and cytomics. Some basic methods of data analysis are provided along with the technology, however, functional analysis and interpretation requires adaptation of existing or development of new software tools. For these steps, structuring and evaluating according to the biological context is extremely important and not only a mathematical problem. This aspect has to be considered much more for molecular big data than for those analyzed in health economy or epidemiology. Molecular data are structured in a first order determined by the applied technology and present quantitative characteristics that follow the principles of their biological nature. These biological dependencies have to be integrated into software solutions, which may require networks of molecular big data of the same or even different technologies in order to achieve cross-technology confirmation. More and more extensive recording of molecular processes also in individual patients are generating personal big data and require new strategies for management in order to develop data-driven individualized interpretation concepts. With this perspective in mind, translation of information derived from molecular big data will also require new specifications for education and professional competence.

libFLASM: a software library for fixed-length approximate string matching.

PubMed

Ayad, Lorraine A K; Pissis, Solon P P; Retha, Ahmad

2016-11-10

Approximate string matching is the problem of finding all factors of a given text that are at a distance at most k from a given pattern. Fixed-length approximate string matching is the problem of finding all factors of a text of length n that are at a distance at most k from any factor of length ℓ of a pattern of length m. There exist bit-vector techniques to solve the fixed-length approximate string matching problem in time [Formula: see text] and space [Formula: see text] under the edit and Hamming distance models, where w is the size of the computer word; as such these techniques are independent of the distance threshold k or the alphabet size. Fixed-length approximate string matching is a generalisation of approximate string matching and, hence, has numerous direct applications in computational molecular biology and elsewhere. We present and make available libFLASM, a free open-source C++ software library for solving fixed-length approximate string matching under both the edit and the Hamming distance models. Moreover we describe how fixed-length approximate string matching is applied to solve real problems by incorporating libFLASM into established applications for multiple circular sequence alignment as well as single and structured motif extraction. Specifically, we describe how it can be used to improve the accuracy of multiple circular sequence alignment in terms of the inferred likelihood-based phylogenies; and we also describe how it is used to efficiently find motifs in molecular sequences representing regulatory or functional regions. The comparison of the performance of the library to other algorithms show how it is competitive, especially with increasing distance thresholds. Fixed-length approximate string matching is a generalisation of the classic approximate string matching problem. We present libFLASM, a free open-source C++ software library for solving fixed-length approximate string matching. The extensive experimental results presented here suggest that other applications could benefit from using libFLASM, and thus further maintenance and development of libFLASM is desirable.

ECUT (Energy Conversion and Utilization Technologies) program: Biocatalysis Project

NASA Technical Reports Server (NTRS)

1988-01-01

Fiscal year 1987 research activities and accomplishments for the Biocatalysis Project of the U.S. Department of Energy, Energy Conversion and Utilization Technologies (ECUT) Division are presented. The project's technical activities were organized into three work elements. The Molecular Modeling and Applied Genetics work element includes modeling and simulation studies to verify a dynamic model of the enzyme carboxypeptidase; plasmid stabilization by chromosomal integration; growth and stability characteristics of plasmid-containing cells; and determination of optional production parameters for hyper-production of polyphenol oxidase. The Bioprocess Engineering work element supports efforts in novel bioreactor concepts that are likely to lead to substantially higher levels of reactor productivity, product yields, and lower separation energetics. The Bioprocess Design and Assessment work element attempts to develop procedures (via user-friendly computer software) for assessing the economics and energetics of a given biocatalyst process.

cDF Theory Software for mesoscopic modeling of equilibrium and transport phenomena

DOE Office of Scientific and Technical Information (OSTI.GOV)

2015-12-01

The approach is based on classical Density Functional Theory ((cDFT) coupled with the Poisson-Nernst-Planck (PNP) transport kinetics model and quantum mechanical description of short-range interaction and elementary transport processes. The model we proposed and implemented is fully atomistic, taking into account pairwise short-range and manybody long-range interactions. But in contrast to standard molecular dynamics (MD) simulations, where long-range manybody interactions are evaluated as a sum of pair-wise atom-atom contributions, we include them analytically based on wellestablished theories of electrostatic and excluded volume interactions in multicomponent systems. This feature of the PNP/cDFT approach allows us to reach well beyond the length-scalesmore » accessible to MD simulations, while retaining the essential physics of interatomic interactions from first principles and in a parameter-free fashion.« less

WebSat--a web software for microsatellite marker development.

PubMed

Martins, Wellington Santos; Lucas, Divino César Soares; Neves, Kelligton Fabricio de Souza; Bertioli, David John

2009-01-01

Simple sequence repeats (SSR), also known as microsatellites, have been extensively used as molecular markers due to their abundance and high degree of polymorphism. We have developed a simple to use web software, called WebSat, for microsatellite molecular marker prediction and development. WebSat is accessible through the Internet, requiring no program installation. Although a web solution, it makes use of Ajax techniques, providing a rich, responsive user interface. WebSat allows the submission of sequences, visualization of microsatellites and the design of primers suitable for their amplification. The program allows full control of parameters and the easy export of the resulting data, thus facilitating the development of microsatellite markers. The web tool may be accessed at http://purl.oclc.org/NET/websat/

Dependability modeling and assessment in UML-based software development.

PubMed

Bernardi, Simona; Merseguer, José; Petriu, Dorina C

2012-01-01

Assessment of software nonfunctional properties (NFP) is an important problem in software development. In the context of model-driven development, an emerging approach for the analysis of different NFPs consists of the following steps: (a) to extend the software models with annotations describing the NFP of interest; (b) to transform automatically the annotated software model to the formalism chosen for NFP analysis; (c) to analyze the formal model using existing solvers; (d) to assess the software based on the results and give feedback to designers. Such a modeling→analysis→assessment approach can be applied to any software modeling language, be it general purpose or domain specific. In this paper, we focus on UML-based development and on the dependability NFP, which encompasses reliability, availability, safety, integrity, and maintainability. The paper presents the profile used to extend UML with dependability information, the model transformation to generate a DSPN formal model, and the assessment of the system properties based on the DSPN results.

Dependability Modeling and Assessment in UML-Based Software Development

PubMed Central

Bernardi, Simona; Merseguer, José; Petriu, Dorina C.

2012-01-01

Assessment of software nonfunctional properties (NFP) is an important problem in software development. In the context of model-driven development, an emerging approach for the analysis of different NFPs consists of the following steps: (a) to extend the software models with annotations describing the NFP of interest; (b) to transform automatically the annotated software model to the formalism chosen for NFP analysis; (c) to analyze the formal model using existing solvers; (d) to assess the software based on the results and give feedback to designers. Such a modeling→analysis→assessment approach can be applied to any software modeling language, be it general purpose or domain specific. In this paper, we focus on UML-based development and on the dependability NFP, which encompasses reliability, availability, safety, integrity, and maintainability. The paper presents the profile used to extend UML with dependability information, the model transformation to generate a DSPN formal model, and the assessment of the system properties based on the DSPN results. PMID:22988428

Software reliability models for fault-tolerant avionics computers and related topics

NASA Technical Reports Server (NTRS)

Miller, Douglas R.

1987-01-01

Software reliability research is briefly described. General research topics are reliability growth models, quality of software reliability prediction, the complete monotonicity property of reliability growth, conceptual modelling of software failure behavior, assurance of ultrahigh reliability, and analysis techniques for fault-tolerant systems.

TANDEM: a two-stage approach to maximize interpretability of drug response models based on multiple molecular data types.

PubMed

Aben, Nanne; Vis, Daniel J; Michaut, Magali; Wessels, Lodewyk F A

2016-09-01

Clinical response to anti-cancer drugs varies between patients. A large portion of this variation can be explained by differences in molecular features, such as mutation status, copy number alterations, methylation and gene expression profiles. We show that the classic approach for combining these molecular features (Elastic Net regression on all molecular features simultaneously) results in models that are almost exclusively based on gene expression. The gene expression features selected by the classic approach are difficult to interpret as they often represent poorly studied combinations of genes, activated by aberrations in upstream signaling pathways. To utilize all data types in a more balanced way, we developed TANDEM, a two-stage approach in which the first stage explains response using upstream features (mutations, copy number, methylation and cancer type) and the second stage explains the remainder using downstream features (gene expression). Applying TANDEM to 934 cell lines profiled across 265 drugs (GDSC1000), we show that the resulting models are more interpretable, while retaining the same predictive performance as the classic approach. Using the more balanced contributions per data type as determined with TANDEM, we find that response to MAPK pathway inhibitors is largely predicted by mutation data, while predicting response to DNA damaging agents requires gene expression data, in particular SLFN11 expression. TANDEM is available as an R package on CRAN (for more information, see http://ccb.nki.nl/software/tandem). m.michaut@nki.nl or l.wessels@nki.nl Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Protocols for Molecular Modeling with Rosetta3 and RosettaScripts

PubMed Central

2016-01-01

Previously, we published an article providing an overview of the Rosetta suite of biomacromolecular modeling software and a series of step-by-step tutorials [Kaufmann, K. W., et al. (2010) Biochemistry 49, 2987–2998]. The overwhelming positive response to this publication we received motivates us to here share the next iteration of these tutorials that feature de novo folding, comparative modeling, loop construction, protein docking, small molecule docking, and protein design. This updated and expanded set of tutorials is needed, as since 2010 Rosetta has been fully redesigned into an object-oriented protein modeling program Rosetta3. Notable improvements include a substantially improved energy function, an XML-like language termed “RosettaScripts” for flexibly specifying modeling task, new analysis tools, the addition of the TopologyBroker to control conformational sampling, and support for multiple templates in comparative modeling. Rosetta’s ability to model systems with symmetric proteins, membrane proteins, noncanonical amino acids, and RNA has also been greatly expanded and improved. PMID:27490953

Developing a physiologically based approach for modeling plutonium decorporation therapy with DTPA.

PubMed

Kastl, Manuel; Giussani, Augusto; Blanchardon, Eric; Breustedt, Bastian; Fritsch, Paul; Hoeschen, Christoph; Lopez, Maria Antonia

2014-11-01

To develop a physiologically based compartmental approach for modeling plutonium decorporation therapy with the chelating agent Diethylenetriaminepentaacetic acid (Ca-DTPA/Zn-DTPA). Model calculations were performed using the software package SAAM II (©The Epsilon Group, Charlottesville, Virginia, USA). The Luciani/Polig compartmental model with age-dependent description of the bone recycling processes was used for the biokinetics of plutonium. The Luciani/Polig model was slightly modified in order to account for the speciation of plutonium in blood and for the different affinities for DTPA of the present chemical species. The introduction of two separate blood compartments, describing low-molecular-weight complexes of plutonium (Pu-LW) and transferrin-bound plutonium (Pu-Tf), respectively, and one additional compartment describing plutonium in the interstitial fluids was performed successfully. The next step of the work is the modeling of the chelation process, coupling the physiologically modified structure with the biokinetic model for DTPA. RESULTS of animal studies performed under controlled conditions will enable to better understand the principles of the involved mechanisms.

Software For Computing Reliability Of Other Software

NASA Technical Reports Server (NTRS)

Nikora, Allen; Antczak, Thomas M.; Lyu, Michael

1995-01-01

Computer Aided Software Reliability Estimation (CASRE) computer program developed for use in measuring reliability of other software. Easier for non-specialists in reliability to use than many other currently available programs developed for same purpose. CASRE incorporates mathematical modeling capabilities of public-domain Statistical Modeling and Estimation of Reliability Functions for Software (SMERFS) computer program and runs in Windows software environment. Provides menu-driven command interface; enabling and disabling of menu options guides user through (1) selection of set of failure data, (2) execution of mathematical model, and (3) analysis of results from model. Written in C language.

Software-Engineering Process Simulation (SEPS) model

NASA Technical Reports Server (NTRS)

Lin, C. Y.; Abdel-Hamid, T.; Sherif, J. S.

1992-01-01

The Software Engineering Process Simulation (SEPS) model is described which was developed at JPL. SEPS is a dynamic simulation model of the software project development process. It uses the feedback principles of system dynamics to simulate the dynamic interactions among various software life cycle development activities and management decision making processes. The model is designed to be a planning tool to examine tradeoffs of cost, schedule, and functionality, and to test the implications of different managerial policies on a project's outcome. Furthermore, SEPS will enable software managers to gain a better understanding of the dynamics of software project development and perform postmodern assessments.

A Chado case study: an ontology-based modular schema for representing genome-associated biological information.

PubMed

Mungall, Christopher J; Emmert, David B

2007-07-01

A few years ago, FlyBase undertook to design a new database schema to store Drosophila data. It would fully integrate genomic sequence and annotation data with bibliographic, genetic, phenotypic and molecular data from the literature representing a distillation of the first 100 years of research on this major animal model system. In developing this new integrated schema, FlyBase also made a commitment to ensure that its design was generic, extensible and available as open source, so that it could be employed as the core schema of any model organism data repository, thereby avoiding redundant software development and potentially increasing interoperability. Our question was whether we could create a relational database schema that would be successfully reused. Chado is a relational database schema now being used to manage biological knowledge for a wide variety of organisms, from human to pathogens, especially the classes of information that directly or indirectly can be associated with genome sequences or the primary RNA and protein products encoded by a genome. Biological databases that conform to this schema can interoperate with one another, and with application software from the Generic Model Organism Database (GMOD) toolkit. Chado is distinctive because its design is driven by ontologies. The use of ontologies (or controlled vocabularies) is ubiquitous across the schema, as they are used as a means of typing entities. The Chado schema is partitioned into integrated subschemas (modules), each encapsulating a different biological domain, and each described using representations in appropriate ontologies. To illustrate this methodology, we describe here the Chado modules used for describing genomic sequences. GMOD is a collaboration of several model organism database groups, including FlyBase, to develop a set of open-source software for managing model organism data. The Chado schema is freely distributed under the terms of the Artistic License (http://www.opensource.org/licenses/artistic-license.php) from GMOD (www.gmod.org).

Software Quality Evaluation Models Applicable in Health Information and Communications Technologies. A Review of the Literature.

PubMed

Villamor Ordozgoiti, Alberto; Delgado Hito, Pilar; Guix Comellas, Eva María; Fernandez Sanchez, Carlos Manuel; Garcia Hernandez, Milagros; Lluch Canut, Teresa

2016-01-01

Information and Communications Technologies in healthcare has increased the need to consider quality criteria through standardised processes. The aim of this study was to analyse the software quality evaluation models applicable to healthcare from the perspective of ICT-purchasers. Through a systematic literature review with the keywords software, product, quality, evaluation and health, we selected and analysed 20 original research papers published from 2005-2016 in health science and technology databases. The results showed four main topics: non-ISO models, software quality evaluation models based on ISO/IEC standards, studies analysing software quality evaluation models, and studies analysing ISO standards for software quality evaluation. The models provide cost-efficiency criteria for specific software, and improve use outcomes. The ISO/IEC25000 standard is shown as the most suitable for evaluating the quality of ICTs for healthcare use from the perspective of institutional acquisition.

Haplotag: Software for Haplotype-Based Genotyping-by-Sequencing Analysis

PubMed Central

Tinker, Nicholas A.; Bekele, Wubishet A.; Hattori, Jiro

2016-01-01

Genotyping-by-sequencing (GBS), and related methods, are based on high-throughput short-read sequencing of genomic complexity reductions followed by discovery of single nucleotide polymorphisms (SNPs) within sequence tags. This provides a powerful and economical approach to whole-genome genotyping, facilitating applications in genomics, diversity analysis, and molecular breeding. However, due to the complexity of analyzing large data sets, applications of GBS may require substantial time, expertise, and computational resources. Haplotag, the novel GBS software described here, is freely available, and operates with minimal user-investment on widely available computer platforms. Haplotag is unique in fulfilling the following set of criteria: (1) operates without a reference genome; (2) can be used in a polyploid species; (3) provides a discovery mode, and a production mode; (4) discovers polymorphisms based on a model of tag-level haplotypes within sequenced tags; (5) reports SNPs as well as haplotype-based genotypes; and (6) provides an intuitive visual “passport” for each inferred locus. Haplotag is optimized for use in a self-pollinating plant species. PMID:26818073

Choosing a genome browser for a Model Organism Database: surveying the Maize community

PubMed Central

Sen, Taner Z.; Harper, Lisa C.; Schaeffer, Mary L.; Andorf, Carson M.; Seigfried, Trent E.; Campbell, Darwin A.; Lawrence, Carolyn J.

2010-01-01

As the B73 maize genome sequencing project neared completion, MaizeGDB began to integrate a graphical genome browser with its existing web interface and database. To ensure that maize researchers would optimally benefit from the potential addition of a genome browser to the existing MaizeGDB resource, personnel at MaizeGDB surveyed researchers’ needs. Collected data indicate that existing genome browsers for maize were inadequate and suggest implementation of a browser with quick interface and intuitive tools would meet most researchers’ needs. Here, we document the survey’s outcomes, review functionalities of available genome browser software platforms and offer our rationale for choosing the GBrowse software suite for MaizeGDB. Because the genome as represented within the MaizeGDB Genome Browser is tied to detailed phenotypic data, molecular marker information, available stocks, etc., the MaizeGDB Genome Browser represents a novel mechanism by which the researchers can leverage maize sequence information toward crop improvement directly. Database URL: http://gbrowse.maizegdb.org/ PMID:20627860

A Semantic Web Management Model for Integrative Biomedical Informatics

PubMed Central

Deus, Helena F.; Stanislaus, Romesh; Veiga, Diogo F.; Behrens, Carmen; Wistuba, Ignacio I.; Minna, John D.; Garner, Harold R.; Swisher, Stephen G.; Roth, Jack A.; Correa, Arlene M.; Broom, Bradley; Coombes, Kevin; Chang, Allen; Vogel, Lynn H.; Almeida, Jonas S.

2008-01-01

Background Data, data everywhere. The diversity and magnitude of the data generated in the Life Sciences defies automated articulation among complementary efforts. The additional need in this field for managing property and access permissions compounds the difficulty very significantly. This is particularly the case when the integration involves multiple domains and disciplines, even more so when it includes clinical and high throughput molecular data. Methodology/Principal Findings The emergence of Semantic Web technologies brings the promise of meaningful interoperation between data and analysis resources. In this report we identify a core model for biomedical Knowledge Engineering applications and demonstrate how this new technology can be used to weave a management model where multiple intertwined data structures can be hosted and managed by multiple authorities in a distributed management infrastructure. Specifically, the demonstration is performed by linking data sources associated with the Lung Cancer SPORE awarded to The University of Texas MDAnderson Cancer Center at Houston and the Southwestern Medical Center at Dallas. A software prototype, available with open source at www.s3db.org, was developed and its proposed design has been made publicly available as an open source instrument for shared, distributed data management. Conclusions/Significance The Semantic Web technologies have the potential to addresses the need for distributed and evolvable representations that are critical for systems Biology and translational biomedical research. As this technology is incorporated into application development we can expect that both general purpose productivity software and domain specific software installed on our personal computers will become increasingly integrated with the relevant remote resources. In this scenario, the acquisition of a new dataset should automatically trigger the delegation of its analysis. PMID:18698353

BRIDG: a domain information model for translational and clinical protocol-driven research.

PubMed

Becnel, Lauren B; Hastak, Smita; Ver Hoef, Wendy; Milius, Robert P; Slack, MaryAnn; Wold, Diane; Glickman, Michael L; Brodsky, Boris; Jaffe, Charles; Kush, Rebecca; Helton, Edward

2017-09-01

It is critical to integrate and analyze data from biological, translational, and clinical studies with data from health systems; however, electronic artifacts are stored in thousands of disparate systems that are often unable to readily exchange data. To facilitate meaningful data exchange, a model that presents a common understanding of biomedical research concepts and their relationships with health care semantics is required. The Biomedical Research Integrated Domain Group (BRIDG) domain information model fulfills this need. Software systems created from BRIDG have shared meaning "baked in," enabling interoperability among disparate systems. For nearly 10 years, the Clinical Data Standards Interchange Consortium, the National Cancer Institute, the US Food and Drug Administration, and Health Level 7 International have been key stakeholders in developing BRIDG. BRIDG is an open-source Unified Modeling Language-class model developed through use cases and harmonization with other models. With its 4+ releases, BRIDG includes clinical and now translational research concepts in its Common, Protocol Representation, Study Conduct, Adverse Events, Regulatory, Statistical Analysis, Experiment, Biospecimen, and Molecular Biology subdomains. The model is a Clinical Data Standards Interchange Consortium, Health Level 7 International, and International Standards Organization standard that has been utilized in national and international standards-based software development projects. It will continue to mature and evolve in the areas of clinical imaging, pathology, ontology, and vocabulary support. BRIDG 4.1.1 and prior releases are freely available at https://bridgmodel.nci.nih.gov . © The Author 2017. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com

TriBITS lifecycle model. Version 1.0, a lean/agile software lifecycle model for research-based computational science and engineering and applied mathematical software.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Willenbring, James M.; Bartlett, Roscoe Ainsworth; Heroux, Michael Allen

2012-01-01

Software lifecycles are becoming an increasingly important issue for computational science and engineering (CSE) software. The process by which a piece of CSE software begins life as a set of research requirements and then matures into a trusted high-quality capability is both commonplace and extremely challenging. Although an implicit lifecycle is obviously being used in any effort, the challenges of this process - respecting the competing needs of research vs. production - cannot be overstated. Here we describe a proposal for a well-defined software lifecycle process based on modern Lean/Agile software engineering principles. What we propose is appropriate for manymore » CSE software projects that are initially heavily focused on research but also are expected to eventually produce usable high-quality capabilities. The model is related to TriBITS, a build, integration and testing system, which serves as a strong foundation for this lifecycle model, and aspects of this lifecycle model are ingrained in the TriBITS system. Here, we advocate three to four phases or maturity levels that address the appropriate handling of many issues associated with the transition from research to production software. The goals of this lifecycle model are to better communicate maturity levels with customers and to help to identify and promote Software Engineering (SE) practices that will help to improve productivity and produce better software. An important collection of software in this domain is Trilinos, which is used as the motivation and the initial target for this lifecycle model. However, many other related and similar CSE (and non-CSE) software projects can also make good use of this lifecycle model, especially those that use the TriBITS system. Indeed this lifecycle process, if followed, will enable large-scale sustainable integration of many complex CSE software efforts across several institutions.« less

Model based on GRID-derived descriptors for estimating CYP3A4 enzyme stability of potential drug candidates

NASA Astrophysics Data System (ADS)

Crivori, Patrizia; Zamora, Ismael; Speed, Bill; Orrenius, Christian; Poggesi, Italo

2004-03-01

A number of computational approaches are being proposed for an early optimization of ADME (absorption, distribution, metabolism and excretion) properties to increase the success rate in drug discovery. The present study describes the development of an in silico model able to estimate, from the three-dimensional structure of a molecule, the stability of a compound with respect to the human cytochrome P450 (CYP) 3A4 enzyme activity. Stability data were obtained by measuring the amount of unchanged compound remaining after a standardized incubation with human cDNA-expressed CYP3A4. The computational method transforms the three-dimensional molecular interaction fields (MIFs) generated from the molecular structure into descriptors (VolSurf and Almond procedures). The descriptors were correlated to the experimental metabolic stability classes by a partial least squares discriminant procedure. The model was trained using a set of 1800 compounds from the Pharmacia collection and was validated using two test sets: the first one including 825 compounds from the Pharmacia collection and the second one consisting of 20 known drugs. This model correctly predicted 75% of the first and 85% of the second test set and showed a precision above 86% to correctly select metabolically stable compounds. The model appears a valuable tool in the design of virtual libraries to bias the selection toward more stable compounds. Abbreviations: ADME - absorption, distribution, metabolism and excretion; CYP - cytochrome P450; MIFs - molecular interaction fields; HTS - high throughput screening; DDI - drug-drug interactions; 3D - three-dimensional; PCA - principal components analysis; CPCA - consensus principal components analysis; PLS - partial least squares; PLSD - partial least squares discriminant; GRIND - grid independent descriptors; GRID - software originally created and developed by Professor Peter Goodford.

Toxicity prediction of ionic liquids based on Daphnia magna by using density functional theory

NASA Astrophysics Data System (ADS)

Nu’aim, M. N.; Bustam, M. A.

2018-04-01

By using a model called density functional theory, the toxicity of ionic liquids can be predicted and forecast. It is a theory that allowing the researcher to have a substantial tool for computation of the quantum state of atoms, molecules and solids, and molecular dynamics which also known as computer simulation method. It can be done by using structural feature based quantum chemical reactivity descriptor. The identification of ionic liquids and its Log[EC50] data are from literature data that available in Ismail Hossain thesis entitled “Synthesis, Characterization and Quantitative Structure Toxicity Relationship of Imidazolium, Pyridinium and Ammonium Based Ionic Liquids”. Each cation and anion of the ionic liquids were optimized and calculated. The geometry optimization and calculation from the software, produce the value of highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO). From the value of HOMO and LUMO, the value for other toxicity descriptors were obtained according to their formulas. The toxicity descriptor that involves are electrophilicity index, HOMO, LUMO, energy gap, chemical potential, hardness and electronegativity. The interrelation between the descriptors are being determined by using a multiple linear regression (MLR). From this MLR, all descriptors being analyzed and the descriptors that are significant were chosen. In order to develop the finest model equation for toxicity prediction of ionic liquids, the selected descriptors that are significant were used. The validation of model equation was performed with the Log[EC50] data from the literature and the final model equation was developed. A bigger range of ionic liquids which nearly 108 of ionic liquids can be predicted from this model equation.

Deep space network software cost estimation model

NASA Technical Reports Server (NTRS)

Tausworthe, R. C.

1981-01-01

A parametric software cost estimation model prepared for Jet PRopulsion Laboratory (JPL) Deep Space Network (DSN) Data System implementation tasks is described. The resource estimation mdel modifies and combines a number of existing models. The model calibrates the task magnitude and difficulty, development environment, and software technology effects through prompted responses to a set of approximately 50 questions. Parameters in the model are adjusted to fit JPL software life-cycle statistics.

MD Simulations of P-Type ATPases in a Lipid Bilayer System.

PubMed

Autzen, Henriette Elisabeth; Musgaard, Maria

2016-01-01

Molecular dynamics (MD) simulation is a computational method which provides insight on protein dynamics with high resolution in both space and time, in contrast to many experimental techniques. MD simulations can be used as a stand-alone method to study P-type ATPases as well as a complementary method aiding experimental studies. In particular, MD simulations have proved valuable in generating and confirming hypotheses relating to the structure and function of P-type ATPases. In the following, we describe a detailed practical procedure on how to set up and run a MD simulation of a P-type ATPase embedded in a lipid bilayer using software free of use for academics. We emphasize general considerations and problems typically encountered when setting up simulations. While full coverage of all possible procedures is beyond the scope of this chapter, we have chosen to illustrate the MD procedure with the Nanoscale Molecular Dynamics (NAMD) and the Visual Molecular Dynamics (VMD) software suites.

GATE: software for the analysis and visualization of high-dimensional time series expression data.

PubMed

MacArthur, Ben D; Lachmann, Alexander; Lemischka, Ihor R; Ma'ayan, Avi

2010-01-01

We present Grid Analysis of Time series Expression (GATE), an integrated computational software platform for the analysis and visualization of high-dimensional biomolecular time series. GATE uses a correlation-based clustering algorithm to arrange molecular time series on a two-dimensional hexagonal array and dynamically colors individual hexagons according to the expression level of the molecular component to which they are assigned, to create animated movies of systems-level molecular regulatory dynamics. In order to infer potential regulatory control mechanisms from patterns of correlation, GATE also allows interactive interroga-tion of movies against a wide variety of prior knowledge datasets. GATE movies can be paused and are interactive, allowing users to reconstruct networks and perform functional enrichment analyses. Movies created with GATE can be saved in Flash format and can be inserted directly into PDF manuscript files as interactive figures. GATE is available for download and is free for academic use from http://amp.pharm.mssm.edu/maayan-lab/gate.htm

DOE Office of Scientific and Technical Information (OSTI.GOV)

McCann, Billy W.; Silva, Nuwan De; Windus, Theresa L.

Computer-aided molecular design and high-throughput screening of viable host architectures can significantly reduce the efforts in the design of novel ligands for efficient extraction of rare earth elements. This paper presents a computational approach to the deliberate design of bis-phosphine oxide host architectures that are structurally organized for complexation of trivalent lanthanides. Molecule building software, HostDesigner, was interfaced with molecular mechanics software, PCModel, providing a tool for generating and screening millions of potential R 2(O)P-link-P(O)R 2 ligand geometries. The molecular mechanics ranking of ligand structures is consistent with both the solution-phase free energies of complexation obtained with density functional theorymore » and the performance of known bis-phosphine oxide extractants. For the case where link is -CH 2-, evaluation of the ligand geometry provides the first characterization of a steric origin for the ‘anomalous aryl strengthening’ effect. The design approach has identified a number of novel bis-phosphine oxide ligands that are better organized for lanthanide complexation than previously studied examples.« less

NASA Software Cost Estimation Model: An Analogy Based Estimation Model

NASA Technical Reports Server (NTRS)

Hihn, Jairus; Juster, Leora; Menzies, Tim; Mathew, George; Johnson, James

2015-01-01

The cost estimation of software development activities is increasingly critical for large scale integrated projects such as those at DOD and NASA especially as the software systems become larger and more complex. As an example MSL (Mars Scientific Laboratory) developed at the Jet Propulsion Laboratory launched with over 2 million lines of code making it the largest robotic spacecraft ever flown (Based on the size of the software). Software development activities are also notorious for their cost growth, with NASA flight software averaging over 50% cost growth. All across the agency, estimators and analysts are increasingly being tasked to develop reliable cost estimates in support of program planning and execution. While there has been extensive work on improving parametric methods there is very little focus on the use of models based on analogy and clustering algorithms. In this paper we summarize our findings on effort/cost model estimation and model development based on ten years of software effort estimation research using data mining and machine learning methods to develop estimation models based on analogy and clustering. The NASA Software Cost Model performance is evaluated by comparing it to COCOMO II, linear regression, and K-­ nearest neighbor prediction model performance on the same data set.

[Preparation of monoclonal antibody against 4-amylphenol and homology modeling of its Fv fragment].

PubMed

Cheng, Lei; Wu, Haizhen; Fei, Jing; Zhang, Lujia; Ye, Jiang; Zhang, Huizhan

2017-03-01

Objective To prepare and characterize a monoclonal antibody (mAb) against 4-amylphenol (4-AP), clone its cDNA sequence and make homology modeling for its Fv fragment. Methods A high-affinity anti-4-AP mAb was generated from a hybridoma cell line F10 using electrofusion between splenocytes from APA-BSA-immunized mouse and Sp2/0 myeloma cells. Then we extracted the mRNA of F10 cells and cloned the cDNA of mAb. The homology modeling and molecular docking of its Fv fragment was conducted with biological software. Results Under the optimum conditions, the ic-ELISA equation was y=A 2 +(A 1 -A 2 )/(1+(x/x 0 ) p ) (A 1 =1.28; A 2 =-0.066; x 0 =12560.75; p=0.74) with a correlation coefficient (R 2 ) of 0.997. The lowest detectable limit was 0.65 μg/mL. The heavy and light chains of mAb respectively belonged to IgG1 and Kappa. The homology modeling and molecular docking studies revealed that the binding of 4-Ap and mAb was attributed to the hydrogen bond and hydrophobic interactions. Conclusion The study successfully established a stable 4-AP mAb-secreting hybridoma cell line. The study on spatial structure of Fv fragment using homology modeling provided a reference for the development and design of single chain variable fragments.

SynBioSS designer: a web-based tool for the automated generation of kinetic models for synthetic biological constructs

PubMed Central

Weeding, Emma; Houle, Jason

2010-01-01

Modeling tools can play an important role in synthetic biology the same way modeling helps in other engineering disciplines: simulations can quickly probe mechanisms and provide a clear picture of how different components influence the behavior of the whole. We present a brief review of available tools and present SynBioSS Designer. The Synthetic Biology Software Suite (SynBioSS) is used for the generation, storing, retrieval and quantitative simulation of synthetic biological networks. SynBioSS consists of three distinct components: the Desktop Simulator, the Wiki, and the Designer. SynBioSS Designer takes as input molecular parts involved in gene expression and regulation (e.g. promoters, transcription factors, ribosome binding sites, etc.), and automatically generates complete networks of reactions that represent transcription, translation, regulation, induction and degradation of those parts. Effectively, Designer uses DNA sequences as input and generates networks of biomolecular reactions as output. In this paper we describe how Designer uses universal principles of molecular biology to generate models of any arbitrary synthetic biological system. These models are useful as they explain biological phenotypic complexity in mechanistic terms. In turn, such mechanistic explanations can assist in designing synthetic biological systems. We also discuss, giving practical guidance to users, how Designer interfaces with the Registry of Standard Biological Parts, the de facto compendium of parts used in synthetic biology applications. PMID:20639523

Presenting an evaluation model of the trauma registry software.

PubMed

Asadi, Farkhondeh; Paydar, Somayeh

2018-04-01

Trauma is a major cause of 10% death in the worldwide and is considered as a global concern. This problem has made healthcare policy makers and managers to adopt a basic strategy in this context. Trauma registry has an important and basic role in decreasing the mortality and the disabilities due to injuries resulted from trauma. Today, different software are designed for trauma registry. Evaluation of this software improves management, increases efficiency and effectiveness of these systems. Therefore, the aim of this study is to present an evaluation model for trauma registry software. The present study is an applied research. In this study, general and specific criteria of trauma registry software were identified by reviewing literature including books, articles, scientific documents, valid websites and related software in this domain. According to general and specific criteria and related software, a model for evaluating trauma registry software was proposed. Based on the proposed model, a checklist designed and its validity and reliability evaluated. Mentioned model by using of the Delphi technique presented to 12 experts and specialists. To analyze the results, an agreed coefficient of %75 was determined in order to apply changes. Finally, when the model was approved by the experts and professionals, the final version of the evaluation model for the trauma registry software was presented. For evaluating of criteria of trauma registry software, two groups were presented: 1- General criteria, 2- Specific criteria. General criteria of trauma registry software were classified into four main categories including: 1- usability, 2- security, 3- maintainability, and 4-interoperability. Specific criteria were divided into four main categories including: 1- data submission and entry, 2- reporting, 3- quality control, 4- decision and research support. The presented model in this research has introduced important general and specific criteria of trauma registry software and sub criteria related to each main criteria separately. This model was validated by experts in this field. Therefore, this model can be used as a comprehensive model and a standard evaluation tool for measuring efficiency and effectiveness and performance improvement of trauma registry software. Copyright © 2018 Elsevier B.V. All rights reserved.

New software for statistical analysis of Cambridge Structural Database data

PubMed Central

Sykes, Richard A.; McCabe, Patrick; Allen, Frank H.; Battle, Gary M.; Bruno, Ian J.; Wood, Peter A.

2011-01-01

A collection of new software tools is presented for the analysis of geometrical, chemical and crystallographic data from the Cambridge Structural Database (CSD). This software supersedes the program Vista. The new functionality is integrated into the program Mercury in order to provide statistical, charting and plotting options alongside three-dimensional structural visualization and analysis. The integration also permits immediate access to other information about specific CSD entries through the Mercury framework, a common requirement in CSD data analyses. In addition, the new software includes a range of more advanced features focused towards structural analysis such as principal components analysis, cone-angle correction in hydrogen-bond analyses and the ability to deal with topological symmetry that may be exhibited in molecular search fragments. PMID:22477784

NHPP-Based Software Reliability Models Using Equilibrium Distribution

NASA Astrophysics Data System (ADS)

Xiao, Xiao; Okamura, Hiroyuki; Dohi, Tadashi

Non-homogeneous Poisson processes (NHPPs) have gained much popularity in actual software testing phases to estimate the software reliability, the number of remaining faults in software and the software release timing. In this paper, we propose a new modeling approach for the NHPP-based software reliability models (SRMs) to describe the stochastic behavior of software fault-detection processes. The fundamental idea is to apply the equilibrium distribution to the fault-detection time distribution in NHPP-based modeling. We also develop efficient parameter estimation procedures for the proposed NHPP-based SRMs. Through numerical experiments, it can be concluded that the proposed NHPP-based SRMs outperform the existing ones in many data sets from the perspective of goodness-of-fit and prediction performance.

An information model for use in software management estimation and prediction

NASA Technical Reports Server (NTRS)

Li, Ningda R.; Zelkowitz, Marvin V.

1993-01-01

This paper describes the use of cluster analysis for determining the information model within collected software engineering development data at the NASA/GSFC Software Engineering Laboratory. We describe the Software Management Environment tool that allows managers to predict development attributes during early phases of a software project and the modifications we propose to allow it to develop dynamic models for better predictions of these attributes.

Bayesian species delimitation in Pleophylla chafers (Coleoptera) - the importance of prior choice and morphology.

PubMed

Eberle, Jonas; Warnock, Rachel C M; Ahrens, Dirk

2016-05-05

Defining species units can be challenging, especially during the earliest stages of speciation, when phylogenetic inference and delimitation methods may be compromised by incomplete lineage sorting (ILS) or secondary gene flow. Integrative approaches to taxonomy, which combine molecular and morphological evidence, have the potential to be valuable in such cases. In this study we investigated the South African scarab beetle genus Pleophylla using data collected from 110 individuals of eight putative morphospecies. The dataset included four molecular markers (cox1, 16S, rrnL, ITS1) and morphometric data based on male genital morphology. We applied a suite of molecular and morphological approaches to species delimitation, and implemented a novel Bayesian approach in the software iBPP, which enables continuous morphological trait and molecular data to be combined. Traditional morphology-based species assignments were supported quantitatively by morphometric analyses of the male genitalia (eigenshape analysis, CVA, LDA). While the ITS1-based delineation was also broadly congruent with the morphospecies, the cox1 data resulted in over-splitting (GMYC modelling, haplotype networks, PTP, ABGD). In the most extreme case morphospecies shared identical haplotypes, which may be attributable to ILS based on statistical tests performed using the software JML. We found the strongest support for putative morphospecies based on phylogenetic evidence using the combined approach implemented in iBPP. However, support for putative species was sensitive to the use of alternative guide trees and alternative combinations of priors on the population size (θ) and rootage (τ 0 ) parameters, especially when the analysis was based on molecular or morphological data alone. We demonstrate that continuous morphological trait data can be extremely valuable in assessing competing hypotheses to species delimitation. In particular, we show that the inclusion of morphological data in an integrative Bayesian framework can improve the resolution of inferred species units. However, we also demonstrate that this approach is extremely sensitive to guide tree and prior parameter choice. These parameters should be chosen with caution - if possible - based on independent empirical evidence, or careful sensitivity analyses should be performed to assess the robustness of results. Young species provide exemplars for investigating the mechanisms of speciation and for assessing the performance of tools used to delimit species on the basis of molecular and/or morphological evidence.

Immersive virtual reality in computational chemistry: Applications to the analysis of QM and MM data.

PubMed

Salvadori, Andrea; Del Frate, Gianluca; Pagliai, Marco; Mancini, Giordano; Barone, Vincenzo

2016-11-15

The role of Virtual Reality (VR) tools in molecular sciences is analyzed in this contribution through the presentation of the Caffeine software to the quantum chemistry community. Caffeine, developed at Scuola Normale Superiore, is specifically tailored for molecular representation and data visualization with VR systems, such as VR theaters and helmets. Usefulness and advantages that can be gained by exploiting VR are here reported, considering few examples specifically selected to illustrate different level of theory and molecular representation.

A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language

PubMed Central

2011-01-01

Shotgun lipidome profiling relies on direct mass spectrometric analysis of total lipid extracts from cells, tissues or organisms and is a powerful tool to elucidate the molecular composition of lipidomes. We present a novel informatics concept of the molecular fragmentation query language implemented within the LipidXplorer open source software kit that supports accurate quantification of individual species of any ionizable lipid class in shotgun spectra acquired on any mass spectrometry platform. PMID:21247462

A molecular fragment cheminformatics roadmap for mesoscopic simulation.

PubMed

Truszkowski, Andreas; Daniel, Mirco; Kuhn, Hubert; Neumann, Stefan; Steinbeck, Christoph; Zielesny, Achim; Epple, Matthias

2014-12-01

Mesoscopic simulation studies the structure, dynamics and properties of large molecular ensembles with millions of atoms: Its basic interacting units (beads) are no longer the nuclei and electrons of quantum chemical ab-initio calculations or the atom types of molecular mechanics but molecular fragments, molecules or even larger molecular entities. For its simulation setup and output a mesoscopic simulation kernel software uses abstract matrix (array) representations for bead topology and connectivity. Therefore a pure kernel-based mesoscopic simulation task is a tedious, time-consuming and error-prone venture that limits its practical use and application. A consequent cheminformatics approach tackles these problems and provides solutions for a considerably enhanced accessibility. This study aims at outlining a complete cheminformatics roadmap that frames a mesoscopic Molecular Fragment Dynamics (MFD) simulation kernel to allow its efficient use and practical application. The molecular fragment cheminformatics roadmap consists of four consecutive building blocks: An adequate fragment structure representation (1), defined operations on these fragment structures (2), the description of compartments with defined compositions and structural alignments (3), and the graphical setup and analysis of a whole simulation box (4). The basis of the cheminformatics approach (i.e. building block 1) is a SMILES-like line notation (denoted f SMILES) with connected molecular fragments to represent a molecular structure. The f SMILES notation and the following concepts and methods for building blocks 2-4 are outlined with examples and practical usage scenarios. It is shown that the requirements of the roadmap may be partly covered by already existing open-source cheminformatics software. Mesoscopic simulation techniques like MFD may be considerably alleviated and broadened for practical use with a consequent cheminformatics layer that successfully tackles its setup subtleties and conceptual usage hurdles. Molecular Fragment Cheminformatics may be regarded as a crucial accelerator to propagate MFD and similar mesoscopic simulation techniques in the molecular sciences. Graphical abstractA molecular fragment cheminformatics roadmap for mesoscopic simulation.

Predicting Software Suitability Using a Bayesian Belief Network

NASA Technical Reports Server (NTRS)

Beaver, Justin M.; Schiavone, Guy A.; Berrios, Joseph S.

2005-01-01

The ability to reliably predict the end quality of software under development presents a significant advantage for a development team. It provides an opportunity to address high risk components earlier in the development life cycle, when their impact is minimized. This research proposes a model that captures the evolution of the quality of a software product, and provides reliable forecasts of the end quality of the software being developed in terms of product suitability. Development team skill, software process maturity, and software problem complexity are hypothesized as driving factors of software product quality. The cause-effect relationships between these factors and the elements of software suitability are modeled using Bayesian Belief Networks, a machine learning method. This research presents a Bayesian Network for software quality, and the techniques used to quantify the factors that influence and represent software quality. The developed model is found to be effective in predicting the end product quality of small-scale software development efforts.

System and Software Reliability (C103)

NASA Technical Reports Server (NTRS)

Wallace, Dolores

2003-01-01

Within the last decade better reliability models (hardware. software, system) than those currently used have been theorized and developed but not implemented in practice. Previous research on software reliability has shown that while some existing software reliability models are practical, they are no accurate enough. New paradigms of development (e.g. OO) have appeared and associated reliability models have been proposed posed but not investigated. Hardware models have been extensively investigated but not integrated into a system framework. System reliability modeling is the weakest of the three. NASA engineers need better methods and tools to demonstrate that the products meet NASA requirements for reliability measurement. For the new models for the software component of the last decade, there is a great need to bring them into a form that they can be used on software intensive systems. The Statistical Modeling and Estimation of Reliability Functions for Systems (SMERFS'3) tool is an existing vehicle that may be used to incorporate these new modeling advances. Adapting some existing software reliability modeling changes to accommodate major changes in software development technology may also show substantial improvement in prediction accuracy. With some additional research, the next step is to identify and investigate system reliability. System reliability models could then be incorporated in a tool such as SMERFS'3. This tool with better models would greatly add value in assess in GSFC projects.

The impact of computer science in molecular medicine: enabling high-throughput research.

PubMed

de la Iglesia, Diana; García-Remesal, Miguel; de la Calle, Guillermo; Kulikowski, Casimir; Sanz, Ferran; Maojo, Víctor

2013-01-01

The Human Genome Project and the explosion of high-throughput data have transformed the areas of molecular and personalized medicine, which are producing a wide range of studies and experimental results and providing new insights for developing medical applications. Research in many interdisciplinary fields is resulting in data repositories and computational tools that support a wide diversity of tasks: genome sequencing, genome-wide association studies, analysis of genotype-phenotype interactions, drug toxicity and side effects assessment, prediction of protein interactions and diseases, development of computational models, biomarker discovery, and many others. The authors of the present paper have developed several inventories covering tools, initiatives and studies in different computational fields related to molecular medicine: medical informatics, bioinformatics, clinical informatics and nanoinformatics. With these inventories, created by mining the scientific literature, we have carried out several reviews of these fields, providing researchers with a useful framework to locate, discover, search and integrate resources. In this paper we present an analysis of the state-of-the-art as it relates to computational resources for molecular medicine, based on results compiled in our inventories, as well as results extracted from a systematic review of the literature and other scientific media. The present review is based on the impact of their related publications and the available data and software resources for molecular medicine. It aims to provide information that can be useful to support ongoing research and work to improve diagnostics and therapeutics based on molecular-level insights.

Integration of Molecular Dynamics Based Predictions into the Optimization of De Novo Protein Designs: Limitations and Benefits.

PubMed

Carvalho, Henrique F; Barbosa, Arménio J M; Roque, Ana C A; Iranzo, Olga; Branco, Ricardo J F

2017-01-01

Recent advances in de novo protein design have gained considerable insight from the intrinsic dynamics of proteins, based on the integration of molecular dynamics simulations protocols on the state-of-the-art de novo protein design protocols used nowadays. With this protocol we illustrate how to set up and run a molecular dynamics simulation followed by a functional protein dynamics analysis. New users will be introduced to some useful open-source computational tools, including the GROMACS molecular dynamics simulation software package and ProDy for protein structural dynamics analysis.

Are Earth System model software engineering practices fit for purpose? A case study.

NASA Astrophysics Data System (ADS)

Easterbrook, S. M.; Johns, T. C.

2009-04-01

We present some analysis and conclusions from a case study of the culture and practices of scientists at the Met Office and Hadley Centre working on the development of software for climate and Earth System models using the MetUM infrastructure. The study examined how scientists think about software correctness, prioritize their requirements in making changes, and develop a shared understanding of the resulting models. We conclude that highly customized techniques driven strongly by scientific research goals have evolved for verification and validation of such models. In a formal software engineering context these represents costly, but invaluable, software integration tests with considerable benefits. The software engineering practices seen also exhibit recognisable features of both agile and open source software development projects - self-organisation of teams consistent with a meritocracy rather than top-down organisation, extensive use of informal communication channels, and software developers who are generally also users and science domain experts. We draw some general conclusions on whether these practices work well, and what new software engineering challenges may lie ahead as Earth System models become ever more complex and petascale computing becomes the norm.

Students' Different Understandings of Class Diagrams

ERIC Educational Resources Information Center

Boustedt, Jonas

2012-01-01

The software industry needs well-trained software designers and one important aspect of software design is the ability to model software designs visually and understand what visual models represent. However, previous research indicates that software design is a difficult task to many students. This article reports empirical findings from a…

Model-based software process improvement

NASA Technical Reports Server (NTRS)

Zettervall, Brenda T.

1994-01-01

The activities of a field test site for the Software Engineering Institute's software process definition project are discussed. Products tested included the improvement model itself, descriptive modeling techniques, the CMM level 2 framework document, and the use of process definition guidelines and templates. The software process improvement model represents a five stage cyclic approach for organizational process improvement. The cycles consist of the initiating, diagnosing, establishing, acting, and leveraging phases.

Facilitating Students' Interaction with Real Gas Properties Using a Discovery-Based Approach and Molecular Dynamics Simulations

ERIC Educational Resources Information Center

Sweet, Chelsea; Akinfenwa, Oyewumi; Foley, Jonathan J., IV

2018-01-01

We present an interactive discovery-based approach to studying the properties of real gases using simple, yet realistic, molecular dynamics software. Use of this approach opens up a variety of opportunities for students to interact with the behaviors and underlying theories of real gases. Students can visualize gas behavior under a variety of…

Concept of a Cloud Service for Data Preparation and Computational Control on Custom HPC Systems in Application to Molecular Dynamics

NASA Astrophysics Data System (ADS)

Puzyrkov, Dmitry; Polyakov, Sergey; Podryga, Viktoriia; Markizov, Sergey

2018-02-01

At the present stage of computer technology development it is possible to study the properties and processes in complex systems at molecular and even atomic levels, for example, by means of molecular dynamics methods. The most interesting are problems related with the study of complex processes under real physical conditions. Solving such problems requires the use of high performance computing systems of various types, for example, GRID systems and HPC clusters. Considering the time consuming computational tasks, the need arises of software for automatic and unified monitoring of such computations. A complex computational task can be performed over different HPC systems. It requires output data synchronization between the storage chosen by a scientist and the HPC system used for computations. The design of the computational domain is also quite a problem. It requires complex software tools and algorithms for proper atomistic data generation on HPC systems. The paper describes the prototype of a cloud service, intended for design of atomistic systems of large volume for further detailed molecular dynamic calculations and computational management for this calculations, and presents the part of its concept aimed at initial data generation on the HPC systems.

Increasing the reliability of ecological models using modern software engineering techniques

Treesearch

Robert M. Scheller; Brian R. Sturtevant; Eric J. Gustafson; Brendan C. Ward; David J. Mladenoff

2009-01-01

Modern software development techniques are largely unknown to ecologists. Typically, ecological models and other software tools are developed for limited research purposes, and additional capabilities are added later, usually in an ad hoc manner. Modern software engineering techniques can substantially increase scientific rigor and confidence in ecological models and...

Tips on Creating Complex Geometry Using Solid Modeling Software

ERIC Educational Resources Information Center

Gow, George

2008-01-01

Three-dimensional computer-aided drafting (CAD) software, sometimes referred to as "solid modeling" software, is easy to learn, fun to use, and becoming the standard in industry. However, many users have difficulty creating complex geometry with the solid modeling software. And the problem is not entirely a student problem. Even some teachers and…

Software engineering and the role of Ada: Executive seminar

NASA Technical Reports Server (NTRS)

Freedman, Glenn B.

1987-01-01

The objective was to introduce the basic terminology and concepts of software engineering and Ada. The life cycle model is reviewed. The application of the goals and principles of software engineering is applied. An introductory understanding of the features of the Ada language is gained. Topics addressed include: the software crises; the mandate of the Space Station Program; software life cycle model; software engineering; and Ada under the software engineering umbrella.

The Phenix Software for Automated Determination of Macromolecular Structures

PubMed Central

Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor; Chen, Vincent B.; Echols, Nathaniel; Headd, Jeffrey J.; Hung, Li-Wei; Jain, Swati; Kapral, Gary J.; Grosse Kunstleve, Ralf W.; McCoy, Airlie J.; Moriarty, Nigel W.; Oeffner, Robert D.; Read, Randy J.; Richardson, David C.; Richardson, Jane S.; Terwilliger, Thomas C.; Zwart, Peter H.

2011-01-01

X-ray crystallography is a critical tool in the study of biological systems. It is able to provide information that has been a prerequisite to understanding the fundamentals of life. It is also a method that is central to the development of new therapeutics for human disease. Significant time and effort are required to determine and optimize many macromolecular structures because of the need for manual interpretation of complex numerical data, often using many different software packages, and the repeated use of interactive three-dimensional graphics. The Phenix software package has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on automation. This has required the development of new algorithms that minimize or eliminate subjective input in favour of built-in expert-systems knowledge, the automation of procedures that are traditionally performed by hand, and the development of a computational framework that allows a tight integration between the algorithms. The application of automated methods is particularly appropriate in the field of structural proteomics, where high throughput is desired. Features in Phenix for the automation of experimental phasing with subsequent model building, molecular replacement, structure refinement and validation are described and examples given of running Phenix from both the command line and graphical user interface. PMID:21821126

Presenting an Evaluation Model for the Cancer Registry Software.

PubMed

Moghaddasi, Hamid; Asadi, Farkhondeh; Rabiei, Reza; Rahimi, Farough; Shahbodaghi, Reihaneh

2017-12-01

As cancer is increasingly growing, cancer registry is of great importance as the main core of cancer control programs, and many different software has been designed for this purpose. Therefore, establishing a comprehensive evaluation model is essential to evaluate and compare a wide range of such software. In this study, the criteria of the cancer registry software have been determined by studying the documents and two functional software of this field. The evaluation tool was a checklist and in order to validate the model, this checklist was presented to experts in the form of a questionnaire. To analyze the results of validation, an agreed coefficient of %75 was determined in order to apply changes. Finally, when the model was approved, the final version of the evaluation model for the cancer registry software was presented. The evaluation model of this study contains tool and method of evaluation. The evaluation tool is a checklist including the general and specific criteria of the cancer registry software along with their sub-criteria. The evaluation method of this study was chosen as a criteria-based evaluation method based on the findings. The model of this study encompasses various dimensions of cancer registry software and a proper method for evaluating it. The strong point of this evaluation model is the separation between general criteria and the specific ones, while trying to fulfill the comprehensiveness of the criteria. Since this model has been validated, it can be used as a standard to evaluate the cancer registry software.

Methods for cost estimation in software project management

NASA Astrophysics Data System (ADS)

Briciu, C. V.; Filip, I.; Indries, I. I.

2016-02-01

The speed in which the processes used in software development field have changed makes it very difficult the task of forecasting the overall costs for a software project. By many researchers, this task has been considered unachievable, but there is a group of scientist for which this task can be solved using the already known mathematical methods (e.g. multiple linear regressions) and the new techniques as genetic programming and neural networks. The paper presents a solution for building a model for the cost estimation models in the software project management using genetic algorithms starting from the PROMISE datasets related COCOMO 81 model. In the first part of the paper, a summary of the major achievements in the research area of finding a model for estimating the overall project costs is presented together with the description of the existing software development process models. In the last part, a basic proposal of a mathematical model of a genetic programming is proposed including here the description of the chosen fitness function and chromosome representation. The perspective of model described it linked with the current reality of the software development considering as basis the software product life cycle and the current challenges and innovations in the software development area. Based on the author's experiences and the analysis of the existing models and product lifecycle it was concluded that estimation models should be adapted with the new technologies and emerging systems and they depend largely by the chosen software development method.

Component-based integration of chemistry and optimization software.

PubMed

Kenny, Joseph P; Benson, Steven J; Alexeev, Yuri; Sarich, Jason; Janssen, Curtis L; McInnes, Lois Curfman; Krishnan, Manojkumar; Nieplocha, Jarek; Jurrus, Elizabeth; Fahlstrom, Carl; Windus, Theresa L

2004-11-15

Typical scientific software designs make rigid assumptions regarding programming language and data structures, frustrating software interoperability and scientific collaboration. Component-based software engineering is an emerging approach to managing the increasing complexity of scientific software. Component technology facilitates code interoperability and reuse. Through the adoption of methodology and tools developed by the Common Component Architecture Forum, we have developed a component architecture for molecular structure optimization. Using the NWChem and Massively Parallel Quantum Chemistry packages, we have produced chemistry components that provide capacity for energy and energy derivative evaluation. We have constructed geometry optimization applications by integrating the Toolkit for Advanced Optimization, Portable Extensible Toolkit for Scientific Computation, and Global Arrays packages, which provide optimization and linear algebra capabilities. We present a brief overview of the component development process and a description of abstract interfaces for chemical optimizations. The components conforming to these abstract interfaces allow the construction of applications using different chemistry and mathematics packages interchangeably. Initial numerical results for the component software demonstrate good performance, and highlight potential research enabled by this platform.

Implementation of metal-friendly EAM/FS-type semi-empirical potentials in HOOMD-blue: A GPU-accelerated molecular dynamics software

DOE PAGES

Yang, Lin; Zhang, Feng; Wang, Cai-Zhuang; ...

2018-01-12

We present an implementation of EAM and FS interatomic potentials, which are widely used in simulating metallic systems, in HOOMD-blue, a software designed to perform classical molecular dynamics simulations using GPU accelerations. We first discuss the details of our implementation and then report extensive benchmark tests. We demonstrate that single-precision floating point operations efficiently implemented on GPUs can produce sufficient accuracy when compared against double-precision codes, as demonstrated in test simulations of calculations of the glass-transition temperature of Cu 64.5Zr 35.5, and pair correlation function of liquid Ni 3Al. Our code scales well with the size of the simulating systemmore » on NVIDIA Tesla M40 and P100 GPUs. Compared with another popular software LAMMPS running on 32 cores of AMD Opteron 6220 processors, the GPU/CPU performance ratio can reach as high as 4.6. In conclusion, the source code can be accessed through the HOOMD-blue web page for free by any interested user.« less

Implementation of metal-friendly EAM/FS-type semi-empirical potentials in HOOMD-blue: A GPU-accelerated molecular dynamics software

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Lin; Zhang, Feng; Wang, Cai-Zhuang

We present an implementation of EAM and FS interatomic potentials, which are widely used in simulating metallic systems, in HOOMD-blue, a software designed to perform classical molecular dynamics simulations using GPU accelerations. We first discuss the details of our implementation and then report extensive benchmark tests. We demonstrate that single-precision floating point operations efficiently implemented on GPUs can produce sufficient accuracy when compared against double-precision codes, as demonstrated in test simulations of calculations of the glass-transition temperature of Cu 64.5Zr 35.5, and pair correlation function of liquid Ni 3Al. Our code scales well with the size of the simulating systemmore » on NVIDIA Tesla M40 and P100 GPUs. Compared with another popular software LAMMPS running on 32 cores of AMD Opteron 6220 processors, the GPU/CPU performance ratio can reach as high as 4.6. In conclusion, the source code can be accessed through the HOOMD-blue web page for free by any interested user.« less

DynamO: a free O(N) general event-driven molecular dynamics simulator.

PubMed

Bannerman, M N; Sargant, R; Lue, L

2011-11-30

Molecular dynamics algorithms for systems of particles interacting through discrete or "hard" potentials are fundamentally different to the methods for continuous or "soft" potential systems. Although many software packages have been developed for continuous potential systems, software for discrete potential systems based on event-driven algorithms are relatively scarce and specialized. We present DynamO, a general event-driven simulation package, which displays the optimal O(N) asymptotic scaling of the computational cost with the number of particles N, rather than the O(N) scaling found in most standard algorithms. DynamO provides reference implementations of the best available event-driven algorithms. These techniques allow the rapid simulation of both complex and large (>10(6) particles) systems for long times. The performance of the program is benchmarked for elastic hard sphere systems, homogeneous cooling and sheared inelastic hard spheres, and equilibrium Lennard-Jones fluids. This software and its documentation are distributed under the GNU General Public license and can be freely downloaded from http://marcusbannerman.co.uk/dynamo. Copyright © 2011 Wiley Periodicals, Inc.

WebSat ‐ A web software for microsatellite marker development

PubMed Central

Martins, Wellington Santos; Soares Lucas, Divino César; de Souza Neves, Kelligton Fabricio; Bertioli, David John

2009-01-01

Simple sequence repeats (SSR), also known as microsatellites, have been extensively used as molecular markers due to their abundance and high degree of polymorphism. We have developed a simple to use web software, called WebSat, for microsatellite molecular marker prediction and development. WebSat is accessible through the Internet, requiring no program installation. Although a web solution, it makes use of Ajax techniques, providing a rich, responsive user interface. WebSat allows the submission of sequences, visualization of microsatellites and the design of primers suitable for their amplification. The program allows full control of parameters and the easy export of the resulting data, thus facilitating the development of microsatellite markers. Availability The web tool may be accessed at http://purl.oclc.org/NET/websat/ PMID:19255650

Program Model Checking as a New Trend

NASA Technical Reports Server (NTRS)

Havelund, Klaus; Visser, Willem; Clancy, Daniel (Technical Monitor)

2002-01-01

This paper introduces a special section of STTT (International Journal on Software Tools for Technology Transfer) containing a selection of papers that were presented at the 7th International SPIN workshop, Stanford, August 30 - September 1, 2000. The workshop was named SPIN Model Checking and Software Verification, with an emphasis on model checking of programs. The paper outlines the motivation for stressing software verification, rather than only design and model verification, by presenting the work done in the Automated Software Engineering group at NASA Ames Research Center within the last 5 years. This includes work in software model checking, testing like technologies and static analysis.

Knowledge-based approach for generating target system specifications from a domain model

NASA Technical Reports Server (NTRS)

Gomaa, Hassan; Kerschberg, Larry; Sugumaran, Vijayan

1992-01-01

Several institutions in industry and academia are pursuing research efforts in domain modeling to address unresolved issues in software reuse. To demonstrate the concepts of domain modeling and software reuse, a prototype software engineering environment is being developed at George Mason University to support the creation of domain models and the generation of target system specifications. This prototype environment, which is application domain independent, consists of an integrated set of commercial off-the-shelf software tools and custom-developed software tools. This paper describes the knowledge-based tool that was developed as part of the environment to generate target system specifications from a domain model.

Software cost/resource modeling: Deep space network software cost estimation model

NASA Technical Reports Server (NTRS)

Tausworthe, R. J.

1980-01-01

A parametric software cost estimation model prepared for JPL deep space network (DSN) data systems implementation tasks is presented. The resource estimation model incorporates principles and data from a number of existing models, such as those of the General Research Corporation, Doty Associates, IBM (Walston-Felix), Rome Air Force Development Center, University of Maryland, and Rayleigh-Norden-Putnam. The model calibrates task magnitude and difficulty, development environment, and software technology effects through prompted responses to a set of approximately 50 questions. Parameters in the model are adjusted to fit JPL software lifecycle statistics. The estimation model output scales a standard DSN work breakdown structure skeleton, which is then input to a PERT/CPM system, producing a detailed schedule and resource budget for the project being planned.

TheoReTS - An information system for theoretical spectra based on variational predictions from molecular potential energy and dipole moment surfaces

NASA Astrophysics Data System (ADS)

Rey, Michaël; Nikitin, Andrei V.; Babikov, Yurii L.; Tyuterev, Vladimir G.

2016-09-01

Knowledge of intensities of rovibrational transitions of various molecules and theirs isotopic species in wide spectral and temperature ranges is essential for the modeling of optical properties of planetary atmospheres, brown dwarfs and for other astrophysical applications. TheoReTS ("Theoretical Reims-Tomsk Spectral data") is an Internet accessible information system devoted to ab initio based rotationally resolved spectra predictions for some relevant molecular species. All data were generated from potential energy and dipole moment surfaces computed via high-level electronic structure calculations using variational methods for vibration-rotation energy levels and transitions. When available, empirical corrections to band centers were applied, all line intensities remaining purely ab initio. The current TheoReTS implementation contains information on four-to-six atomic molecules, including phosphine, methane, ethylene, silane, methyl-fluoride, and their isotopic species 13CH4 , 12CH3D , 12CH2D2 , 12CD4 , 13C2H4, … . Predicted hot methane line lists up to T = 2000 K are included. The information system provides the associated software for spectra simulation including absorption coefficient, absorption and emission cross-sections, transmittance and radiance. The simulations allow Lorentz, Gauss and Voight line shapes. Rectangular, triangular, Lorentzian, Gaussian, sinc and sinc squared apparatus function can be used with user-defined specifications for broadening parameters and spectral resolution. All information is organized as a relational database with the user-friendly graphical interface according to Model-View-Controller architectural tools. The full-featured web application is written on PHP using Yii framework and C++ software modules. In case of very large high-temperature line lists, a data compression is implemented for fast interactive spectra simulations of a quasi-continual absorption due to big line density. Applications for the TheoReTS may include: education/training in molecular absorption/emission, radiative and non-LTE processes, spectroscopic applications, opacity calculations for planetary and astrophysical applications. The system is freely accessible via internet on the two mirror sites: in Reims, France

LC-IMS-MS Feature Finder: detecting multidimensional liquid chromatography, ion mobility and mass spectrometry features in complex datasets.

PubMed

Crowell, Kevin L; Slysz, Gordon W; Baker, Erin S; LaMarche, Brian L; Monroe, Matthew E; Ibrahim, Yehia M; Payne, Samuel H; Anderson, Gordon A; Smith, Richard D

2013-11-01

The addition of ion mobility spectrometry to liquid chromatography-mass spectrometry experiments requires new, or updated, software tools to facilitate data processing. We introduce a command line software application LC-IMS-MS Feature Finder that searches for molecular ion signatures in multidimensional liquid chromatography-ion mobility spectrometry-mass spectrometry (LC-IMS-MS) data by clustering deisotoped peaks with similar monoisotopic mass, charge state, LC elution time and ion mobility drift time values. The software application includes an algorithm for detecting and quantifying co-eluting chemical species, including species that exist in multiple conformations that may have been separated in the IMS dimension. LC-IMS-MS Feature Finder is available as a command-line tool for download at http://omics.pnl.gov/software/LC-IMS-MS_Feature_Finder.php. The Microsoft.NET Framework 4.0 is required to run the software. All other dependencies are included with the software package. Usage of this software is limited to non-profit research to use (see README). rds@pnnl.gov. Supplementary data are available at Bioinformatics online.

AN EFFICIENT HIGHER-ORDER FAST MULTIPOLE BOUNDARY ELEMENT SOLUTION FOR POISSON-BOLTZMANN BASED MOLECULAR ELECTROSTATICS

PubMed Central

Bajaj, Chandrajit; Chen, Shun-Chuan; Rand, Alexander

2011-01-01

In order to compute polarization energy of biomolecules, we describe a boundary element approach to solving the linearized Poisson-Boltzmann equation. Our approach combines several important features including the derivative boundary formulation of the problem and a smooth approximation of the molecular surface based on the algebraic spline molecular surface. State of the art software for numerical linear algebra and the kernel independent fast multipole method is used for both simplicity and efficiency of our implementation. We perform a variety of computational experiments, testing our method on a number of actual proteins involved in molecular docking and demonstrating the effectiveness of our solver for computing molecular polarization energy. PMID:21660123

Physics Computing '92: Proceedings of the 4th International Conference

NASA Astrophysics Data System (ADS)

de Groot, Robert A.; Nadrchal, Jaroslav

1993-04-01

The Table of Contents for the book is as follows: * Preface * INVITED PAPERS * Ab Initio Theoretical Approaches to the Structural, Electronic and Vibrational Properties of Small Clusters and Fullerenes: The State of the Art * Neural Multigrid Methods for Gauge Theories and Other Disordered Systems * Multicanonical Monte Carlo Simulations * On the Use of the Symbolic Language Maple in Physics and Chemistry: Several Examples * Nonequilibrium Phase Transitions in Catalysis and Population Models * Computer Algebra, Symmetry Analysis and Integrability of Nonlinear Evolution Equations * The Path-Integral Quantum Simulation of Hydrogen in Metals * Digital Optical Computing: A New Approach of Systolic Arrays Based on Coherence Modulation of Light and Integrated Optics Technology * Molecular Dynamics Simulations of Granular Materials * Numerical Implementation of a K.A.M. Algorithm * Quasi-Monte Carlo, Quasi-Random Numbers and Quasi-Error Estimates * What Can We Learn from QMC Simulations * Physics of Fluctuating Membranes * Plato, Apollonius, and Klein: Playing with Spheres * Steady States in Nonequilibrium Lattice Systems * CONVODE: A REDUCE Package for Differential Equations * Chaos in Coupled Rotators * Symplectic Numerical Methods for Hamiltonian Problems * Computer Simulations of Surfactant Self Assembly * High-dimensional and Very Large Cellular Automata for Immunological Shape Space * A Review of the Lattice Boltzmann Method * Electronic Structure of Solids in the Self-interaction Corrected Local-spin-density Approximation * Dedicated Computers for Lattice Gauge Theory Simulations * Physics Education: A Survey of Problems and Possible Solutions * Parallel Computing and Electronic-Structure Theory * High Precision Simulation Techniques for Lattice Field Theory * CONTRIBUTED PAPERS * Case Study of Microscale Hydrodynamics Using Molecular Dynamics and Lattice Gas Methods * Computer Modelling of the Structural and Electronic Properties of the Supported Metal Catalysis * Ordered Particle Simulations for Serial and MIMD Parallel Computers * "NOLP" -- Program Package for Laser Plasma Nonlinear Optics * Algorithms to Solve Nonlinear Least Square Problems * Distribution of Hydrogen Atoms in Pd-H Computed by Molecular Dynamics * A Ray Tracing of Optical System for Protein Crystallography Beamline at Storage Ring-SIBERIA-2 * Vibrational Properties of a Pseudobinary Linear Chain with Correlated Substitutional Disorder * Application of the Software Package Mathematica in Generalized Master Equation Method * Linelist: An Interactive Program for Analysing Beam-foil Spectra * GROMACS: A Parallel Computer for Molecular Dynamics Simulations * GROMACS Method of Virial Calculation Using a Single Sum * The Interactive Program for the Solution of the Laplace Equation with the Elimination of Singularities for Boundary Functions * Random-Number Generators: Testing Procedures and Comparison of RNG Algorithms * Micro-TOPIC: A Tokamak Plasma Impurities Code * Rotational Molecular Scattering Calculations * Orthonormal Polynomial Method for Calibrating of Cryogenic Temperature Sensors * Frame-based System Representing Basis of Physics * The Role of Massively Data-parallel Computers in Large Scale Molecular Dynamics Simulations * Short-range Molecular Dynamics on a Network of Processors and Workstations * An Algorithm for Higher-order Perturbation Theory in Radiative Transfer Computations * Hydrostochastics: The Master Equation Formulation of Fluid Dynamics * HPP Lattice Gas on Transputers and Networked Workstations * Study on the Hysteresis Cycle Simulation Using Modeling with Different Functions on Intervals * Refined Pruning Techniques for Feed-forward Neural Networks * Random Walk Simulation of the Motion of Transient Charges in Photoconductors * The Optical Hysteresis in Hydrogenated Amorphous Silicon * Diffusion Monte Carlo Analysis of Modern Interatomic Potentials for He * A Parallel Strategy for Molecular Dynamics Simulations of Polar Liquids on Transputer Arrays * Distribution of Ions Reflected on Rough Surfaces * The Study of Step Density Distribution During Molecular Beam Epitaxy Growth: Monte Carlo Computer Simulation * Towards a Formal Approach to the Construction of Large-scale Scientific Applications Software * Correlated Random Walk and Discrete Modelling of Propagation through Inhomogeneous Media * Teaching Plasma Physics Simulation * A Theoretical Determination of the Au-Ni Phase Diagram * Boson and Fermion Kinetics in One-dimensional Lattices * Computational Physics Course on the Technical University * Symbolic Computations in Simulation Code Development and Femtosecond-pulse Laser-plasma Interaction Studies * Computer Algebra and Integrated Computing Systems in Education of Physical Sciences * Coordinated System of Programs for Undergraduate Physics Instruction * Program Package MIRIAM and Atomic Physics of Extreme Systems * High Energy Physics Simulation on the T_Node * The Chapman-Kolmogorov Equation as Representation of Huygens' Principle and the Monolithic Self-consistent Numerical Modelling of Lasers * Authoring System for Simulation Developments * Molecular Dynamics Study of Ion Charge Effects in the Structure of Ionic Crystals * A Computational Physics Introductory Course * Computer Calculation of Substrate Temperature Field in MBE System * Multimagnetical Simulation of the Ising Model in Two and Three Dimensions * Failure of the CTRW Treatment of the Quasicoherent Excitation Transfer * Implementation of a Parallel Conjugate Gradient Method for Simulation of Elastic Light Scattering * Algorithms for Study of Thin Film Growth * Algorithms and Programs for Physics Teaching in Romanian Technical Universities * Multicanonical Simulation of 1st order Transitions: Interface Tension of the 2D 7-State Potts Model * Two Numerical Methods for the Calculation of Periodic Orbits in Hamiltonian Systems * Chaotic Behavior in a Probabilistic Cellular Automata? * Wave Optics Computing by a Networked-based Vector Wave Automaton * Tensor Manipulation Package in REDUCE * Propagation of Electromagnetic Pulses in Stratified Media * The Simple Molecular Dynamics Model for the Study of Thermalization of the Hot Nucleon Gas * Electron Spin Polarization in PdCo Alloys Calculated by KKR-CPA-LSD Method * Simulation Studies of Microscopic Droplet Spreading * A Vectorizable Algorithm for the Multicolor Successive Overrelaxation Method * Tetragonality of the CuAu I Lattice and Its Relation to Electronic Specific Heat and Spin Susceptibility * Computer Simulation of the Formation of Metallic Aggregates Produced by Chemical Reactions in Aqueous Solution * Scaling in Growth Models with Diffusion: A Monte Carlo Study * The Nucleus as the Mesoscopic System * Neural Network Computation as Dynamic System Simulation * First-principles Theory of Surface Segregation in Binary Alloys * Data Smooth Approximation Algorithm for Estimating the Temperature Dependence of the Ice Nucleation Rate * Genetic Algorithms in Optical Design * Application of 2D-FFT in the Study of Molecular Exchange Processes by NMR * Advanced Mobility Model for Electron Transport in P-Si Inversion Layers * Computer Simulation for Film Surfaces and its Fractal Dimension * Parallel Computation Techniques and the Structure of Catalyst Surfaces * Educational SW to Teach Digital Electronics and the Corresponding Text Book * Primitive Trinomials (Mod 2) Whose Degree is a Mersenne Exponent * Stochastic Modelisation and Parallel Computing * Remarks on the Hybrid Monte Carlo Algorithm for the ∫4 Model * An Experimental Computer Assisted Workbench for Physics Teaching * A Fully Implicit Code to Model Tokamak Plasma Edge Transport * EXPFIT: An Interactive Program for Automatic Beam-foil Decay Curve Analysis * Mapping Technique for Solving General, 1-D Hamiltonian Systems * Freeway Traffic, Cellular Automata, and Some (Self-Organizing) Criticality * Photonuclear Yield Analysis by Dynamic Programming * Incremental Representation of the Simply Connected Planar Curves * Self-convergence in Monte Carlo Methods * Adaptive Mesh Technique for Shock Wave Propagation * Simulation of Supersonic Coronal Streams and Their Interaction with the Solar Wind * The Nature of Chaos in Two Systems of Ordinary Nonlinear Differential Equations * Considerations of a Window-shopper * Interpretation of Data Obtained by RTP 4-Channel Pulsed Radar Reflectometer Using a Multi Layer Perceptron * Statistics of Lattice Bosons for Finite Systems * Fractal Based Image Compression with Affine Transformations * Algorithmic Studies on Simulation Codes for Heavy-ion Reactions * An Energy-Wise Computer Simulation of DNA-Ion-Water Interactions Explains the Abnormal Structure of Poly[d(A)]:Poly[d(T)] * Computer Simulation Study of Kosterlitz-Thouless-Like Transitions * Problem-oriented Software Package GUN-EBT for Computer Simulation of Beam Formation and Transport in Technological Electron-Optical Systems * Parallelization of a Boundary Value Solver and its Application in Nonlinear Dynamics * The Symbolic Classification of Real Four-dimensional Lie Algebras * Short, Singular Pulses Generation by a Dye Laser at Two Wavelengths Simultaneously * Quantum Monte Carlo Simulations of the Apex-Oxygen-Model * Approximation Procedures for the Axial Symmetric Static Einstein-Maxwell-Higgs Theory * Crystallization on a Sphere: Parallel Simulation on a Transputer Network * FAMULUS: A Software Product (also) for Physics Education * MathCAD vs. FAMULUS -- A Brief Comparison * First-principles Dynamics Used to Study Dissociative Chemisorption * A Computer Controlled System for Crystal Growth from Melt * A Time Resolved Spectroscopic Method for Short Pulsed Particle Emission * Green's Function Computation in Radiative Transfer Theory * Random Search Optimization Technique for One-criteria and Multi-criteria Problems * Hartley Transform Applications to Thermal Drift Elimination in Scanning Tunneling Microscopy * Algorithms of Measuring, Processing and Interpretation of Experimental Data Obtained with Scanning Tunneling Microscope * Time-dependent Atom-surface Interactions * Local and Global Minima on Molecular Potential Energy Surfaces: An Example of N3 Radical * Computation of Bifurcation Surfaces * Symbolic Computations in Quantum Mechanics: Energies in Next-to-solvable Systems * A Tool for RTP Reactor and Lamp Field Design * Modelling of Particle Spectra for the Analysis of Solid State Surface * List of Participants

Art Advancing Science: Filmmaking Leads to Molecular Insights at the Nanoscale.

PubMed

Reilly, Charles; Ingber, Donald E

2017-12-26

Many have recognized the potential value of facilitating activities that span the art-science interface for the benefit of society; however, there are few examples that demonstrate how pursuit of an artistic agenda can lead to scientific insights. Here, we describe how we set out to produce an entertaining short film depicting the fertilization of the egg by sperm as a parody of a preview for another Star Wars movie to excite the public about science, but ended up developing a simulation tool for multiscale modeling. To produce an aesthetic that communicates mechanical continuity across spatial scales, we developed custom strategies that integrate physics-based animation software from the entertainment industry with molecular dynamics simulation tools, using experimental data from research publications. Using this approach, we were able to depict biological physicality across multiple spatial scales, from how sperm tails move to collective molecular behavior within the axoneme to how the molecular motor, dynein, produces force at the nanometer scale. The dynein simulations, which were validated by replicating results of past simulations and cryo-electron microscopic studies, also predicted a potential mechanism for how ATP hydrolysis drives dynein motion along the microtubule as well as how dynein changes its conformation when it goes through the power stroke. Thus, pursuit of an artistic work led to insights into biology at the nanoscale as well as the development of a highly generalizable modeling and simulation technology that has utility for nanoscience and any other area of scientific investigation that involves analysis of complex multiscale systems.

Molecular imaging assessment of periodontitis lesions in an experimental mouse model.

PubMed

Ideguchi, Hidetaka; Yamashiro, Keisuke; Yamamoto, Tadashi; Shimoe, Masayuki; Hongo, Shoichi; Kochi, Shinsuke; Yoshihara-Hirata, Chiaki; Aoyagi, Hiroaki; Kawamura, Mari; Takashiba, Shogo

2018-06-06

We aimed to evaluate molecular imaging as a novel diagnostic tool for mice periodontitis model induced by ligature and Porphyromonas gingivalis (Pg) inoculation. Twelve female mice were assigned to the following groups: no treatment as control group (n = 4); periodontitis group induced by ligature and Pg as Pg group (n = 4); and Pg group treated with glycyrrhizinic acid (GA) as Pg + GA group (n = 4). All mice were administered a myeloperoxidase (MPO) activity-specific luminescent probe and observed using a charge-coupled device camera on day 14. Image analysis on all mice was conducted using software to determine the signal intensity of inflammation. Additionally, histological and radiographic evaluation for periodontal inflammation and bone resorption at the site of periodontitis, and quantitative enzyme-linked immunosorbent assay (ELISA) were conducted on three mice for each group. Each experiment was performed three times. Levels of serum IgG antibody against P. gingivalis were significantly higher in the Pg than in the Pg + GA group. Histological analyses indicated that the number of osteoclasts and neutrophils were significantly lower in the Pg + GA than in the Pg group. Micro-CT image analysis indicated no difference in bone resorption between the Pg and Pg + GA groups. The signal intensity of MPO activity was detected on the complete craniofacial image; moreover, strong signal intensity was localized specifically at the periodontitis site in the ex vivo palate, with group-wise differences. Molecular imaging analysis based on MPO activity showed high sensitivity of detection of periodontal inflammation in mice. Molecular imaging analysis based on MPO activity has potential as a diagnostic tool for periodontitis.

An enhanced Petri-net model to predict synergistic effects of pairwise drug combinations from gene microarray data.

PubMed

Jin, Guangxu; Zhao, Hong; Zhou, Xiaobo; Wong, Stephen T C

2011-07-01

Prediction of synergistic effects of drug combinations has traditionally been relied on phenotypic response data. However, such methods cannot be used to identify molecular signaling mechanisms of synergistic drug combinations. In this article, we propose an enhanced Petri-Net (EPN) model to recognize the synergistic effects of drug combinations from the molecular response profiles, i.e. drug-treated microarray data. We addressed the downstream signaling network of the targets for the two individual drugs used in the pairwise combinations and applied EPN to the identified targeted signaling network. In EPN, drugs and signaling molecules are assigned to different types of places, while drug doses and molecular expressions are denoted by color tokens. The changes of molecular expressions caused by treatments of drugs are simulated by two actions of EPN: firing and blasting. Firing is to transit the drug and molecule tokens from one node or place to another, and blasting is to reduce the number of molecule tokens by drug tokens in a molecule node. The goal of EPN is to mediate the state characterized by control condition without any treatment to that of treatment and to depict the drug effects on molecules by the drug tokens. We applied EPN to our generated pairwise drug combination microarray data. The synergistic predictions using EPN are consistent with those predicted using phenotypic response data. The molecules responsible for the synergistic effects with their associated feedback loops display the mechanisms of synergism. The software implemented in Python 2.7 programming language is available from request. stwong@tmhs.org.

Software Cost-Estimation Model

NASA Technical Reports Server (NTRS)

Tausworthe, R. C.

1985-01-01

Software Cost Estimation Model SOFTCOST provides automated resource and schedule model for software development. Combines several cost models found in open literature into one comprehensive set of algorithms. Compensates for nearly fifty implementation factors relative to size of task, inherited baseline, organizational and system environment and difficulty of task.

Software Program: Software Management Guidebook

NASA Technical Reports Server (NTRS)

1996-01-01

The purpose of this NASA Software Management Guidebook is twofold. First, this document defines the core products and activities required of NASA software projects. It defines life-cycle models and activity-related methods but acknowledges that no single life-cycle model is appropriate for all NASA software projects. It also acknowledges that the appropriate method for accomplishing a required activity depends on characteristics of the software project. Second, this guidebook provides specific guidance to software project managers and team leaders in selecting appropriate life cycles and methods to develop a tailored plan for a software engineering project.

Scalable nanohelices for predictive studies and enhanced 3D visualization.

PubMed

Meagher, Kwyn A; Doblack, Benjamin N; Ramirez, Mercedes; Davila, Lilian P

2014-11-12

Spring-like materials are ubiquitous in nature and of interest in nanotechnology for energy harvesting, hydrogen storage, and biological sensing applications. For predictive simulations, it has become increasingly important to be able to model the structure of nanohelices accurately. To study the effect of local structure on the properties of these complex geometries one must develop realistic models. To date, software packages are rather limited in creating atomistic helical models. This work focuses on producing atomistic models of silica glass (SiO₂) nanoribbons and nanosprings for molecular dynamics (MD) simulations. Using an MD model of "bulk" silica glass, two computational procedures to precisely create the shape of nanoribbons and nanosprings are presented. The first method employs the AWK programming language and open-source software to effectively carve various shapes of silica nanoribbons from the initial bulk model, using desired dimensions and parametric equations to define a helix. With this method, accurate atomistic silica nanoribbons can be generated for a range of pitch values and dimensions. The second method involves a more robust code which allows flexibility in modeling nanohelical structures. This approach utilizes a C++ code particularly written to implement pre-screening methods as well as the mathematical equations for a helix, resulting in greater precision and efficiency when creating nanospring models. Using these codes, well-defined and scalable nanoribbons and nanosprings suited for atomistic simulations can be effectively created. An added value in both open-source codes is that they can be adapted to reproduce different helical structures, independent of material. In addition, a MATLAB graphical user interface (GUI) is used to enhance learning through visualization and interaction for a general user with the atomistic helical structures. One application of these methods is the recent study of nanohelices via MD simulations for mechanical energy harvesting purposes.

Touching proteins with virtual bare hands - Visualizing protein-drug complexes and their dynamics in self-made virtual reality using gaming hardware

NASA Astrophysics Data System (ADS)

Ratamero, Erick Martins; Bellini, Dom; Dowson, Christopher G.; Römer, Rudolf A.

2018-06-01

The ability to precisely visualize the atomic geometry of the interactions between a drug and its protein target in structural models is critical in predicting the correct modifications in previously identified inhibitors to create more effective next generation drugs. It is currently common practice among medicinal chemists while attempting the above to access the information contained in three-dimensional structures by using two-dimensional projections, which can preclude disclosure of useful features. A more accessible and intuitive visualization of the three-dimensional configuration of the atomic geometry in the models can be achieved through the implementation of immersive virtual reality (VR). While bespoke commercial VR suites are available, in this work, we present a freely available software pipeline for visualising protein structures through VR. New consumer hardware, such as the uc(HTC Vive) and the uc(Oculus Rift) utilized in this study, are available at reasonable prices. As an instructive example, we have combined VR visualization with fast algorithms for simulating intramolecular motions of protein flexibility, in an effort to further improve structure-led drug design by exposing molecular interactions that might be hidden in the less informative static models. This is a paradigmatic test case scenario for many similar applications in computer-aided molecular studies and design.

Touching proteins with virtual bare hands : Visualizing protein-drug complexes and their dynamics in self-made virtual reality using gaming hardware.

PubMed

Ratamero, Erick Martins; Bellini, Dom; Dowson, Christopher G; Römer, Rudolf A

2018-06-07

The ability to precisely visualize the atomic geometry of the interactions between a drug and its protein target in structural models is critical in predicting the correct modifications in previously identified inhibitors to create more effective next generation drugs. It is currently common practice among medicinal chemists while attempting the above to access the information contained in three-dimensional structures by using two-dimensional projections, which can preclude disclosure of useful features. A more accessible and intuitive visualization of the three-dimensional configuration of the atomic geometry in the models can be achieved through the implementation of immersive virtual reality (VR). While bespoke commercial VR suites are available, in this work, we present a freely available software pipeline for visualising protein structures through VR. New consumer hardware, such as the HTC VIVE and the OCULUS RIFT utilized in this study, are available at reasonable prices. As an instructive example, we have combined VR visualization with fast algorithms for simulating intramolecular motions of protein flexibility, in an effort to further improve structure-led drug design by exposing molecular interactions that might be hidden in the less informative static models. This is a paradigmatic test case scenario for many similar applications in computer-aided molecular studies and design.

Analysis of high vacuum systems using SINDA'85

NASA Technical Reports Server (NTRS)

Spivey, R. A.; Clanton, S. E.; Moore, J. D.

1993-01-01

The theory, algorithms, and test data correlation analysis of a math model developed to predict performance of the Space Station Freedom Vacuum Exhaust System are presented. The theory used to predict the flow characteristics of viscous, transition, and molecular flow is presented in detail. Development of user subroutines which predict the flow characteristics in conjunction with the SINDA'85/FLUINT analysis software are discussed. The resistance-capacitance network approach with application to vacuum system analysis is demonstrated and results from the model are correlated with test data. The model was developed to predict the performance of the Space Station Freedom Vacuum Exhaust System. However, the unique use of the user subroutines developed in this model and written into the SINDA'85/FLUINT thermal analysis model provides a powerful tool that can be used to predict the transient performance of vacuum systems and gas flow in tubes of virtually any geometry. This can be accomplished using a resistance-capacitance (R-C) method very similar to the methods used to perform thermal analyses.

Modeling and simulation of the debonding process of composite solid propellants

NASA Astrophysics Data System (ADS)

Feng, Tao; Xu, Jin-sheng; Han, Long; Chen, Xiong

2017-07-01

In order to study the damage evolution law of composite solid propellants, the molecular dynamics particle filled algorithm was used to establish the mesoscopic structure model of HTPB(Hydroxyl-terminated polybutadiene) propellants. The cohesive element method was employed for the adhesion interface between AP(Ammonium perchlorate) particle and HTPB matrix and the bilinear cohesive zone model was used to describe the mechanical response of the interface elements. The inversion analysis method based on Hooke-Jeeves optimization algorithm was employed to identify the parameters of cohesive zone model(CZM) of the particle/binder interface. Then, the optimized parameters were applied to the commercial finite element software ABAQUS to simulate the damage evolution process for AP particle and HTPB matrix, including the initiation, development, gathering and macroscopic crack. Finally, the stress-strain simulation curve was compared with the experiment curves. The result shows that the bilinear cohesive zone model can accurately describe the debonding and fracture process between the AP particles and HTPB matrix under the uniaxial tension loading.

Cell illustrator 4.0: a computational platform for systems biology.

PubMed

Nagasaki, Masao; Saito, Ayumu; Jeong, Euna; Li, Chen; Kojima, Kaname; Ikeda, Emi; Miyano, Satoru

2011-01-01

Cell Illustrator is a software platform for Systems Biology that uses the concept of Petri net for modeling and simulating biopathways. It is intended for biological scientists working at bench. The latest version of Cell Illustrator 4.0 uses Java Web Start technology and is enhanced with new capabilities, including: automatic graph grid layout algorithms using ontology information; tools using Cell System Markup Language (CSML) 3.0 and Cell System Ontology 3.0; parameter search module; high-performance simulation module; CSML database management system; conversion from CSML model to programming languages (FORTRAN, C, C++, Java, Python and Perl); import from SBML, CellML, and BioPAX; and, export to SVG and HTML. Cell Illustrator employs an extension of hybrid Petri net in an object-oriented style so that biopathway models can include objects such as DNA sequence, molecular density, 3D localization information, transcription with frame-shift, translation with codon table, as well as biochemical reactions.

Cell Illustrator 4.0: a computational platform for systems biology.

PubMed

Nagasaki, Masao; Saito, Ayumu; Jeong, Euna; Li, Chen; Kojima, Kaname; Ikeda, Emi; Miyano, Satoru

2010-01-01

Cell Illustrator is a software platform for Systems Biology that uses the concept of Petri net for modeling and simulating biopathways. It is intended for biological scientists working at bench. The latest version of Cell Illustrator 4.0 uses Java Web Start technology and is enhanced with new capabilities, including: automatic graph grid layout algorithms using ontology information; tools using Cell System Markup Language (CSML) 3.0 and Cell System Ontology 3.0; parameter search module; high-performance simulation module; CSML database management system; conversion from CSML model to programming languages (FORTRAN, C, C++, Java, Python and Perl); import from SBML, CellML, and BioPAX; and, export to SVG and HTML. Cell Illustrator employs an extension of hybrid Petri net in an object-oriented style so that biopathway models can include objects such as DNA sequence, molecular density, 3D localization information, transcription with frame-shift, translation with codon table, as well as biochemical reactions.

Empirical studies of software design: Implications for SSEs

NASA Technical Reports Server (NTRS)

Krasner, Herb

1988-01-01

Implications for Software Engineering Environments (SEEs) are presented in viewgraph format for characteristics of projects studied; significant problems and crucial problem areas in software design for large systems; layered behavioral model of software processes; implications of field study results; software project as an ecological system; results of the LIFT study; information model of design exploration; software design strategies; results of the team design study; and a list of publications.

Software Metrics

DTIC Science & Technology

1988-12-01

software development scene is often charac- c. SPQR Model-Jones terized by: * schedule and cost estimates that are gross-d. COPMO-Thebaut ly inaccurate, SEI...time c. SPQR Model-Jones (in seconds) is simply derived from E by dividing T. Capers Jones has developed a software cost by the Stroud number, S...estimation model called the Software Produc- T=E/S tivity, Quality, and Reliability ( SPQR ) model. The basic approach is similar to that of Boehm’s The value

The contribution of the hydrogen bond acidity on the lipophilicity of drugs estimated from chromatographic measurements.

PubMed

Pallicer, Juan M; Pascual, Rosalia; Port, Adriana; Rosés, Martí; Ràfols, Clara; Bosch, Elisabeth

2013-02-14

The influence of the hydrogen bond acidity when the 1-octanol/water partition coefficient (log P(o/w)) of drugs is determined from chromatographic measurements was studied in this work. This influence was firstly evaluated by means of the comparison between the Abraham solvation parameter model when it is applied to express the 1-octanol/water partitioning and the chromatographic retention, expressed as the solute polarity p. Then, several hydrogen bond acidity descriptors were compared in order to determine properly the log P(o/w) of drugs. These descriptors were obtained from different software and comprise two-dimensional parameters such as the calculated Abraham hydrogen bond acidity A and three-dimensional descriptors like HDCA-2 from CODESSA program or WO1 and DRDODO descriptors calculated from Volsurf+software. The additional HOMO-LUMO polarizability descriptor should be added when the three-dimensional descriptors are used to complement the chromatographic retention. The models generated using these descriptors were compared studying the correlations between the determined log P(o/w) values and the reference ones. The comparison showed that there was no significant difference between the tested models and any of them was able to determine the log P(o/w) of drugs from a single chromatographic measurement and the correspondent molecular descriptors terms. However, the model that involved the calculated A descriptor was simpler and it is thus recommended for practical uses. Copyright © 2012 Elsevier B.V. All rights reserved.

Studying the Accuracy of Software Process Elicitation: The User Articulated Model

ERIC Educational Resources Information Center

Crabtree, Carlton A.

2010-01-01

Process models are often the basis for demonstrating improvement and compliance in software engineering organizations. A descriptive model is a type of process model describing the human activities in software development that actually occur. The purpose of a descriptive model is to provide a documented baseline for further process improvement…

Overview of the TriBITS Lifecycle Model: Lean/Agile Software Lifecycle Model for Research-based Computational Science and Engineering Software

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bartlett, Roscoe A; Heroux, Dr. Michael A; Willenbring, James

2012-01-01

Software lifecycles are becoming an increasingly important issue for computational science & engineering (CSE) software. The process by which a piece of CSE software begins life as a set of research requirements and then matures into a trusted high-quality capability is both commonplace and extremely challenging. Although an implicit lifecycle is obviously being used in any effort, the challenges of this process--respecting the competing needs of research vs. production--cannot be overstated. Here we describe a proposal for a well-defined software lifecycle process based on modern Lean/Agile software engineering principles. What we propose is appropriate for many CSE software projects thatmore » are initially heavily focused on research but also are expected to eventually produce usable high-quality capabilities. The model is related to TriBITS, a build, integration and testing system, which serves as a strong foundation for this lifecycle model, and aspects of this lifecycle model are ingrained in the TriBITS system. Indeed this lifecycle process, if followed, will enable large-scale sustainable integration of many complex CSE software efforts across several institutions.« less

Biology Needs Evolutionary Software Tools: Let’s Build Them Right

PubMed Central

Team, Galaxy; Goecks, Jeremy; Taylor, James

2018-01-01

Abstract Research in population genetics and evolutionary biology has always provided a computational backbone for life sciences as a whole. Today evolutionary and population biology reasoning are essential for interpretation of large complex datasets that are characteristic of all domains of today’s life sciences ranging from cancer biology to microbial ecology. This situation makes algorithms and software tools developed by our community more important than ever before. This means that we, developers of software tool for molecular evolutionary analyses, now have a shared responsibility to make these tools accessible using modern technological developments as well as provide adequate documentation and training. PMID:29688462

A conceptual model for megaprogramming

NASA Technical Reports Server (NTRS)

Tracz, Will

1990-01-01

Megaprogramming is component-based software engineering and life-cycle management. Magaprogramming and its relationship to other research initiatives (common prototyping system/common prototyping language, domain specific software architectures, and software understanding) are analyzed. The desirable attributes of megaprogramming software components are identified and a software development model and resulting prototype megaprogramming system (library interconnection language extended by annotated Ada) are described.

Deep space network software cost estimation model

NASA Technical Reports Server (NTRS)

Tausworthe, R. C.

1981-01-01

A parametric software cost estimation model prepared for Deep Space Network (DSN) Data Systems implementation tasks is presented. The resource estimation model incorporates principles and data from a number of existing models. The model calibrates task magnitude and difficulty, development environment, and software technology effects through prompted responses to a set of approximately 50 questions. Parameters in the model are adjusted to fit DSN software life cycle statistics. The estimation model output scales a standard DSN Work Breakdown Structure skeleton, which is then input into a PERT/CPM system, producing a detailed schedule and resource budget for the project being planned.

Consistent Evolution of Software Artifacts and Non-Functional Models

DTIC Science & Technology

2014-11-14

induce bad software performance)? 15. SUBJECT TERMS EOARD, Nano particles, Photo-Acoustic Sensors, Model-Driven Engineering ( MDE ), Software Performance...Università degli Studi dell’Aquila, Via Vetoio, 67100 L’Aquila, Italy Email: vittorio.cortellessa@univaq.it Web : http: // www. di. univaq. it/ cortelle/ Phone...Model-Driven Engineering ( MDE ), Software Performance Engineering (SPE), Change Propagation, Performance Antipatterns. For sake of readability of the

The Effect of a Computerized Simulation on Middle School Students' Understanding of the Kinetic Molecular Theory

ERIC Educational Resources Information Center

Stern, Luli; Barnea, Nitza; Shauli, Sofia

2008-01-01

The objective of this study was to evaluate the effect of a dynamic software simulation on the understanding of the kinetic molecular theory by 7th graders. Students in the control group (n = 62) studied a curricular unit that addressed the differences in arrangement and motion of molecules in the three phases of matter. The experimental group (n…

Sources and Sinks: Elucidating Mechanisms, Documenting Patterns, and Forecasting Impacts

DTIC Science & Technology

2017-01-18

Molecular Ecology 17: 3628-3639. Fazio III, V. W., Miles, D. B., & White, M. M. 2004. Genetic differentiation in the endangered Black-capped Vireo...exploration of accuracy and power. Molecular Ecology 13: 55–65. Raymond, M., & Rousset, F. 1995. GENEPOP (version 1.2): population genetics software for...SUPPLEMENTAL GENETICS MEMO Sources and Sinks: Elucidating Mechanisms, Documenting Patterns, and Forecasting Impacts SERDP Project RC-2120

RuleMonkey: software for stochastic simulation of rule-based models

PubMed Central

2010-01-01

Background The system-level dynamics of many molecular interactions, particularly protein-protein interactions, can be conveniently represented using reaction rules, which can be specified using model-specification languages, such as the BioNetGen language (BNGL). A set of rules implicitly defines a (bio)chemical reaction network. The reaction network implied by a set of rules is often very large, and as a result, generation of the network implied by rules tends to be computationally expensive. Moreover, the cost of many commonly used methods for simulating network dynamics is a function of network size. Together these factors have limited application of the rule-based modeling approach. Recently, several methods for simulating rule-based models have been developed that avoid the expensive step of network generation. The cost of these "network-free" simulation methods is independent of the number of reactions implied by rules. Software implementing such methods is now needed for the simulation and analysis of rule-based models of biochemical systems. Results Here, we present a software tool called RuleMonkey, which implements a network-free method for simulation of rule-based models that is similar to Gillespie's method. The method is suitable for rule-based models that can be encoded in BNGL, including models with rules that have global application conditions, such as rules for intramolecular association reactions. In addition, the method is rejection free, unlike other network-free methods that introduce null events, i.e., steps in the simulation procedure that do not change the state of the reaction system being simulated. We verify that RuleMonkey produces correct simulation results, and we compare its performance against DYNSTOC, another BNGL-compliant tool for network-free simulation of rule-based models. We also compare RuleMonkey against problem-specific codes implementing network-free simulation methods. Conclusions RuleMonkey enables the simulation of rule-based models for which the underlying reaction networks are large. It is typically faster than DYNSTOC for benchmark problems that we have examined. RuleMonkey is freely available as a stand-alone application http://public.tgen.org/rulemonkey. It is also available as a simulation engine within GetBonNie, a web-based environment for building, analyzing and sharing rule-based models. PMID:20673321

Binomial tau-leap spatial stochastic simulation algorithm for applications in chemical kinetics.

PubMed

Marquez-Lago, Tatiana T; Burrage, Kevin

2007-09-14

In cell biology, cell signaling pathway problems are often tackled with deterministic temporal models, well mixed stochastic simulators, and/or hybrid methods. But, in fact, three dimensional stochastic spatial modeling of reactions happening inside the cell is needed in order to fully understand these cell signaling pathways. This is because noise effects, low molecular concentrations, and spatial heterogeneity can all affect the cellular dynamics. However, there are ways in which important effects can be accounted without going to the extent of using highly resolved spatial simulators (such as single-particle software), hence reducing the overall computation time significantly. We present a new coarse grained modified version of the next subvolume method that allows the user to consider both diffusion and reaction events in relatively long simulation time spans as compared with the original method and other commonly used fully stochastic computational methods. Benchmarking of the simulation algorithm was performed through comparison with the next subvolume method and well mixed models (MATLAB), as well as stochastic particle reaction and transport simulations (CHEMCELL, Sandia National Laboratories). Additionally, we construct a model based on a set of chemical reactions in the epidermal growth factor receptor pathway. For this particular application and a bistable chemical system example, we analyze and outline the advantages of our presented binomial tau-leap spatial stochastic simulation algorithm, in terms of efficiency and accuracy, in scenarios of both molecular homogeneity and heterogeneity.

Aminoguanidine hydrazones (AGH's) as modulators of norfloxacin resistance in Staphylococcus aureus that overexpress NorA efflux pump.

PubMed

Dantas, Natalina; de Aquino, Thiago Mendonça; de Araújo-Júnior, João Xavier; da Silva-Júnior, Edeildo; Gomes, Ednaldo Almeida; Gomes, Antoniel Augusto Severo; Siqueira-Júnior, José Pinto; Mendonça Junior, Francisco Jaime Bezerra

2018-01-25

One of the promising fields for improving the effectiveness of antimicrobial agents is their combination with efflux pump inhibitors (EPIs), which besides expanding the use of existing antibiotics. The goal of this research was to evaluate a series of aminoguanidine hydrazones (AGH's, 1-19) as antibacterial agents and NorA efflux pump inhibitors in Staphylococcus aureus strain SA-1199B. Molecular modeling and docking studies were also performed in order to explain at the molecular level the interactions of the compounds with the generated NorA efflux pump model. The MICs of the antibiotic and ethidium bromide were determined by microdilution assay in absence or presence of a subinhibitory concentration of aminoguanidine hydrazones and macrophages viability was determined through MTT assay. Bioinformatic software Swiss-Model and AutoDock 4.2 were used to perform modeling and docking studies, respectively. As results, all AGH's were able to potentiate the action for the antibiotic norfloxacin, causing MIC's reduction of 16-fold and 32-fold to ethidium bromide. In the cell viability test, the concentration of 10 μg/mL showed better results than 90% and the concentration of 1000 μg/mL showed the lowest viability, reaching a maximum of 50% for the analyzed aminoguanidine hydrazones. Molecular docking studies showed that both norfloxacin and derivative 13 were recognized by the same binding site of NorA pump, suggesting a competitive mechanism. The present work demonstrated for the first time that AGH derivatives have potential to be putative inhibitors of NorA efflux pump, showing a promising activity as an antibacterial drug development. Copyright © 2017 Elsevier B.V. All rights reserved.

THE EPA MULTIMEDIA INTEGRATED MODELING SYSTEM SOFTWARE SUITE

EPA Science Inventory

The U.S. EPA is developing a Multimedia Integrated Modeling System (MIMS) framework that will provide a software infrastructure or environment to support constructing, composing, executing, and evaluating complex modeling studies. The framework will include (1) common software ...

Senior Computational Scientist | Center for Cancer Research

Cancer.gov

The Basic Science Program (BSP) pursues independent, multidisciplinary research in basic and applied molecular biology, immunology, retrovirology, cancer biology, and human genetics. Research efforts and support are an integral part of the Center for Cancer Research (CCR) at the Frederick National Laboratory for Cancer Research (FNLCR). The Cancer & Inflammation Program (CIP), Basic Science Program, HLA Immunogenetics Section, under the leadership of Dr. Mary Carrington, studies the influence of human leukocyte antigens (HLA) and specific KIR/HLA genotypes on risk of and outcomes to infection, cancer, autoimmune disease, and maternal-fetal disease. Recent studies have focused on the impact of HLA gene expression in disease, the molecular mechanism regulating expression levels, and the functional basis for the effect of differential expression on disease outcome. The lab’s further focus is on the genetic basis for resistance/susceptibility to disease conferred by immunogenetic variation. KEY ROLES/RESPONSIBILITIES The Senior Computational Scientist will provide research support to the CIP-BSP-HLA Immunogenetics Section performing bio-statistical design, analysis and reporting of research projects conducted in the lab. This individual will be involved in the implementation of statistical models and data preparation. Successful candidate should have 5 or more years of competent, innovative biostatistics/bioinformatics research experience, beyond doctoral training Considerable experience with statistical software, such as SAS, R and S-Plus Sound knowledge, and demonstrated experience of theoretical and applied statistics Write program code to analyze data using statistical analysis software Contribute to the interpretation and publication of research results

Educational aspects of molecular simulation

NASA Astrophysics Data System (ADS)

Allen, Michael P.

This article addresses some aspects of teaching simulation methods to undergraduates and graduate students. Simulation is increasingly a cross-disciplinary activity, which means that the students who need to learn about simulation methods may have widely differing backgrounds. Also, they may have a wide range of views on what constitutes an interesting application of simulation methods. Almost always, a successful simulation course includes an element of practical, hands-on activity: a balance always needs to be struck between treating the simulation software as a 'black box', and becoming bogged down in programming issues. With notebook computers becoming widely available, students often wish to take away the programs to run themselves, and access to raw computer power is not the limiting factor that it once was; on the other hand, the software should be portable and, if possible, free. Examples will be drawn from the author's experience in three different contexts. (1) An annual simulation summer school for graduate students, run by the UK CCP5 organization, in which practical sessions are combined with an intensive programme of lectures describing the methodology. (2) A molecular modelling module, given as part of a doctoral training centre in the Life Sciences at Warwick, for students who might not have a first degree in the physical sciences. (3) An undergraduate module in Physics at Warwick, also taken by students from other disciplines, teaching high performance computing, visualization, and scripting in the context of a physical application such as Monte Carlo simulation.

Development and Application of New Quality Model for Software Projects

PubMed Central

Karnavel, K.; Dillibabu, R.

2014-01-01

The IT industry tries to employ a number of models to identify the defects in the construction of software projects. In this paper, we present COQUALMO and its limitations and aim to increase the quality without increasing the cost and time. The computation time, cost, and effort to predict the residual defects are very high; this was overcome by developing an appropriate new quality model named the software testing defect corrective model (STDCM). The STDCM was used to estimate the number of remaining residual defects in the software product; a few assumptions and the detailed steps of the STDCM are highlighted. The application of the STDCM is explored in software projects. The implementation of the model is validated using statistical inference, which shows there is a significant improvement in the quality of the software projects. PMID:25478594

Development and application of new quality model for software projects.

PubMed

Karnavel, K; Dillibabu, R

2014-01-01

The IT industry tries to employ a number of models to identify the defects in the construction of software projects. In this paper, we present COQUALMO and its limitations and aim to increase the quality without increasing the cost and time. The computation time, cost, and effort to predict the residual defects are very high; this was overcome by developing an appropriate new quality model named the software testing defect corrective model (STDCM). The STDCM was used to estimate the number of remaining residual defects in the software product; a few assumptions and the detailed steps of the STDCM are highlighted. The application of the STDCM is explored in software projects. The implementation of the model is validated using statistical inference, which shows there is a significant improvement in the quality of the software projects.

Visualization Skills: A Prerequisite to Advanced Solid Modeling

ERIC Educational Resources Information Center

Gow, George

2007-01-01

Many educators believe that solid modeling software has made teaching two- and three-dimensional visualization skills obsolete. They claim that the visual tools built into the solid modeling software serve as a replacement for the CAD operator's personal visualization skills. They also claim that because solid modeling software can produce…

Software engineering the mixed model for genome-wide association studies on large samples.

PubMed

Zhang, Zhiwu; Buckler, Edward S; Casstevens, Terry M; Bradbury, Peter J

2009-11-01

Mixed models improve the ability to detect phenotype-genotype associations in the presence of population stratification and multiple levels of relatedness in genome-wide association studies (GWAS), but for large data sets the resource consumption becomes impractical. At the same time, the sample size and number of markers used for GWAS is increasing dramatically, resulting in greater statistical power to detect those associations. The use of mixed models with increasingly large data sets depends on the availability of software for analyzing those models. While multiple software packages implement the mixed model method, no single package provides the best combination of fast computation, ability to handle large samples, flexible modeling and ease of use. Key elements of association analysis with mixed models are reviewed, including modeling phenotype-genotype associations using mixed models, population stratification, kinship and its estimation, variance component estimation, use of best linear unbiased predictors or residuals in place of raw phenotype, improving efficiency and software-user interaction. The available software packages are evaluated, and suggestions made for future software development.

Development of a calibrated software reliability model for flight and supporting ground software for avionic systems

NASA Technical Reports Server (NTRS)

Lawrence, Stella

1991-01-01

The object of this project was to develop and calibrate quantitative models for predicting the quality of software. Reliable flight and supporting ground software is a highly important factor in the successful operation of the space shuttle program. The models used in the present study consisted of SMERFS (Statistical Modeling and Estimation of Reliability Functions for Software). There are ten models in SMERFS. For a first run, the results obtained in modeling the cumulative number of failures versus execution time showed fairly good results for our data. Plots of cumulative software failures versus calendar weeks were made and the model results were compared with the historical data on the same graph. If the model agrees with actual historical behavior for a set of data then there is confidence in future predictions for this data. Considering the quality of the data, the models have given some significant results, even at this early stage. With better care in data collection, data analysis, recording of the fixing of failures and CPU execution times, the models should prove extremely helpful in making predictions regarding the future pattern of failures, including an estimate of the number of errors remaining in the software and the additional testing time required for the software quality to reach acceptable levels. It appears that there is no one 'best' model for all cases. It is for this reason that the aim of this project was to test several models. One of the recommendations resulting from this study is that great care must be taken in the collection of data. When using a model, the data should satisfy the model assumptions.

Revealing the ISO/IEC 9126-1 Clique Tree for COTS Software Evaluation

NASA Technical Reports Server (NTRS)

Morris, A. Terry

2007-01-01

Previous research has shown that acyclic dependency models, if they exist, can be extracted from software quality standards and that these models can be used to assess software safety and product quality. In the case of commercial off-the-shelf (COTS) software, the extracted dependency model can be used in a probabilistic Bayesian network context for COTS software evaluation. Furthermore, while experts typically employ Bayesian networks to encode domain knowledge, secondary structures (clique trees) from Bayesian network graphs can be used to determine the probabilistic distribution of any software variable (attribute) using any clique that contains that variable. Secondary structures, therefore, provide insight into the fundamental nature of graphical networks. This paper will apply secondary structure calculations to reveal the clique tree of the acyclic dependency model extracted from the ISO/IEC 9126-1 software quality standard. Suggestions will be provided to describe how the clique tree may be exploited to aid efficient transformation of an evaluation model.

Predicting Monoamine Oxidase Inhibitory Activity through Ligand-Based Models

PubMed Central

Vilar, Santiago; Ferino, Giulio; Quezada, Elias; Santana, Lourdes; Friedman, Carol

2013-01-01

The evolution of bio- and cheminformatics associated with the development of specialized software and increasing computer power has produced a great interest in theoretical in silico methods applied in drug rational design. These techniques apply the concept that “similar molecules have similar biological properties” that has been exploited in Medicinal Chemistry for years to design new molecules with desirable pharmacological profiles. Ligand-based methods are not dependent on receptor structural data and take into account two and three-dimensional molecular properties to assess similarity of new compounds in regards to the set of molecules with the biological property under study. Depending on the complexity of the calculation, there are different types of ligand-based methods, such as QSAR (Quantitative Structure-Activity Relationship) with 2D and 3D descriptors, CoMFA (Comparative Molecular Field Analysis) or pharmacophoric approaches. This work provides a description of a series of ligand-based models applied in the prediction of the inhibitory activity of monoamine oxidase (MAO) enzymes. The controlled regulation of the enzymes’ function through the use of MAO inhibitors is used as a treatment in many psychiatric and neurological disorders, such as depression, anxiety, Alzheimer’s and Parkinson’s disease. For this reason, multiple scaffolds, such as substituted coumarins, indolylmethylamine or pyridazine derivatives were synthesized and assayed toward MAO-A and MAO-B inhibition. Our intention is to focus on the description of ligand-based models to provide new insights in the relationship between the MAO inhibitory activity and the molecular structure of the different inhibitors, and further study enzyme selectivity and possible mechanisms of action. PMID:23231398

Collected software engineering papers, volume 9

NASA Technical Reports Server (NTRS)

1991-01-01

This document is a collection of selected technical papers produced by participants in the Software Engineering Laboratory (SEL) from November 1990 through October 1991. The purpose of the document is to make available, in one reference, some results of SEL research that originally appeared in a number of different forums. This is the ninth such volume of technical papers produced by the SEL. Although these papers cover several topics related to software engineering, they do not encompass the entire scope of SEL activities and interests. For the convenience of this presentation, the eight papers contained here are grouped into three major categories: (1) software models studies; (2) software measurement studies; and (3) Ada technology studies. The first category presents studies on reuse models, including a software reuse model applied to maintenance and a model for an organization to support software reuse. The second category includes experimental research methods and software measurement techniques. The third category presents object-oriented approaches using Ada and object-oriented features proposed for Ada. The SEL is actively working to understand and improve the software development process at GSFC.

The TAME Project: Towards improvement-oriented software environments

NASA Technical Reports Server (NTRS)

Basili, Victor R.; Rombach, H. Dieter

1988-01-01

Experience from a dozen years of analyzing software engineering processes and products is summarized as a set of software engineering and measurement principles that argue for software engineering process models that integrate sound planning and analysis into the construction process. In the TAME (Tailoring A Measurement Environment) project at the University of Maryland, such an improvement-oriented software engineering process model was developed that uses the goal/question/metric paradigm to integrate the constructive and analytic aspects of software development. The model provides a mechanism for formalizing the characterization and planning tasks, controlling and improving projects based on quantitative analysis, learning in a deeper and more systematic way about the software process and product, and feeding the appropriate experience back into the current and future projects. The TAME system is an instantiation of the TAME software engineering process model as an ISEE (integrated software engineering environment). The first in a series of TAME system prototypes has been developed. An assessment of experience with this first limited prototype is presented including a reassessment of its initial architecture.

Using software security analysis to verify the secure socket layer (SSL) protocol

NASA Technical Reports Server (NTRS)

Powell, John D.

2004-01-01

nal Aeronautics and Space Administration (NASA) have tens of thousands of networked computer systems and applications. Software Security vulnerabilities present risks such as lost or corrupted data, information the3, and unavailability of critical systems. These risks represent potentially enormous costs to NASA. The NASA Code Q research initiative 'Reducing Software Security Risk (RSSR) Trough an Integrated Approach '' offers, among its capabilities, formal verification of software security properties, through the use of model based verification (MBV) to address software security risks. [1,2,3,4,5,6] MBV is a formal approach to software assurance that combines analysis of software, via abstract models, with technology, such as model checkers, that provide automation of the mechanical portions of the analysis process. This paper will discuss: The need for formal analysis to assure software systems with respect to software and why testing alone cannot provide it. The means by which MBV with a Flexible Modeling Framework (FMF) accomplishes the necessary analysis task. An example of FMF style MBV in the verification of properties over the Secure Socket Layer (SSL) communication protocol as a demonstration.

Software-defined Quantum Networking Ecosystem

DOE Office of Scientific and Technical Information (OSTI.GOV)

Humble, Travis S.; Sadlier, Ronald

The software enables a user to perform modeling and simulation of software-defined quantum networks. The software addresses the problem of how to synchronize transmission of quantum and classical signals through multi-node networks and to demonstrate quantum information protocols such as quantum teleportation. The software approaches this problem by generating a graphical model of the underlying network and attributing properties to each node and link in the graph. The graphical model is then simulated using a combination of discrete-event simulators to calculate the expected state of each node and link in the graph at a future time. A user interacts withmore » the software by providing an initial network model and instantiating methods for the nodes to transmit information with each other. This includes writing application scripts in python that make use of the software library interfaces. A user then initiates the application scripts, which invokes the software simulation. The user then uses the built-in diagnostic tools to query the state of the simulation and to collect statistics on synchronization.« less

A Prototype for the Support of Integrated Software Process Development and Improvement

NASA Astrophysics Data System (ADS)

Porrawatpreyakorn, Nalinpat; Quirchmayr, Gerald; Chutimaskul, Wichian

An efficient software development process is one of key success factors for quality software. Not only can the appropriate establishment but also the continuous improvement of integrated project management and of the software development process result in efficiency. This paper hence proposes a software process maintenance framework which consists of two core components: an integrated PMBOK-Scrum model describing how to establish a comprehensive set of project management and software engineering processes and a software development maturity model advocating software process improvement. Besides, a prototype tool to support the framework is introduced.

Evaluation of sequence alignments and oligonucleotide probes with respect to three-dimensional structure of ribosomal RNA using ARB software package

PubMed Central

Kumar, Yadhu; Westram, Ralf; Kipfer, Peter; Meier, Harald; Ludwig, Wolfgang

2006-01-01

Background Availability of high-resolution RNA crystal structures for the 30S and 50S ribosomal subunits and the subsequent validation of comparative secondary structure models have prompted the biologists to use three-dimensional structure of ribosomal RNA (rRNA) for evaluating sequence alignments of rRNA genes. Furthermore, the secondary and tertiary structural features of rRNA are highly useful and successfully employed in designing rRNA targeted oligonucleotide probes intended for in situ hybridization experiments. RNA3D, a program to combine sequence alignment information with three-dimensional structure of rRNA was developed. Integration into ARB software package, which is used extensively by the scientific community for phylogenetic analysis and molecular probe designing, has substantially extended the functionality of ARB software suite with 3D environment. Results Three-dimensional structure of rRNA is visualized in OpenGL 3D environment with the abilities to change the display and overlay information onto the molecule, dynamically. Phylogenetic information derived from the multiple sequence alignments can be overlaid onto the molecule structure in a real time. Superimposition of both statistical and non-statistical sequence associated information onto the rRNA 3D structure can be done using customizable color scheme, which is also applied to a textual sequence alignment for reference. Oligonucleotide probes designed by ARB probe design tools can be mapped onto the 3D structure along with the probe accessibility models for evaluation with respect to secondary and tertiary structural conformations of rRNA. Conclusion Visualization of three-dimensional structure of rRNA in an intuitive display provides the biologists with the greater possibilities to carry out structure based phylogenetic analysis. Coupled with secondary structure models of rRNA, RNA3D program aids in validating the sequence alignments of rRNA genes and evaluating probe target sites. Superimposition of the information derived from the multiple sequence alignment onto the molecule dynamically allows the researchers to observe any sequence inherited characteristics (phylogenetic information) in real-time environment. The extended ARB software package is made freely available for the scientific community via . PMID:16672074

Processing-microstructure relationships in thermotropic liquid crystalline polymers: Experimental and numerical modeling studies

NASA Astrophysics Data System (ADS)

Fang, Jun

Thermotropic liquid crystalline polymers (TLCPs) are a class of promising engineering materials for high-demanding structural applications. Their excellent mechanical properties are highly correlated to the underlying molecular orientation states, which may be affected by complex flow fields during melt processing. Thus, understanding and eventually predicting how processing flows impact molecular orientation is a critical step towards rational design work in order to achieve favorable, balanced physical properties in finished products. This thesis aims to develop deeper understanding of orientation development in commercial TLCPs during processing by coordinating extensive experimental measurements with numerical computations. In situ measurements of orientation development of LCPs during processing are a focal point of this thesis. An x-ray capable injection molding apparatus is enhanced and utilized for time-resolved measurements of orientation development in multiple commercial TLCPs during injection molding. Ex situ wide angle x-ray scattering is also employed for more thorough characterization of molecular orientation distributions in molded plaques. Incompletely injection molded plaques ("short shots") are studied to gain further insights into the intermediate orientation states during mold filling. Finally, two surface orientation characterization techniques, near edge x-ray absorption fine structure (NEXAFS) and infrared attenuated total reflectance (FTIR-ATR) are combined to investigate the surface orientation distribution of injection molded plaques. Surface orientation states are found to be vastly different from their bulk counterparts due to different kinematics involved in mold filling. In general, complex distributions of orientation in molded plaques reflect the spatially varying competition between shear and extension during mold filling. To complement these experimental measurements, numerical calculations based on the Larson-Doi polydomain model are performed. The implementation of the Larson-Doi in complex processing flows is performed using a commercial process modeling software suite (MOLDFLOWRTM), exploiting a nearly exact analogy between the Larson-Doi model and a fiber orientation model that has been widely used in composites processing simulations. The modeling scheme is first verified by predicting many qualitative and quantitative features of molecular orientation distributions in isothermal extrusion-fed channel flows. In coordination with experiments, the model predictions are found to capture many qualitative features observed in injection molded plaques (including short shots). The final, stringent test of Larson-Doi model performance is prediction of in situ transient orientation data collected during mold filling. The model yields satisfactory results, though certain numerical approximations limit performance near the mold front.

Idea Paper: The Lifecycle of Software for Scientific Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dubey, Anshu; McInnes, Lois C.

The software lifecycle is a well researched topic that has produced many models to meet the needs of different types of software projects. However, one class of projects, software development for scientific computing, has received relatively little attention from lifecycle researchers. In particular, software for end-to-end computations for obtaining scientific results has received few lifecycle proposals and no formalization of a development model. An examination of development approaches employed by the teams implementing large multicomponent codes reveals a great deal of similarity in their strategies. This idea paper formalizes these related approaches into a lifecycle model for end-to-end scientific applicationmore » software, featuring loose coupling between submodels for development of infrastructure and scientific capability. We also invite input from stakeholders to converge on a model that captures the complexity of this development processes and provides needed lifecycle guidance to the scientific software community.« less

JavaGenes Molecular Evolution

NASA Technical Reports Server (NTRS)

Lohn, Jason; Smith, David; Frank, Jeremy; Globus, Al; Crawford, James

2007-01-01

JavaGenes is a general-purpose, evolutionary software system written in Java. It implements several versions of a genetic algorithm, simulated annealing, stochastic hill climbing, and other search techniques. This software has been used to evolve molecules, atomic force field parameters, digital circuits, Earth Observing Satellite schedules, and antennas. This version differs from version 0.7.28 in that it includes the molecule evolution code and other improvements. Except for the antenna code, JaveGenes is available for NASA Open Source distribution.

Quantitative Image Informatics for Cancer Research (QIICR) | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

Imaging has enormous untapped potential to improve cancer research through software to extract and process morphometric and functional biomarkers. In the era of non-cytotoxic treatment agents, multi- modality image-guided ablative therapies and rapidly evolving computational resources, quantitative imaging software can be transformative in enabling minimally invasive, objective and reproducible evaluation of cancer treatment response. Post-processing algorithms are integral to high-throughput analysis and fine- grained differentiation of multiple molecular targets.

Tetramethylpyrazine-Loaded Hydrogels: Preparation, Penetration Through a Subcutaneous-Mucous-Membrane Model, and a Molecular Dynamics Simulation.

PubMed

Xia, Hongmei; Xu, Yinxiang; Cheng, Zhiqing; Cheng, Yongfeng

2017-07-01

Tetramethylpyrazine (TMP) was extracted from Ligusticum chuanxiong hort. The compound is known to have a variety of medicinal functions; in particular, it is used for the treatment of cerebral ischemic diseases. TMP-loaded hydrogels offer an excellent preparation with the capacity to bypass the blood-brain barrier, allowing treatment of the brain through intranasal administration. We prepared TMP-loaded hydrogels using carbomer 940 and evaluated the release of TMP from the hydrogel. We determined the release rate using Franz-type diffusion cell experiments with a subcutaneous-mucous-membrane model and also by a molecular dynamics (MD) simulation. In general, the former method was more complicated than the latter was. The dynamic behavior of TMP release from the hydrogel was revealed by analysis of the mean square displacement of the trajectory in the MD simulation. The coefficient of TMP diffusion from the hydrogel was calculated at different temperatures (277, 298, and 310 K) by using MD software. The results showed that the coefficient of diffusion increased with an increase in temperature. This trend was observed both experimentally and in the MD simulation. Therefore, the MD simulation was a complementary method to verify the experimental data.

Mathematical biology modules based on modern molecular biology and modern discrete mathematics.

PubMed

Robeva, Raina; Davies, Robin; Hodge, Terrell; Enyedi, Alexander

2010-01-01

We describe an ongoing collaborative curriculum materials development project between Sweet Briar College and Western Michigan University, with support from the National Science Foundation. We present a collection of modules under development that can be used in existing mathematics and biology courses, and we address a critical national need to introduce students to mathematical methods beyond the interface of biology with calculus. Based on ongoing research, and designed to use the project-based-learning approach, the modules highlight applications of modern discrete mathematics and algebraic statistics to pressing problems in molecular biology. For the majority of projects, calculus is not a required prerequisite and, due to the modest amount of mathematical background needed for some of the modules, the materials can be used for an early introduction to mathematical modeling. At the same time, most modules are connected with topics in linear and abstract algebra, algebraic geometry, and probability, and they can be used as meaningful applied introductions into the relevant advanced-level mathematics courses. Open-source software is used to facilitate the relevant computations. As a detailed example, we outline a module that focuses on Boolean models of the lac operon network.

Molecular basis of crystal morphology-dependent adhesion behavior of mefenamic acid during tableting.

PubMed

Waknis, Vrushali; Chu, Elza; Schlam, Roxana; Sidorenko, Alexander; Badawy, Sherif; Yin, Shawn; Narang, Ajit S

2014-01-01

The molecular basis of crystal surface adhesion leading to sticking was investigated by exploring the correlation of crystal adhesion to oxidized iron coated atomic force microscope (AFM) tips and bulk powder sticking behavior during tableting of two morphologically different crystals of a model drug, mefenamic acid (MA), to differences in their surface functional group orientation and energy. MA was recrystallized into two morphologies (plates and needles) of the same crystalline form. Crystal adhesion to oxidized iron coated AFM tips and bulk powder sticking to tablet punches was assessed using a direct compression formulation. Surface functional group orientation and energies on crystal faces were modeled using Accelrys Material Studio software. Needle-shaped morphology showed higher sticking tendency than plates despite similar particle size. This correlated with higher crystal surface adhesion of needle-shaped morphology to oxidized iron coated AFM probe tips, and greater surface energy and exposure of polar functional groups. Higher surface exposure of polar functional groups correlates with higher tendency to stick to metal surfaces and AFM tips, indicating involvement of specific polar interactions in the adhesion behavior. In addition, an AFM method is identified to prospectively assess the risk of sticking during the early stages of drug development.

Multipolar electrostatics.

PubMed

Cardamone, Salvatore; Hughes, Timothy J; Popelier, Paul L A

2014-06-14

Atomistic simulation of chemical systems is currently limited by the elementary description of electrostatics that atomic point-charges offer. Unfortunately, a model of one point-charge for each atom fails to capture the anisotropic nature of electronic features such as lone pairs or π-systems. Higher order electrostatic terms, such as those offered by a multipole moment expansion, naturally recover these important electronic features. The question remains as to why such a description has not yet been widely adopted by popular molecular mechanics force fields. There are two widely-held misconceptions about the more rigorous formalism of multipolar electrostatics: (1) Accuracy: the implementation of multipole moments, compared to point-charges, offers little to no advantage in terms of an accurate representation of a system's energetics, structure and dynamics. (2) Efficiency: atomistic simulation using multipole moments is computationally prohibitive compared to simulation using point-charges. Whilst the second of these may have found some basis when computational power was a limiting factor, the first has no theoretical grounding. In the current work, we disprove the two statements above and systematically demonstrate that multipole moments are not discredited by either. We hope that this perspective will help in catalysing the transition to more realistic electrostatic modelling, to be adopted by popular molecular simulation software.

Mathematical Biology Modules Based on Modern Molecular Biology and Modern Discrete Mathematics

PubMed Central

Davies, Robin; Hodge, Terrell; Enyedi, Alexander

2010-01-01

We describe an ongoing collaborative curriculum materials development project between Sweet Briar College and Western Michigan University, with support from the National Science Foundation. We present a collection of modules under development that can be used in existing mathematics and biology courses, and we address a critical national need to introduce students to mathematical methods beyond the interface of biology with calculus. Based on ongoing research, and designed to use the project-based-learning approach, the modules highlight applications of modern discrete mathematics and algebraic statistics to pressing problems in molecular biology. For the majority of projects, calculus is not a required prerequisite and, due to the modest amount of mathematical background needed for some of the modules, the materials can be used for an early introduction to mathematical modeling. At the same time, most modules are connected with topics in linear and abstract algebra, algebraic geometry, and probability, and they can be used as meaningful applied introductions into the relevant advanced-level mathematics courses. Open-source software is used to facilitate the relevant computations. As a detailed example, we outline a module that focuses on Boolean models of the lac operon network. PMID:20810955

Symposium overview the Shell Conference on computer-aided molecular modelling

NASA Astrophysics Data System (ADS)

Hays, G. R.; de Bruijn, D. P.

1988-10-01

The `Shell Conference on ...' series began in 1985 and meetings are held approximately twice a year. The idea behind the conferences is to bring together invited scientists from both universities and industry, and representatives from different Shell Research laboratories, to create a forum to discuss the future directions of the chosen research area. These meetings have embraced a wide range of topics of interest to Shell Research as a whole. This particular conference, organised by the Analytical Department of the Koninklijke/ShellLaboratorium, Amsterdam (KSLA), was held on 4-6 October, 1987 at Hoenderloo in the Netherlands. The aim was to review the state-of-the-art and to discuss the future of molecular modelling and design. The programme itself consisted of a series of presentations on prescribed topics, panel discussions, and software and hardware demonstrations. Many of the presentations given consisted of overviews, experiences, advice and predictions for the future. The panel sessions, which involved the speakers within that session and a discussion leader who summarised some of the points made in an introduction, encouraged even further discussion and speculation. This overview attempts to catch the flavour of the meeting and convey some personal views that were expressed and conclusions drawn.

Matriarch: A Python Library for Materials Architecture.

PubMed

Giesa, Tristan; Jagadeesan, Ravi; Spivak, David I; Buehler, Markus J

2015-10-12

Biological materials, such as proteins, often have a hierarchical structure ranging from basic building blocks at the nanoscale (e.g., amino acids) to assembled structures at the macroscale (e.g., fibers). Current software for materials engineering allows the user to specify polypeptide chains and simple secondary structures prior to molecular dynamics simulation, but is not flexible in terms of the geometric arrangement of unequilibrated structures. Given some knowledge of a larger-scale structure, instructing the software to create it can be very difficult and time-intensive. To this end, the present paper reports a mathematical language, using category theory, to describe the architecture of a material, i.e., its set of building blocks and instructions for combining them. While this framework applies to any hierarchical material, here we concentrate on proteins. We implement this mathematical language as an open-source Python library called Matriarch. It is a domain-specific language that gives the user the ability to create almost arbitrary structures with arbitrary amino acid sequences and, from them, generate Protein Data Bank (PDB) files. In this way, Matriarch is more powerful than commercial software now available. Matriarch can be used in tandem with molecular dynamics simulations and helps engineers design and modify biologically inspired materials based on their desired functionality. As a case study, we use our software to alter both building blocks and building instructions for tropocollagen, and determine their effect on its structure and mechanical properties.

Software development predictors, error analysis, reliability models and software metric analysis

NASA Technical Reports Server (NTRS)

Basili, Victor

1983-01-01

The use of dynamic characteristics as predictors for software development was studied. It was found that there are some significant factors that could be useful as predictors. From a study on software errors and complexity, it was shown that meaningful results can be obtained which allow insight into software traits and the environment in which it is developed. Reliability models were studied. The research included the field of program testing because the validity of some reliability models depends on the answers to some unanswered questions about testing. In studying software metrics, data collected from seven software engineering laboratory (FORTRAN) projects were examined and three effort reporting accuracy checks were applied to demonstrate the need to validate a data base. Results are discussed.

The Molecular Modeling Workbook for Organic Chemistry (by Warren J. Hehre, Alan J. Shusterman, and Janet E. Nelson)

NASA Astrophysics Data System (ADS)

Crouch, R. David

1999-09-01

Wavefunction, Inc.: Irvine, CA, 1998. 307 pp. ISBN 1-890661-06-6. 30.00. This workbook is the latest in a series of "lab manuals" designed to increase the presence of molecular modeling and computational chemistry in undergraduate courses. The authors have designed the workbook to differ from its predecessors in two ways: the target audience is introductory organic chemistry students, and a CD-ROM containing files of molecules and data replaces the need for expensive molecular modeling software. It also differs from its predecessors in that the exercises in it are not really molecular modeling experiments. Instead, students are introduced to the field by viewing the results of computational work stored on the CD-ROM. The workbook is divided into 21 chapters, each of which covers a topic encountered in introductory-level organic chemistry. The sequence of chapters follows the sequence of topics that instructors of introductory organic courses might employ, allowing the workbook to be used with most modern organic chemistry texts. The heart of the workbook, though, is the CD-ROM included with the book. It contains files of molecules and their accompanying computational results as well as Spartan View, a software package that allows these models to be visualized. Although it does not allow actual calculations to be performed, Spartan View permits the user to rotate molecules, intermediates, and transition states and retrieve "precalculated" values of bond and dihedral angles, bond lengths, energies, dipole moments, charge, and frequency of vibration. Spartan View also allows the user to search molecules and intermediates for electron-rich or electron-poor regions by showing electrostatic potential as well as HOMOs and LUMOs. Some files allow for animation of reactions or conformational changes. Note, however, that since the data are just stored on the CD-ROM, not all the data are available for all files. Although performing calculations is not an option, Spartan View can be used to display models and data obtained using Spartan or MacSpartan and stored on a disk. In this way, student exercises can be customized by the instructor or the instructor can prepare customized examples for use in lecture. Each chapter in the workbook contains a series of 3 to 17 exercises that use models and associated data contained on the accompanying CD-ROM. The exercises are not simply cookbook procedures in which the student is directed how to solve a problem. Instead, the authors provide background in a two-part tutorial and several essays that describe the information that can be obtained through molecular modeling, and then introduce a problem in organic chemistry that can be addressed using molecular modeling. The student is left to determine how best to obtain the requested data. For example, an exercise in the chapter Acids & Bases directs the student to determine the atomic charges and view the electrostatic potential map of the conjugate bases of three organic acids. The student is not, however, told which menu to pull or button to push. At the end of the exercise, the student is directed to compare the reactivity of the acids with the data collected from Spartan View. The exercises are relatively easy to complete after spending a few minutes with the tutorials, and many require students to compare the results of calculations with the reactivity of the molecules as discussed in the traditional lecture portion of the course. In this sense, the workbook provides a meaningful link between molecular modeling exercises outside of class and activities in the classroom. While some exercises involve comparing the energies of intermediates or transition states, others are more like videos of processes. Instructors will find many of these to be useful as visual aids in lecture. Mechanisms of Ring Inversion, for example, allows the instructor to show the stepwise ring flip of cyclohexane. Although some of the animations are very similar to those contained on CD-ROMs that sometimes accompany textbooks, the exercises in this workbook allow for the retrieval of data such as the energies of the various conformations cyclohexane. Not only can the student see the stepwise conversion of one chair conformation into another, but the changes in energy as the ring flip occurs are available. Also, unlike many of the visualizations on the CD-ROMs packaged with textbooks, these give the student control over the orientation of the structures on the screen, allowing views from numerous angles. The possibility of the instructor's customizing the exercises adds to the appeal of this workbook. In reviewing this book, I noted a couple of problems. The energy of molecules is presented in hartrees or atomic units (au). Although a factor is given for converting these values into the more familiar kcal/mol or kJ/mol, wouldn't it be easier to use these results if they were given in the units that are more typically used in introductory organic chemistry texts? Similarly, a number of exercises ask the student to plot data that they have calculated in the exercise. However, no routine for plotting the data is included with Spartan View and students must go through the cumbersome process of copying the values and preparing the plots using another program or by hand. And, finally, in Tutorial B, animations are introduced by showing "the SN2 displacement of chloride in tert-butyl chloride by bromide." Although the animation shows an SN1 mechanism with the C-Cl bond breaking before approach of the incoming bromide ion, students who are new to organic mechanisms will be misled by the erroneous description in the workbook. Although instructors may want to carefully consider whether to add an additional 30 to the already high cost of required texts, this workbook provides a unique and potentially valuable addition to the introductory organic chemistry course. With many exercises involving the visualization of electrostatic potentials and HOMOs and LUMOs, it adds an increased presence of physical organic chemistry in the introductory course. And, although the exercises are not really molecular modeling, this workbook also provides a low-cost introduction to the field without the considerable cost of modeling software. If Spartan or MacSpartan is already available in the department, the possible tie-in with the workbook and the capability to project the results should make this an attractive addition to any instructor's repertoire of visualization tools for lecture. The Molecular Modeling Workbook for Organic Chemistry is definitely worthy of consideration by anyone interested in adding molecular modeling to the organic course.

NASA Tech Briefs, March 2012

NASA Technical Reports Server (NTRS)

2012-01-01

The topics include: 1) Spectral Profiler Probe for In Situ Snow Grain Size and Composition Stratigraphy; 2) Portable Fourier Transform Spectroscopy for Analysis of Surface Contamination and Quality Control; 3) In Situ Geochemical Analysis and Age Dating of Rocks Using Laser Ablation-Miniature Mass Spectrometer; 4) Physics Mining of Multi-Source Data Sets; 5) Photogrammetry Tool for Forensic Analysis; 6) Connect Global Positioning System RF Module; 7) Simple Cell Balance Circuit; 8) Miniature EVA Software Defined Radio; 9) Remotely Accessible Testbed for Software Defined Radio Development; 10) System-of-Systems Technology-Portfolio-Analysis Tool; 11) VESGEN Software for Mapping and Quantification of Vascular Regulators; 12) Constructing a Database From Multiple 2D Images for Camera Pose Estimation and Robot Localization; 13) Adaption of G-TAG Software for Validating Touch and Go Asteroid Sample Return Design Methodology; 14) 3D Visualization for Phoenix Mars Lander Science Operations; 15) RxGen General Optical Model Prescription Generator; 16) Carbon Nanotube Bonding Strength Enhancement Using Metal Wicking Process; 17) Multi-Layer Far-Infrared Component Technology; 18) Germanium Lift-Off Masks for Thin Metal Film Patterning; 19) Sealing Materials for Use in Vacuum at High Temperatures; 20) Radiation Shielding System Using a Composite of Carbon Nanotubes Loaded With Electropolymers; 21) Nano Sponges for Drug Delivery and Medicinal Applications; 22) Molecular Technique to Understand Deep Microbial Diversity; 23) Methods and Compositions Based on Culturing Microorganisms in Low Sedimental Fluid Shear Conditions; 24) Secure Peer-to-Peer Networks for Scientific Information Sharing; 25) Multiplexer/Demultiplexer Loading Tool (MDMLT); 26) High-Rate Data-Capture for an Airborne Lidar System; 27) Wavefront Sensing Analysis of Grazing Incidence Optical Systems; 28) Foam-on-Tile Damage Model; 29) Instrument Package Manipulation Through the Generation and Use of an Attenuated-Fluent Gas Fold; 30) Multicolor Detectors for Ultrasensitive Long-Wave Imaging Cameras; 31) Lunar Reconnaissance Orbiter (LRO) Command and Data Handling Flight Electronics Subsystem; and 32) Electro-Optic Segment-Segment Sensors for Radio and Optical Telescopes.

Resource utilization during software development

NASA Technical Reports Server (NTRS)

Zelkowitz, Marvin V.

1988-01-01

This paper discusses resource utilization over the life cycle of software development and discusses the role that the current 'waterfall' model plays in the actual software life cycle. Software production in the NASA environment was analyzed to measure these differences. The data from 13 different projects were collected by the Software Engineering Laboratory at NASA Goddard Space Flight Center and analyzed for similarities and differences. The results indicate that the waterfall model is not very realistic in practice, and that as technology introduces further perturbations to this model with concepts like executable specifications, rapid prototyping, and wide-spectrum languages, we need to modify our model of this process.

phylo-node: A molecular phylogenetic toolkit using Node.js.

PubMed

O'Halloran, Damien M

2017-01-01

Node.js is an open-source and cross-platform environment that provides a JavaScript codebase for back-end server-side applications. JavaScript has been used to develop very fast and user-friendly front-end tools for bioinformatic and phylogenetic analyses. However, no such toolkits are available using Node.js to conduct comprehensive molecular phylogenetic analysis. To address this problem, I have developed, phylo-node, which was developed using Node.js and provides a stable and scalable toolkit that allows the user to perform diverse molecular and phylogenetic tasks. phylo-node can execute the analysis and process the resulting outputs from a suite of software options that provides tools for read processing and genome alignment, sequence retrieval, multiple sequence alignment, primer design, evolutionary modeling, and phylogeny reconstruction. Furthermore, phylo-node enables the user to deploy server dependent applications, and also provides simple integration and interoperation with other Node modules and languages using Node inheritance patterns, and a customized piping module to support the production of diverse pipelines. phylo-node is open-source and freely available to all users without sign-up or login requirements. All source code and user guidelines are openly available at the GitHub repository: https://github.com/dohalloran/phylo-node.

Coarse-grained molecular dynamics simulations of polymerization with forward and backward reactions.

PubMed

Krajniak, Jakub; Zhang, Zidan; Pandiyan, Sudharsan; Nies, Eric; Samaey, Giovanni

2018-06-11

We develop novel parallel algorithms that allow molecular dynamics simulations in which byproduct molecules are created and removed because of the chemical reactions during the molecular dynamics simulation. To prevent large increases in the potential energy, we introduce the byproduct molecules smoothly by changing the non-bonded interactions gradually. To simulate complete equilibrium reactions, we allow the byproduct molecules attack and destroy created bonds. Modeling of such reactions are, for instance, important to study the pore formation due to the presence of e.g. water molecules or development of polymer morphology during the process of splitting off byproduct molecules. Another concept that could be studied is the degradation of polymeric materials, a very important topic in a recycling of polymer waste. We illustrate the method by simulating the polymerization of polyethylene terephthalate (PET) at the coarse-grained level as an example of a polycondensation reaction with water as a byproduct. The algorithms are implemented in a publicly available software package and are easily accessible using a domain-specific language that describes chemical reactions in an input configuration file. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Comparison of 3D reconstruction of mandible for pre-operative planning using commercial and open-source software

NASA Astrophysics Data System (ADS)

Abdullah, Johari Yap; Omar, Marzuki; Pritam, Helmi Mohd Hadi; Husein, Adam; Rajion, Zainul Ahmad

2016-12-01

3D printing of mandible is important for pre-operative planning, diagnostic purposes, as well as for education and training. Currently, the processing of CT data is routinely performed with commercial software which increases the cost of operation and patient management for a small clinical setting. Usage of open-source software as an alternative to commercial software for 3D reconstruction of the mandible from CT data is scarce. The aim of this study is to compare two methods of 3D reconstruction of the mandible using commercial Materialise Mimics software and open-source Medical Imaging Interaction Toolkit (MITK) software. Head CT images with a slice thickness of 1 mm and a matrix of 512x512 pixels each were retrieved from the server located at the Radiology Department of Hospital Universiti Sains Malaysia. The CT data were analysed and the 3D models of mandible were reconstructed using both commercial Materialise Mimics and open-source MITK software. Both virtual 3D models were saved in STL format and exported to 3matic and MeshLab software for morphometric and image analyses. Both models were compared using Wilcoxon Signed Rank Test and Hausdorff Distance. No significant differences were obtained between the 3D models of the mandible produced using Mimics and MITK software. The 3D model of the mandible produced using MITK open-source software is comparable to the commercial MIMICS software. Therefore, open-source software could be used in clinical setting for pre-operative planning to minimise the operational cost.

3D modeling based on CityEngine

NASA Astrophysics Data System (ADS)

Jia, Guangyin; Liao, Kaiju

2017-03-01

Currently, there are many 3D modeling softwares, like 3DMAX, AUTOCAD, and more populous BIM softwares represented by REVIT. CityEngine modeling software introduced in this paper can fully utilize the existing GIS data and combine other built models to make 3D modeling on internal and external part of buildings in a rapid and batch manner, so as to improve the 3D modeling efficiency.

Global review of open access risk assessment software packages valid for global or continental scale analysis

NASA Astrophysics Data System (ADS)

Daniell, James; Simpson, Alanna; Gunasekara, Rashmin; Baca, Abigail; Schaefer, Andreas; Ishizawa, Oscar; Murnane, Rick; Tijssen, Annegien; Deparday, Vivien; Forni, Marc; Himmelfarb, Anne; Leder, Jan

2015-04-01

Over the past few decades, a plethora of open access software packages for the calculation of earthquake, volcanic, tsunami, storm surge, wind and flood have been produced globally. As part of the World Bank GFDRR Review released at the Understanding Risk 2014 Conference, over 80 such open access risk assessment software packages were examined. Commercial software was not considered in the evaluation. A preliminary analysis was used to determine whether the 80 models were currently supported and if they were open access. This process was used to select a subset of 31 models that include 8 earthquake models, 4 cyclone models, 11 flood models, and 8 storm surge/tsunami models for more detailed analysis. By using multi-criteria analysis (MCDA) and simple descriptions of the software uses, the review allows users to select a few relevant software packages for their own testing and development. The detailed analysis evaluated the models on the basis of over 100 criteria and provides a synopsis of available open access natural hazard risk modelling tools. In addition, volcano software packages have since been added making the compendium of risk software tools in excess of 100. There has been a huge increase in the quality and availability of open access/source software over the past few years. For example, private entities such as Deltares now have an open source policy regarding some flood models (NGHS). In addition, leaders in developing risk models in the public sector, such as Geoscience Australia (EQRM, TCRM, TsuDAT, AnuGA) or CAPRA (ERN-Flood, Hurricane, CRISIS2007 etc.), are launching and/or helping many other initiatives. As we achieve greater interoperability between modelling tools, we will also achieve a future wherein different open source and open access modelling tools will be increasingly connected and adapted towards unified multi-risk model platforms and highly customised solutions. It was seen that many software tools could be improved by enabling user-defined exposure and vulnerability. Without this function, many tools can only be used regionally and not at global or continental scale. It is becoming increasingly easy to use multiple packages for a single region and/or hazard to characterize the uncertainty in the risk, or use as checks for the sensitivities in the analysis. There is a potential for valuable synergy between existing software. A number of open source software packages could be combined to generate a multi-risk model with multiple views of a hazard. This extensive review has simply attempted to provide a platform for dialogue between all open source and open access software packages and to hopefully inspire collaboration between developers, given the great work done by all open access and open source developers.

Models and metrics for software management and engineering

NASA Technical Reports Server (NTRS)

Basili, V. R.

1988-01-01

This paper attempts to characterize and present a state of the art view of several quantitative models and metrics of the software life cycle. These models and metrics can be used to aid in managing and engineering software projects. They deal with various aspects of the software process and product, including resources allocation and estimation, changes and errors, size, complexity and reliability. Some indication is given of the extent to which the various models have been used and the success they have achieved.

A software quality model and metrics for risk assessment

NASA Technical Reports Server (NTRS)

Hyatt, L.; Rosenberg, L.

1996-01-01

A software quality model and its associated attributes are defined and used as the model for the basis for a discussion on risk. Specific quality goals and attributes are selected based on their importance to a software development project and their ability to be quantified. Risks that can be determined by the model's metrics are identified. A core set of metrics relating to the software development process and its products is defined. Measurements for each metric and their usability and applicability are discussed.